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# RNA-Seq Blog

Transcriptome Research & Industry News

## Posts

- [Blog](https://www.rna-seqblog.com/blog/)
- [Caris Life Sciences announces launch of Caris ChromoSeq, the world's first whole genome and whole transcriptome tumor profiling assay for myeloid malignancies](https://www.rna-seqblog.com/caris-life-sciences-announces-launch-of-caris-chromoseq-the-worlds-first-whole-genome-and-whole-transcriptome-tumor-profiling-assay-for-myeloid-malignancies/) - Integrating RNA sequencing with whole genome analysis, Caris ChromoSeq delivers...
- [Medgenome unveils india’s first study demonstrating the clinical impact of RNA-based NGS in sarcoma diagnosis](https://www.rna-seqblog.com/medgenome-unveils-indias-first-study-demonstrating-the-clinical-impact-of-rna-based-ngs-in-sarcoma-diagnosis/) - On the occasion of World Health Day, MedGenome, India’s leading genomics-driven diagnostics and research services company announced the outcomes of India’s first prospective study assessing the clinical utility of RNA-based next-generation sequencing (NGS) for soft tissue and bone sarcoma diagnosis. Aligning with this year’s theme “Together for health. Stand with science,” the study highlights the
- [The trRosettaRNA server for RNA structure prediction](https://www.rna-seqblog.com/the-trrosettarna-server-for-rna-structure-prediction/) - Deep learning combined with RNA sequencing enables rapid prediction of RNA 3D structures, helping researchers understand RNA function and accelerate therapeutic development...
- [Unraveling hair aging: a molecular atlas of human hair follicle senescence drawn by single-cell and spatiotemporal sequencing](https://www.rna-seqblog.com/unraveling-hair-aging-a-molecular-atlas-of-human-hair-follicle-senescence-drawn-by-single-cell-and-spatiotemporal-sequencing-2/) - Hair loss and graying, the earliest visible signs of skin aging, are fundamentally driven by the functional decline of the hair follicle stem cells (HFSCs) and their surrounding niche. The research, led researchers at BGI Cell, leveraging single-cell RNA sequencing of 11 human scalp samples and spatial transcriptomic sequencing of 1 sample, has created a
- [New sequencing method exposes hidden gaps in immune signaling](https://www.rna-seqblog.com/new-sequencing-method-exposes-hidden-gaps-in-immune-signaling/) - A new single-cell technology is giving scientists their clearest view yet of immune cell behavior—capturing not just genetic intent but real-time activity. By measuring RNA and proteins simultaneously, it reveals cytokine activity with greater accuracy, strengthening the foundation for understanding cancer, inflammation and treatment resistance. Published in the April 8 issue of Scientific Reports, the findings
- [Who Is Missing Out on Next-Generation Sequencing in Cancer?](https://www.rna-seqblog.com/who-is-missing-out-on-next-generation-sequencing-in-cancer/) - RNA sequencing and genomic profiling adoption is rising across cancers, yet disparities in access and delayed testing continue to limit timely precision oncology treatment decisions...
- [Next-generation sequencing has had a huge impact on molecular pathology lab](https://www.rna-seqblog.com/next-generation-sequencing-has-had-a-huge-impact-on-molecular-pathology-lab/) - Allison Cushman-Vokoun, MD, PhD, professor and director of Diagnostic Molecular Pathology and Human Genetics, has seen next-generation sequencing (NGS) transform the molecular pathology laboratory in the 10 years since it was launched. “When I started in 2009, everything was a single-gene test,” she said. “Which meant you had one gene where you were looking at
- [Researchers identify cellular pathways that drive precancerous lesions to form pancreatic tumors](https://www.rna-seqblog.com/researchers-identify-cellular-pathways-that-drive-precancerous-lesions-to-form-pancreatic-tumors/) - Decreased NADPH production, which powers cellular processes, results in cancer progression Tissue sample from a mouse without lesions (left) and with precancerous lesions due to loss of malic enzyme 1. Credit: Megan Radyk Pancreatic ductal adenocarcinoma is the most common type of pancreatic cancer and has a low five-year survival rate. It begins with a
- [In vivo RNA sequencing reveals real-time immune response to infection](https://www.rna-seqblog.com/in-vivo-rna-sequencing-reveals-real-time-immune-response-to-infection/) - Understanding how the immune system responds to infection requires tracking how cells change over time. Researchers at the Chinese Academy of Sciences have developed a new method to observe how immune cells activate and respond during infection at the single-cell level. Traditional RNA sequencing methods measure total RNA in cells, which provides a snapshot but
- [Parse biosciences launches FFPE-compatible barcoding technology for whole transcriptome single cell analysis](https://www.rna-seqblog.com/parse-biosciences-launches-ffpe-compatible-barcoding-technology-for-whole-transcriptome-single-cell-analysis/) - Parse Biosciences, a QIAGEN company and the leading provider of scalable and accessible single-cell sequencing solutions, today announced the commercial availability of Evercode™ Whole Transcriptome FFPE kits that are now shipping to customers. This new solution is a breakthrough that enables true whole transcriptome single cell RNA sequencing from formalin-fixed, paraffin-embedded samples. Beginning today, cancer,
- [Scientists use RNA sequencing to identify trigger of Crohn’s disease bowel scarring](https://www.rna-seqblog.com/scientists-use-rna-sequencing-to-identify-trigger-of-crohns-disease-bowel-scarring/) - Researchers have uncovered what drives the development of scar tissue in the intestines of people with Crohn’s disease. The study, led by researchers at the Institute of Genetics and Cancer, found clusters of immune cells in the gut which may be stimulating nearby cells to generate excess scar tissue, known as fibrosis. The discovery could
- [RNA sequencing moves toward absolute measurement of gene expression](https://www.rna-seqblog.com/rna-sequencing-moves-toward-absolute-measurement-of-gene-expression/) - RNA sequencing has become a powerful tool for measuring gene activity, but it has an important limitation. The number of sequencing reads does not always directly reflect the true amount of RNA in a sample. Researchers at Fudan University have developed a new method to make RNA sequencing measurements more accurate and comparable across experiments.
- [MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy](https://www.rna-seqblog.com/mitoperturb-seq-identifies-gene-specific-single-cell-responses-to-mitochondrial-dna-depletion-and-heteroplasmy/) - Mitochondria are often called the powerhouses of the cell, and they have their own genetic material known as mitochondrial DNA, or mtDNA. Unlike most DNA in the cell, mtDNA exists in many copies, and mutations may only affect some of those copies, a condition known as heteroplasmy. Researchers at the University of Cambridge explored how
- [SPTEdU-seq - parallel optics-free newborn cell tracking and spatial total transcriptional dynamics](https://www.rna-seqblog.com/sptedu-seq-parallel-optics-free-newborn-cell-tracking-and-spatial-total-transcriptional-dynamics/) - Understanding how cells grow, divide, and change over time is essential for studying development, disease, and tissue repair. Researchers at the Zhejiang University School of Medicine have developed a new method that combines spatial RNA sequencing with cell proliferation tracking to capture both where cells are and what they are doing. Traditional spatial transcriptomics methods
- [Deep learning improves analysis of single cell RNA sequencing data](https://www.rna-seqblog.com/deep-learning-improves-analysis-of-single-cell-rna-sequencing-data/) - Understanding how different cells behave within the same tissue is a major goal in modern biology. Single cell RNA sequencing allows researchers to measure gene activity in individual cells, revealing important differences between cell types. Researchers at the Guilin University of Electronic Technology have developed a new computational method to better analyze this complex data.
- [Bostongene RNA transcriptome profiling reveals new ADC targets in advanced solid tumor](https://www.rna-seqblog.com/bostongene-rna-transcriptome-profiling-reveals-new-adc-targets-in-advanced-solid-tumor/) - Prospective UT MD Anderson Study Shows RNA Analysis Expands Treatment Options Beyond DNA Testing BostonGene, developer of the leading AI foundation model for tumor and immune biology, announced results from the FEASY study in collaboration with The University of Texas MD Anderson Cancer Center, evaluating the clinical utility of comprehensive transcriptome testing in patients with
- [Programmable RNA detection enables multiplex virus identification](https://www.rna-seqblog.com/programmable-rna-detection-enables-multiplex-virus-identification/) - Rapid detection of viral infections is critical for controlling disease spread and guiding treatment decisions. In this work, researchers at the University of California, Berkeley have developed a new approach to detect multiple viruses and variants at once using RNA-based technology. Traditional diagnostic methods like PCR are highly sensitive but require converting RNA into DNA
- [RNA sequencing improves early detection of bile duct cancer](https://www.rna-seqblog.com/rna-sequencing-improves-early-detection-of-bile-duct-cancer/) - Diagnosing bile duct strictures can be difficult because it is often unclear whether a narrowing is benign or caused by cancer. A team led by researchers at the University of Pittsburgh Medical Center evaluated how next-generation sequencing using both DNA and RNA could improve diagnostic accuracy in real clinical settings. Traditionally, doctors collect samples during
- [longcallR - SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads](https://www.rna-seqblog.com/longcallr-snp-calling-haplotype-phasing-and-allele-specific-analysis-with-long-rna-seq-reads/) - Understanding how genes are expressed is not just about which genes are turned on or off, but also how different versions of those genes are produced. A team led by researcher at the Dana-Farber Cancer Institute have developed a new tool called longcallR to better analyze long-read RNA sequencing data. Long-read RNA sequencing is especially
- [Single-cell RNA sequencing gives insight to dermatomyositis treatment](https://www.rna-seqblog.com/single-cell-rna-sequencing-gives-insight-to-dermatomyositis-treatment/) - The comparisons of skin lesions in dermatomyositis and lupus give answers to treatment targets for dermatomyositis patients Dermatomyositis is a rare and devastating autoimmune disease primarily affecting the skin and skeletal muscle. While both can affect the muscle, dermatomyositis and lupus show many overlapping clinical and pathological features in their associated skin rashes but a
- [10th Berlin Summer School in NGS Data Analysis 2026](https://www.rna-seqblog.com/10th-berlin-summer-school-in-ngs-data-analysis-2026/) - Join our 10th Berlin Summer School in NGS Data Analysis, taking place June 15–19, 2026 in Berlin, Germany. Over five intensive days, you’ll work hands-on with real sequencing data and learn how to perform and understand key steps of modern NGS analysis — from quality control and mapping to RNA-seq workflows and variant interpretation. It’s
- [Non-invasive tape strip RNA sequencing tracks disease activity in alopecia areata](https://www.rna-seqblog.com/non-invasive-tape-strip-rna-sequencing-tracks-disease-activity-in-alopecia-areata/) - Researchers are exploring new ways to study skin diseases without needing invasive biopsies. In this work from the IMIBIC/University of Córdoba, scientists evaluated whether a simple tape-strip method could capture meaningful biological signals in alopecia areata, an autoimmune condition that targets hair follicles. Alopecia areata occurs when the immune system mistakenly attacks hair follicles, leading
- [Improving small RNA analysis with a new miRNA alignment tool](https://www.rna-seqblog.com/improving-small-rna-analysis-with-a-new-mirna-alignment-tool/) - Small non-coding RNAs, often abbreviated as sncRNAs, are short RNA molecules that play important roles in regulating gene expression. Among them, microRNAs, or miRNAs, are especially well known for controlling how messenger RNA is translated into proteins. Because of their role in many biological processes and diseases, including cancer, accurately identifying and measuring these molecules
- [Researchers identify the most common recessive neurodevelopmental disorder ever discovered](https://www.rna-seqblog.com/researchers-identify-the-most-common-recessive-neurodevelopmental-disorder-ever-discovered/) - Researchers at the Icahn School of Medicine at Mount Sinai in New York have identified and described a previously unknown recessive neurodevelopmental disorder (NDD) that appears to be the most prevalent ever discovered. The condition is caused by changes in a small noncoding gene called RNU2-2. It is estimated to affect thousands of individuals in the United States and account for about 10 percent of all recessive NDD cases with a known genetic cause. The work was done
- [Improving nucleic acid amplification with machine learning](https://www.rna-seqblog.com/improving-nucleic-acid-amplification-with-machine-learning/) - Amplifying DNA or RNA is a key step in many areas of biology, from disease diagnostics to emerging technologies like DNA-based data storage. However, controlling how efficiently genetic material is copied during amplification is not always easy. Small changes in sequence or reaction conditions can lead to uneven results, which can limit sensitivity and accuracy.
- [Understanding alternative splicing with long read sequencing](https://www.rna-seqblog.com/understanding-alternative-splicing-with-long-read-sequencing/) - Alternative splicing is a process that allows a single gene to produce multiple RNA transcripts, called isoforms. This greatly increases the diversity of proteins that cells can make, and it plays an important role in many biological processes. When alternative splicing is disrupted, it can contribute to diseases such as cancer and neurological disorders. Traditional
- [Researchers create revolutionary database to map neocortical development across species](https://www.rna-seqblog.com/researchers-create-revolutionary-database-to-map-neocortical-development-across-species/) - Result Could Lead to Treatments for ASD, Schizophrenia, and Dementia Researchers have described major advances in the understanding of the development of the neocortex —layer-by-layer and cell-by-cell—thanks to a pioneering database developed at the University of Maryland School of Medicine (UMSOM) that combines multiomic data from 188 different studies. The revolutionary and publicly accessible database,
- [Benchmarking circular RNA detection with long read sequencing](https://www.rna-seqblog.com/benchmarking-circular-rna-detection-with-long-read-sequencing/) - Circular RNAs, often called circRNAs, are a special type of RNA molecule that form a closed loop instead of the usual linear shape. Because they do not have loose ends, they are more stable than many other RNA types and can persist in cells longer. Scientists are increasingly interested in circRNAs because they can vary
- [tRIBO-seq reveals how active tRNAs regulate translation under stress](https://www.rna-seqblog.com/profiling-active-trnas-reveals-how-cells-adapt-protein-synthesis-under-stress/) - Protein production in cells depends on transfer RNAs, or tRNAs, which deliver amino acids to the ribosome based on instructions encoded in messenger RNA. While tRNAs are essential for translation, it has been difficult to measure how they behave during active protein synthesis, especially under different cellular conditions. Researchers at the Centre for Genomic Regulation
- [Cellular ‘atlas’ of prostate cancer opens new avenues for earlier detection](https://www.rna-seqblog.com/cellular-atlas-of-prostate-cancer-opens-new-avenues-for-earlier-detection/) - The newly discovered cell type (yellow) shown clustering around a prostate cancer nerve bundle. Prostate cancer affects one in five Australian men, making it the most common cancer in the country. Now, researchers at the Garvan Institute of Medical Research have produced the world’s most detailed cellular ‘atlas’ of early-stage prostate cancer, revealing the earliest
- [scSurv - a deep generative model for single-cell survival analysis](https://www.rna-seqblog.com/scsurv-a-deep-generative-model-for-single-cell-survival-analysis/) - A computational method called scSurv, developed by researchers at Institute of Science Tokyo, links individual cells to patient outcomes using widely available bulk RNA sequencing data. The approach uses single-cell reference datasets together with patient survival data to infer the contributions of individual cells within complex tissues. The model identified cell populations associated with survival
- [New research reveals how development and sex shape the brain](https://www.rna-seqblog.com/new-research-reveals-how-development-and-sex-shape-the-brain/) - Two companion studies, published in Cell Genomics, reveal how brain development lays the foundation for both shared and sex-specific circuits, redefining how neural diversity arises. A preview article linked to the report highlights the broader significance of these findings and places them in context for the field. Researchers from the University of Oxford have created the first
- [Cirena Launches High-Purity Long RNA to Accelerate CRISPR and Genome-Editing Research](https://www.rna-seqblog.com/cirena-launches-high-purity-long-rna-to-accelerate-crispr-and-genome-editing-research/) - Breakthrough technology delivers 100–400nt RNA with exceptional purity, enabling faster design cycles and improved editing precision Cirena, pioneers in long and ultra-long, high purity RNA synthesis for gene editing and functional genomics, today announced its public launch following successful delivery of high-quality long RNA to leading academic and pharmaceutical research teams across the U.S., Europe,
- [Improving RNA sequencing workflows for single cell plant research](https://www.rna-seqblog.com/improving-rna-sequencing-workflows-for-single-cell-plant-research/) - Understanding how different cell types function within a plant is important for studying growth, development, and responses to environmental stress. Single cell RNA sequencing allows scientists to examine gene expression in individual cells, revealing details that are often hidden in traditional bulk measurements. However, applying this technology to plants has been challenging due to difficulties
- [From pathology image to biological discovery: A journey with LazySlide](https://www.rna-seqblog.com/from-pathology-image-to-biological-discovery-a-journey-with-lazyslide/) - Cell detection with LazySlide in human colon tissue: Immune cells (green), connective tissue cells (blue) and epithelial cells (orange) Microscopic images of human tissue are a cornerstone of biomedical research and clinical diagnostics. Yet despite their importance, these images often remain difficult to analyze systematically and to connect with other types of biological data. A
- [RNA sequencing reveals codon driven control of mRNA stability](https://www.rna-seqblog.com/rna-sequencing-reveals-codon-driven-control-of-mrna-stability/) - Our genes are written in long strings of three-letter units composed of four different nucleotides. These units — or codons — specify one of many amino acids, the building blocks of proteins. Multiple codons can encode the same amino acid, which seems to point to some redundancy in our genetic code. Yet growing evidence suggests that these
- [Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets](https://www.rna-seqblog.com/souporcell3-robust-demultiplexing-for-high-donor-single-cell-rna-seq-datasets/) - Single cell RNA sequencing allows scientists to study gene expression in thousands or even millions of individual cells at once. To make experiments more efficient, researchers often pool samples from multiple donors into a single sequencing run. After sequencing, the data must be separated back into the correct individual sources, a process called demultiplexing. However,
- [Scientists turn cells’ most mysterious structures into spies on genetic activity](https://www.rna-seqblog.com/scientists-turn-cells-most-mysterious-structures-into-spies-on-genetic-activity/) - The barrel-shaped structures found by the thousands in most animal cells are one of biology’s biggest mysteries. But although researchers haven’t figured out the function of these “vaults,” they now report a new use for the puzzling particles...
- [Mapping mutation-driven RNA drug interactions with sequencing-based profiling](https://www.rna-seqblog.com/mapping-mutation-driven-rna-drug-interactions-with-sequencing-based-profiling/) - Small changes in DNA can have a big impact on how cells function. In cancer, mutations often alter how RNA molecules fold and behave. These structural changes can affect how RNA interacts with drugs, especially small molecules designed to bind RNA targets. Until now, it has been difficult to systematically measure how individual mutations influence
- [Direct RNA sequencing improves detection of RNA modifications for clinical use](https://www.rna-seqblog.com/direct-rna-sequencing-improves-detection-of-rna-modifications-for-clinical-use/) - RNA sequencing has become an essential tool for understanding gene expression and identifying biomarkers for disease. Most sequencing methods require converting RNA into DNA before analysis, which can introduce biases and miss important molecular details. A newer approach called direct RNA sequencing allows scientists to read RNA molecules in their natural form, preserving critical information
- [Taking pressure off the lungs](https://www.rna-seqblog.com/taking-pressure-off-the-lungs/) - Pulmonary arterial hypertension, or PAH, is a rare and severe disease characterized by elevated blood pressure in the pulmonary arteries, which transport blood from the heart to the lungs. This can eventually lead to right heart failure, when the heart’s right ventricle becomes too weak to pump sufficient blood through the lungs and to the
- [Building in silico patients using RNA sequencing and AI](https://www.rna-seqblog.com/building-in-silico-patients-using-rna-sequencing-and-ai/) - Cancer is not made up of identical cells. Tumors often contain a mix of different cell types, each behaving in its own way. This complexity, known as cellular heterogeneity, makes it difficult to predict how a patient will respond to treatment and is a major reason why some therapies fail. Researchers Northwestern Polytechnical University in
- [Using RNA sequencing and AI to design new drugs from scratch](https://www.rna-seqblog.com/using-rna-sequencing-and-ai-to-design-new-drugs-from-scratch/) - Discovering new drugs is a long and complex process that often starts with screening thousands of chemical compounds. In recent years, scientists have also explored how RNA sequencing data, which shows how genes are turned on or off in cells, can help identify drugs that reverse disease related changes in gene expression. Most of this
- [CellVoyager - AI agents expand insights from single cell RNA sequencing data](https://www.rna-seqblog.com/cellvoyager-ai-agents-expand-insights-from-single-cell-rna-sequencing-data/) - Modern biology generates massive datasets, especially from technologies like single cell RNA sequencing, which measures gene expression in individual cells. While these datasets contain valuable information, analyzing them fully can be challenging and often depends on the experience and creativity of the researcher. Researchers at Stanford University have developed a new AI system called CellVoyager
- [RNA barcodes enable high-speed mapping of connections in the brain](https://www.rna-seqblog.com/rna-barcodes-enable-high-speed-mapping-of-connections-in-the-brain/) - Comingling RNA barcodes, each correlating to a neuron, indicate where neurons connect in the brain, letting researchers map neural connection with speed, scale and resolution. Graphic by Michael Vincent. By tagging neurons with molecular “barcodes,” researchers mapped connections among thousands of neurons in the mouse brain with unprecedented speed and resolution. The approach could expand
- [Evaluating semi supervised methods for single cell RNA sequencing integration](https://www.rna-seqblog.com/evaluating-semi-supervised-methods-for-single-cell-rna-sequencing-integration/) - Single cell RNA sequencing allows scientists to study gene expression in individual cells, helping reveal how different cell types function and interact. However, combining datasets from different experiments can be difficult because of technical differences known as batch effects, which can make similar cells appear different. Researchers at Yale University conducted a large scale comparison
- [An open single-cell RNA-seq atlas reveals neural differentiation dynamics in sea urchin development](https://www.rna-seqblog.com/an-open-single-cell-rna-seq-atlas-reveals-neural-differentiation-dynamics-in-sea-urchin-development/) - RNA sequencing at single-cell resolution reveals developmental cell states in sea urchin embryos, helping researchers trace neurogenesis and explore gene expression...
- [RNA-seq analysis in seconds using GPUs](https://www.rna-seqblog.com/rna-seq-analysis-in-seconds-using-gpus/) - Modern biology generates enormous amounts of sequencing data, especially from RNA sequencing, which measures how genes are expressed inside cells. Analyzing these datasets can take significant computing time, even with efficient tools. A new report led by researchers at the University of Iceland shows how graphics processing units, GPUs, can dramatically accelerate this process. Many
- [Capsule technology opens new window into individual cells](https://www.rna-seqblog.com/capsule-technology-opens-new-window-into-individual-cells/) - Researchers have developed a capsule-based method that makes it possible to analyse the same cell through multiple experimental steps. The technology overcomes a long-standing limitation in cell research and could open new ways to study disease mechanisms at the single-cell level. The capsule-based technology opens up new possibilities for studying individual cells and their genetic
- [Research Advisor - Computational RNA Genomics](https://www.rna-seqblog.com/research-advisor-computational-rna-genomics/) - Lilly Genetic Medicine is at the forefront of developing innovative genetic therapies to treat and cure disease, combining cutting‑edge science with advanced technologies to translate genetic insights into breakthrough medicines. This Research Advisor role sits within a dynamic team applying deep sequencing and bioinformatic approaches to advance our therapeutic pipeline. The successful candidate will bridge
- [RNA sequencing advances are improving cell lineage tracing and reconstruction of cell fate decisions](https://www.rna-seqblog.com/rna-sequencing-advances-are-improving-cell-lineage-tracing-and-reconstruction-of-cell-fate-decisions/) - Over the past two decades, cell biologists and computational biologists have worked to develop lineage tracing techniques that can decode the relationships between progenitor cells and their differentiated progeny. Despite steady progress, the field has long been constrained by the limited specificity and scalability of experimental labeling methods, as well as the insufficient accuracy and
- [Crop Diagnostix launches RNA-based crop health early-warning system](https://www.rna-seqblog.com/crop-diagnostix-launches-rna-based-crop-health-early-warning-system/) - RNA reveals plants’ real-time biological response to stress, which occurs long before conventional tools detect problems, says the firm. A visual inspection of crops may suggest all is well. A tissue sample analyzed with spectroscopy may reveal otherwise. But both are lagging indicators of crop health, says California-based startup Crop Diagnostix, which is pioneering an approach
- [Improving mRNA therapeutics using RNA sequencing guided 5′UTR design](https://www.rna-seqblog.com/improving-mrna-therapeutics-using-rna-sequencing-guided-5′utr-design/) - Since the COVID-19 pandemic, mRNA vaccines have been attracting attention as a next-generation pharmaceutical technology. mRNA medicines deliver genetic information that directs cells to produce specific proteins, resulting in therapeutic effects. However, limitations have been raised, such as reduced efficacy in the elderly or obese. To address this issue, a team of Korean researchers has
- [HiFi long-read RNA sequencing enhances clinical diagnostics in rare disorders](https://www.rna-seqblog.com/hifi-long-read-rna-sequencing-enhances-clinical-diagnostics-in-rare-disorders/) - Many genetic diseases are caused by small changes in DNA that disrupt how genes are processed into RNA. One important step in this process is called RNA splicing. During splicing, segments of RNA called introns are removed and the remaining pieces called exons are joined together to produce a mature RNA molecule that can be
- [Moving from correlation to causation in gene regulatory networks](https://www.rna-seqblog.com/moving-from-correlation-to-causation-in-gene-regulatory-networks/) - Every cell in the body contains the same DNA, yet different cells behave in very different ways. Some become neurons, others muscle cells, and others form tissues and organs. This diversity is controlled by gene regulatory networks, often called GRNs, which describe how genes interact with one another to control when and how genes are
- [Single-cell RNA sequencing and spatial transcriptomics map complex interplay between cells, metabolism, and immunity in breast cancer lymph node metastasis](https://www.rna-seqblog.com/single-cell-rna-sequencing-and-spatial-transcriptomics-map-complex-interplay-between-cells-metabolism-and-immunity-in-breast-cancer-lymph-node-metastasis/) - A recent integrative analysis of single-cell sequencing and single-cell spatial mapping of lymph node metastasis in breast cancer reveals novel mechanisms of the metabolic-immune interaction that drive the spread of breast cancer. The findings from the study in The American Journal of Pathology, published by Elsevier, offer novel insights into the characteristics of the metastatic
- [Assessing mRNA and sgRNA quality for cell and gene therapy applications using nanopore direct RNA sequencing](https://www.rna-seqblog.com/assessing-mrna-and-sgrna-quality-for-cell-and-gene-therapy-applications-using-nanopore-direct-rna-sequencing/) - RNA based therapeutics are rapidly expanding across modern medicine. Messenger RNA vaccines, gene editing systems, and RNA based immunotherapies all rely on carefully designed RNA molecules to work correctly. Because these molecules directly influence biological processes inside cells, scientists must carefully measure their quality and structure before they can be used in clinical applications. Researchers
- [A streamlined workflow for multiomic single cell analysis from low input clinical samples](https://www.rna-seqblog.com/a-streamlined-workflow-for-multiomic-single-cell-analysis-from-low-input-clinical-samples/) - Clinical samples collected from patients often contain only a small number of cells. Despite this limitation, these samples can provide valuable information about how diseases develop, how the immune system responds, and how patients react to treatments. Extracting as much biological information as possible from these limited samples is therefore a major goal in biomedical
- [Piecing together parasitic plant pathways](https://www.rna-seqblog.com/piecing-together-parasitic-plant-pathways/) - Determining the developmental pathway for an organ that parasitic plants use to siphon off nutrients from hosts could help scientists find ways to curb the parasite A confocal microscopy image showing the initial stages of an haustorium developing in Phtheirospermum japonicum, as a model plant for parasitic Striga. © 2026 RIKEN Center for Sustainable Resource Science Genes
- [Minaris launches AgentSCREEN adventitious virus RNA detection by NGS](https://www.rna-seqblog.com/minaris-launches-agentscreen-adventitious-virus-rna-detection-by-ngs/) - GMP-qualified NGS adventitious virus detection with a predictable 28-day turnaround and U.S.-based end-to-end support Minaris, a global cell and gene therapy (CGT) contract development and manufacturing organization (CDMO) and multimodality biosafety testing provider, today announced the launch of AgentSCREEN Adventitious Virus Detection by Next Generation Sequencing (NGS). The GMP-qualified platform is designed to streamline adventitious agent
- [Spatial RNA sequencing reveals how microbes and host cells interact in the gut](https://www.rna-seqblog.com/spatial-rna-sequencing-reveals-how-microbes-and-host-cells-interact-in-the-gut/) - The human gut is home to trillions of microbes that constantly interact with each other and with the cells lining the intestine. These interactions influence digestion, immune responses, and even disease development. However, studying these relationships has been difficult because many techniques cannot show exactly where microbes and host cells are located relative to one
- [HIV-seq improves detection of HIV-transcribing cells using RNA sequencing](https://www.rna-seqblog.com/hiv-seq-improves-detection-of-hiv-transcribing-cells-using-rna-sequencing/) - People living with HIV who are receiving antiretroviral therapy, often called ART, can suppress the virus to very low levels. Even with effective treatment, some infected cells continue to produce small amounts of HIV RNA. These rare cells are thought to contribute to chronic inflammation and may play a role in viral rebound if therapy
- [Decoding citronella - first haplotype-resolved genome illuminates citronelloid biosynthesis](https://www.rna-seqblog.com/decoding-citronella-first-haplotype-resolved-genome-illuminates-citronelloid-biosynthesis/) - Citronelloid compounds such as citronellal and citronellol function in plant defense and ecological communication, and they are also widely used in pharmaceuticals and essential oils. Within the Poaceae family, species of the genus Cymbopogon display striking differences in citronelloid accumulation, yet the evolutionary origin and biosynthetic regulation of these compounds have remained poorly understood. The absence of
- [Northside Hospital introduces advanced leukemia test](https://www.rna-seqblog.com/northside-hospital-introduces-advanced-leukemia-test/) - Northside Hospital is introducing a new test to help diagnose leukemia faster and more accurately, giving patients quicker answers and helping doctors choose the most effective treatments sooner. Acute myeloid leukemia (AML) and related blood cancers are not all the same. They can look similar but behave differently based on specific genetic changes inside the
- [Alithea Genomics Closes CHF 6.9 M Seed Round, Using Proceeds to Unlock Industrial-Scale RNA-seq for Primary Drug Screening and Toxicology](https://www.rna-seqblog.com/alithea-genomics-closes-chf-6-9-m-seed-round-using-proceeds-to-unlock-industrial-scale-rna-seq-for-primary-drug-screening-and-toxicology/) - Alithea Genomics, an emerging leader in the field of large-scale RNA sequencing and transcriptomics, announced today the closing of its seed financing round with an additional CHF 3 million ($3.9 million), led by Genku Ventures and joined by Novalis Biotech and Zürcher Kantonalbank as well as several private investors. This additional funding brings the total seed
- [A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction](https://www.rna-seqblog.com/a-functionally-integrated-cross-tissue-alternative-splicing-program-during-short-term-calorie-restriction/) - Calorie restriction, reducing calorie intake without causing malnutrition, has long been studied for its effects on metabolism, aging, and overall health. Scientists have observed that lowering calorie intake can influence many biological pathways, but the underlying molecular mechanisms are still being explored. In new research led by researchers at the University of Aberdeen, investigators examined
- [High-performance cell atlas workflow driven by manifold fitting](https://www.rna-seqblog.com/high-performance-cell-atlas-workflow-driven-by-manifold-fitting/) - Researchers from the National University of Singapore (NUS) have developed CellScope, a high-performance single-cell analysis framework that uses manifold fitting to analyse single-cell RNA sequencing (scRNA-seq) data. This framework helps build detailed “cell atlases” that map different cell types and show how they further group into finer subtypes. As single-cell atlases grow in size and
- [Pancreatic cancer may begin hiding from the immune system earlier than we thought](https://www.rna-seqblog.com/pancreatic-cancer-may-begin-hiding-from-the-immune-system-earlier-than-we-thought/) - A new study suggests that pancreatic cancer may start preparing to “hide” from the immune system long before the disease becomes full-blown cancer. Researchers found that very early, precancerous cells in the pancreas don’t spread randomly, they gather into specific clusters and create small “neighborhoods” inside the tissue. These early cell groups also seem to
- [Immune cells remember their location](https://www.rna-seqblog.com/immune-cells-remember-their-location/) - Researchers in Bonn use an AI algorithm to reconstruct the spatial origin of macrophages A new AI-based method reconstructs spatial information about where immune cells were originally located in an organ, even after these cells have been removed from the tissue and analyzed individually. To accomplish this, researchers at the University Hospital Bonn (UKB) and
- [Smoking triggers molecular changes that may drive macular degeneration](https://www.rna-seqblog.com/smoking-triggers-molecular-changes-that-may-drive-macular-degeneration/) - Through a series of experiments supported by the National Institutes of Health, Johns Hopkins Medicine (JHM) researchers say they have advanced understanding of how smoking damages the eye and contributes to the development of age-related macular degeneration (AMD), the leading worldwide cause of visual impairment and blindness among people 50 and older. It has long been
- [Ultima Genomics launches UG200 series and Solaris 2.0 workflows for scalable sequencing](https://www.rna-seqblog.com/ultima-genomics-launches-ug200-series-and-solaris-2-0-workflows-for-scalable-sequencing/) - Twice the output, half the runtime, and half the footprint of the UG 100® with greater flexibility and improved genomic coverage Introducing two new high-throughput instrument configurations accessible for as low as $850,000 Next-gen amplification eliminates the need for a dedicated ePCR instrument and greatly improves coverage in clinically relevant regions of the genome, while maintaining Ultima’s
- [A new framework improves integration of single cell data](https://www.rna-seqblog.com/a-new-framework-improves-integration-of-single-cell-data/) - Modern biology can now measure many types of information from the same single cell. For example, scientists can examine gene expression using RNA sequencing, measure chromatin accessibility, quantify protein abundance, and even analyze spatial imaging data. While these technologies are powerful, combining the different data types into one clear picture of cell state remains challenging.
- [A chatbot simplifies RNA sequencing data analysis](https://www.rna-seqblog.com/a-chatbot-simplifies-rna-sequencing-data-analysis/) - RNA sequencing has become a standard method for measuring gene expression across thousands of genes at once. While the technology itself is powerful, analyzing the resulting data can be complex. Researchers often need bioinformatics expertise to select appropriate statistical tests, perform normalization, filter low quality data, and interpret results correctly. For many laboratories, this creates
- [SUM-seq - single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing](https://www.rna-seqblog.com/sum-seq-single-cell-ultra-high-throughput-multiplexed-chromatin-accessibility-and-gene-expression-sequencing/) - Understanding how genes are turned on and off requires looking at both gene expression and the regulatory elements that control it. Single cell technologies now allow scientists to examine these processes in individual cells, helping reveal cellular diversity and regulatory networks. However, combining measurements of chromatin accessibility and gene expression in the same cell can
- [A user friendly tool brings RNA sequencing analysis to the classroom](https://www.rna-seqblog.com/a-user-friendly-tool-brings-rna-sequencing-analysis-to-the-classroom/) - RNA sequencing, often called RNA-seq, has become one of the most important tools for studying how genes are turned on and off in cells. It allows researchers to measure gene expression across the entire genome, helping scientists understand diseases, development, and biological responses to treatment. However, analyzing RNA sequencing data can be complicated and often
- [Mapping gene activity in three dimensions with volumetric DNA microscopy](https://www.rna-seqblog.com/mapping-gene-activity-in-three-dimensions-with-volumetric-dna-microscopy/) - Biological tissues are three dimensional structures. Cells are arranged in complex layers and neighborhoods, and their position often influences how they behave. However, many spatial transcriptomics methods rely on very thin tissue sections. While these techniques provide valuable information, they do not fully capture the three dimensional organization of intact tissues. Researchers at the University
- [A new method reveals hidden rules of gene control](https://www.rna-seqblog.com/a-new-method-reveals-hidden-rules-of-gene-control/) - An artistic rendition of Mtb transcription. (credit: Andrew Tivon) Inside every cell, thousands of molecular signals collide, overlap, and compensate, obscuring the true drivers of gene expression. Scientists have now developed a way to silence that cellular noise, revealing transcription drivers by reconstructing transcription outside of the cell. This approach, described in a paper published in Molecular
- [RNA-Seq identifies aging-associated mitochondrial circular RNAs](https://www.rna-seqblog.com/rna-seq-identifies-aging-associated-mitochondrial-circular-rnas/) - Led by first author Hyejin Mun from the University of Oklahoma, with corresponding authors Je-Hyun Yoon from the University of Oklahoma and Young-Kook Kim from Chonnam National University Medical School, the study profiles mitochondrial circular RNAs in Peripheral Blood Mononuclear Cells (PBMCs) from young and old human cohorts and probes how mitochondrial circRNAs and the mitochondrial RNA-binding protein GRSF1
- [New single-cell transcriptomic clock reveals intrinsic and systemic T cell aging in COVID-19 and HIV](https://www.rna-seqblog.com/new-single-cell-transcriptomic-clock-reveals-intrinsic-and-systemic-t-cell-aging-in-covid-19-and-hiv/) - Researchers Alan Tomusiak from the Buck Institute for Research on Aging and the University of Southern California, and Sierra Lore from the Buck Institute for Research on Aging and the University of Copenhagen, together with corresponding author Eric Verdin from the Buck Institute for Research on Aging, developed a new single-cell transcriptomic clock called T immune cell transcriptomic clock (Tictock) to
- [Simple methods rival ai models in single cell RNA analysis](https://www.rna-seqblog.com/simple-methods-rival-ai-models-in-single-cell-rna-analysis/) - Single-cell RNA sequencing, often called scRNA-seq, allows scientists to measure gene activity in thousands or even millions of individual cells. Because these datasets are large and complex, researchers have recently developed powerful artificial intelligence systems, including transformer-based foundation models like TranscriptFormer, to learn patterns in gene expression. These deep learning models create mathematical representations of
- [RNA sequencing reveals STING driven immunotherapy targets in meningioma](https://www.rna-seqblog.com/rna-sequencing-reveals-sting-driven-immunotherapy-targets-in-meningioma/) - Northwestern Medicine scientists have discovered a potent immunotherapy approach for treating meningiomas, the most common type of primary brain tumor, according to a recent study published in Nature Communications. More than 39,000 Americans are diagnosed with meningioma each year, according to the National Brain Tumor Society. The tumor originates from cells in the meninges, a fibrous membrane that
- [Key proteins found to drive abnormal bone growth after injury](https://www.rna-seqblog.com/key-proteins-found-to-drive-abnormal-bone-growth-after-injury/) - After serious injuries, burns, fractures, or major surgeries, the body normally repairs damaged tissues and restores movement. However, in some patients, the healing process takes an unexpected and harmful turn. Instead of rebuilding healthy muscle and tendon, new bone begins to form inside soft tissues, causing pain, stiffness, and long-term disability. This condition, known as
- [Element Biosciences Introduces VITARI™](https://www.rna-seqblog.com/element-biosciences-introduces-vitari-redefining-what-high-throughput-sequencing-makes-possible/) - Element Biosciences Inc. today announced VITARI, the first ever high-throughput benchtop sequencing system capable of delivering a high-quality whole genome at $100. With the introduction of VITARI, Element now offers a comprehensive and cohesive portfolio of systems curated to support laboratories as they grow, while maintaining a foundation designed so scientists never have to choose between quality,
- [Improving batch correction for single-cell RNA sequencing data](https://www.rna-seqblog.com/improving-batch-correction-for-single-cell-rna-sequencing-data/) - Over the past decade, single-cell technologies have allowed scientists to measure gene activity in thousands to millions of individual cells. These large datasets have made it possible to build detailed cell atlases of tissues, organs, and even entire organisms. However, as these datasets grow, so do the challenges in comparing results generated at different times,
- [Droplet vs picowell - considerations for single-cell transcriptomic profiling](https://www.rna-seqblog.com/droplet-vs-picowell-considerations-for-single-cell-transcriptomic-profiling/) - Understanding diseases of the gastrointestinal tract, including colon cancer, often depends on studying how genes are turned on or off inside individual cells. Single cell RNA sequencing has become an important tool for this purpose because it allows researchers to examine gene expression in thousands of individual cells at once. However, working with human colon
- [Mapping protein production in brain cells yields new insights for brain disease](https://www.rna-seqblog.com/mapping-protein-production-in-brain-cells-yields-new-insights-for-brain-disease/) - UC San Diego and Scripps Research scientists used a novel method to show that some memory neurons produce proteins at higher rates than others. A new method lets researchers visualize messenger RNA translation across different brain cell types. In this image, CA3 pyramidal neurons of the mouse hippocampus glow magenta, indicating especially high rates of
- [scHiCAR - trimodal single-cell profiling of transcriptome, epigenome and 3D genome](https://www.rna-seqblog.com/schicar-trimodal-single-cell-profiling-of-transcriptome-epigenome-and-3d-genome/) - Understanding how genes are turned on and off requires more than simply measuring RNA levels. Inside the nucleus, DNA is folded in three dimensions, and this folding helps bring regulatory DNA elements, called cis regulatory elements, into contact with the genes they control. These long-range interactions play a critical role in transcription, the process by
- [CubaseBio emerges from stealth to scale true 3D spatial transcriptomics with €5.9M in financing](https://www.rna-seqblog.com/cubasebio-emerges-from-stealth-to-scale-true-3d-spatial-transcriptomics-with-e5-9m-in-financing/) - CubaseBio, a biotechnology company founded by pioneers in spatial biology, today announced it has secured €5.9 million in blended financing. The funding comprises a €2 million non-dilutive grant from the European Innovation Council (EIC) Transition program and €3.9 million in private capital and convertibles from Voima Ventures, Nordic Science Investments (NSI), Illumina Ventures, Almi invest,
- [AI-enabled gene discovery opens door to personalised psoriasis treatment](https://www.rna-seqblog.com/ai-enabled-gene-discovery-opens-door-to-personalised-psoriasis-treatment/) - Using RNA sequencing and machine learning, researchers identified gene signatures that define psoriasis subtypes and severity...
- [Breakthrough in human norovirus research: scientists overcome major obstacle to grow and study the virus](https://www.rna-seqblog.com/breakthrough-in-human-norovirus-research-scientists-overcome-major-obstacle-to-grow-and-study-the-virus/) - Researchers at Baylor College of Medicine report in Science Advances a breakthrough in human norovirus (HuNoV) research. Norovirus is a leading cause of acute viral gastroenteritis worldwide with severe outcomes mostly among young children, the elderly and people with weakened or compromised immune systems. There are currently no approved vaccines or antiviral therapies, and management strategies rely
- [First cell type-specific gene regulatory maps for Alzheimer's disease](https://www.rna-seqblog.com/first-cell-type-specific-gene-regulatory-maps-for-alzheimers-disease/) - Newly developed data analysis method uncovers causal mechanisms of disease Public health researchers use newly developed data analysis method to build the first cell type-specific gene regulatory maps for Alzheimer’s disease, revealing the genetic mechanisms operating within patients’ brains. The study also identified numerous influential “hub genes” that offer promising new targets for early detection and
- [A practical guide to targeted single-cell RNA sequencing technologies](https://www.rna-seqblog.com/a-practical-guide-to-targeted-single-cell-rna-sequencing-technologies/) - Single cell RNA sequencing has become one of the most powerful tools in modern biology. It allows researchers to measure gene activity in individual cells, helping scientists understand cell types, developmental processes, and disease mechanisms. However, current single cell RNA sequencing methods have important limitations. Most widely used approaches only detect about 10 to 40
- [Nanopore sequencing of intact aminoacylated tRNAs](https://www.rna-seqblog.com/nanopore-sequencing-of-intact-aminoacylated-trnas/) - Transfer RNAs, or tRNAs, play a central role in building proteins. Each tRNA carries a specific amino acid and delivers it to the ribosome, where proteins are assembled. For this process to work correctly, the tRNA must be properly modified and correctly attached to its matching amino acid, a step known as aminoacylation. Studying tRNAs
- [Researchers identify potential immune evasion mechanism in premalignant lung lesions](https://www.rna-seqblog.com/researchers-identify-potential-immune-evasion-mechanism-in-premalignant-lung-lesions/) - Intercepting these molecular and cellular changes may prevent or delay lung cancer development, reducing lung cancer–related mortality. Throughout a person’s lifetime, the cells lining the respiratory tract are exposed to inhaled pollutants, including cigarette smoke. These exposures can cause molecular changes that disrupt normal cell behavior, leading to abnormal growth and function. Over time, these
- [Breakthrough UC study sheds light on survival of new neurons in adult brain](https://www.rna-seqblog.com/breakthrough-uc-study-sheds-light-on-survival-of-new-neurons-in-adult-brain/) - Breakthrough research from the University of Cincinnati College of Medicine is revealing how immune cells in the adult brain can regulate the generation of new neurons. The study is leading to a new understanding of how immune cells can influence adult neurogenesis, the process of creating new neurons in the brain. Neurons are the brain’s
- [RMzyme - regulations of RNA-modifying enzymes in humans](https://www.rna-seqblog.com/rmzyme-regulations-of-rna-modifying-enzymes-in-humans/) - Inside every cell, RNA molecules help carry genetic instructions and guide the production of proteins. These RNA molecules are not static. They can be chemically modified after they are made, and these modifications can influence how stable the RNA is, how efficiently it is translated into protein, and how genes are regulated. Scientists call this
- [Quiescent or senescent? Cancer center research helps identify cancer that is more likely to recur](https://www.rna-seqblog.com/quiescent-or-senescent-cancer-center-research-helps-identify-cancer-that-is-more-likely-to-recur/) - In a study that could have implications for more effective cancer therapies and preventing cancer recurrence, University of Colorado Anschutz Cancer Center member Sabrina Spencer, PhD, working with graduate student Brianna Fernandez, used single-cell RNA sequencing to investigate the cell-cycle state of cells following chemotherapy. Specifically, the researchers were looking to characterize cells in one of
- [Using gene expression in blood to personalize care for APS](https://www.rna-seqblog.com/using-gene-expression-in-blood-to-personalize-care-for-aps/) - Treating antiphospholipid syndrome by focusing on blood clots falls short of addressing the underlying biology driving each individual patient’s disease Antiphospholipid syndrome, also known as APS, is an autoimmune disease that sits at the intersection of inflammation and blood clotting. Antiphospholipid syndrome is best known for increasing the risk of blood clots or pregnancy complications.
- [MEBOCOST - mapping metabolite-mediated intercellular communications using single-cell RNA-seq](https://www.rna-seqblog.com/mebocost-mapping-metabolite-mediated-intercellular-communications-using-single-cell-rna-seq-2/) - Cells are constantly communicating with each other to keep tissues healthy and functioning properly. Much of what we know about cell to cell communication focuses on proteins, such as hormones or signaling molecules that bind to receptors on neighboring cells. However, cells also communicate using small molecules called metabolites. These metabolite driven signals are harder
- [AI model may improve RNA sequencing research](https://www.rna-seqblog.com/ai-model-may-improve-rna-sequencing-research/) - Scientists in the laboratory of Rendong Yang, PhD, associate professor of Urology, have developed a new large language model that can interpret transcriptomic data in cancer cell lines more accurately than conventional approaches, as detailed in a recent study published in Nature Communications. Long-read RNA sequencing technologies have transformed transcriptomics research by detecting complex RNA splicing and gene fusion events that have often been missed by conventional short-read RNA-sequencing methods. Among these technologies includes nanopore
- [MUTACLASH - identifying functional small RNA target sites with crosslinking footprints](https://www.rna-seqblog.com/mutaclash-identifying-functional-small-rna-target-sites-with-crosslinking-footprints/) - Small RNAs such as microRNAs and piRNAs help control how genes are turned on or off. They do this by binding to messenger RNAs, which carry the instructions for making proteins. However, figuring out exactly where these small RNAs bind, and which binding events actually matter for gene regulation, has been challenging. Researchers at National
- [scSNViz - visualization and analysis of cell-specific expressed SNVs](https://www.rna-seqblog.com/scsnviz-visualization-and-analysis-of-cell-specific-expressed-snvs/) - Single-cell RNA sequencing has transformed how researchers study complex tissues by revealing differences in gene expression from one cell to the next. But understanding variation goes beyond expression alone. Cells can differ in the genetic variants they express, including single-nucleotide variants, which can reflect mutations, allele-specific expression, or regulatory processes such as imprinting and transcriptional
- [Rutgers develops new tool for examining cancer genomic data that could improve treatment](https://www.rna-seqblog.com/rutgers-develops-new-tool-for-examining-cancer-genomic-data-that-could-improve-treatment/) - When scientists sequence tumor DNA, they typically find small amounts of genetic code from bacteria, viruses and fungi – microorganisms that, if actually present in tumor tissues, could influence how they grow, evade immunity or respond to treatment. But do microorganisms truly reside in tumors, or do the samples become contaminated before sequencing occurs? Independent
- [Ribo-seq Guide: Workflow, QC Metrics, Translational Efficiency, and Method Comparison](https://www.rna-seqblog.com/ribo-seq-guide-workflow-qc-metrics-translational-efficiency-and-method-comparison/) - Translatomics sequencing complements RNA sequencing by revealing which mRNAs are actively translated, uncovering translational efficiency, ribosome dynamics, and regulatory mechanisms invisible at the transcript level...
- [Identification of the central pathological substrate of bipolar disorder as paraventricular thalamic nucleus](https://www.rna-seqblog.com/identification-of-the-central-pathological-substrate-of-bipolar-disorder-as-paraventricular-thalamic-nucleus/) - Insights into a novel diagnostic and therapeutic target in bipolar disorder Bipolar disorder is a significant global health issue, affecting millions worldwide. To address the urgent need for novel therapeutic approaches, it is important to deepen the understanding of its pathology. A group of researchers from the Juntendo University has demonstrated how alterations and abnormalities
- [Reading RNA modifications directly with nanopore sequencing](https://www.rna-seqblog.com/reading-rna-modifications-directly-with-nanopore-sequencing/) - RNA molecules carry more information than just their sequence. Many RNAs contain chemical modifications, often called the epitranscriptome, that influence how RNA is processed, translated, and regulated. Mapping these modifications across the transcriptome is essential for understanding development, stress responses, and disease, but doing so at scale has been technically difficult. Researchers at the University
- [One immune variable predicts poor outcomes across tumor types and species](https://www.rna-seqblog.com/one-immune-variable-predicts-poor-outcomes-across-tumor-types-and-species/) - Renowned as first responders to threatening infections, neutrophils also happen to feature prominently in the microenvironment of tumors, where they and other immune cells play opposing and frequently mutable roles in promoting—or resisting—cancer progression. Though they’ve been linked to the growth of multiple cancers, including those of the lung and breast, neutrophils can assume multiple
- [ULMnet - inferring physical cell-cell communication networks from scRNAseq data using univariate linear models](https://www.rna-seqblog.com/ulmnet-inferring-physical-cell-cell-communication-networks-from-scrnaseq-data-using-univariate-linear-models/) - Cells in tissues communicate in many ways, by sending signals over distance or by directly touching neighboring cells. Single-cell RNA sequencing has become a standard tool for studying these interactions, but it has an important limitation. To sequence individual cells, tissues must be dissociated, and this process breaks apart physical cell contacts, making it hard
- [Understanding what’s going on inside of cells: the dimensionality of gene expression](https://www.rna-seqblog.com/understanding-whats-going-on-inside-of-cells-the-dimensionality-of-gene-expression/) - Researchers at the University of Miami Miller School of Medicine research provided strong evidence that a new platform is a viable, accurate approach to mapping cell development. Dr. Leor Weinberger, chair and professor in the Miller School’s Department of Cell and Systems Biology, and Binyamin Zuckerman, Ph.D., performed single-cell sequencing on C elegans embryos extracted
- [ADAM-tRNA-seq - an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing](https://www.rna-seqblog.com/adam-trna-seq-an-optimized-approach-for-demultiplexing-and-enhanced-hierarchal-mapping-in-direct-trna-sequencing/) - Transfer RNAs, or tRNAs, are small but essential molecules that help cells turn genetic information into proteins. Beyond this classic role, changes in tRNA levels, chemical modifications, or charging with amino acids have been linked to cancer, neurodegeneration, and other diseases. Understanding these molecules in detail has been difficult, largely because many tRNAs are extremely
- [Research uses cutting-edge technology to map how gums become diseased](https://www.rna-seqblog.com/research-uses-cutting-edge-technology-to-map-how-gums-become-diseased-2/) - Millions of people worldwide suffer from gum disease, yet we still don’t fully understand how healthy gums turn into damaged, scar-like tissue. Researchers are using cutting-edge single-cell technology to map every individual cell in the gums, uncovering new clues that could transform how periodontitis is treated. The research was led by Vitor C. M. Neves, Senior
- [Hierarchical analysis of RNA secondary structures with pseudoknots based on sections](https://www.rna-seqblog.com/hierarchical-analysis-of-rna-secondary-structures-with-pseudoknots-based-on-sections/) - RNA molecules do much more than carry genetic messages. They fold into specific shapes that help control how genes are regulated, how proteins are made, and how enzymes function. One of the most challenging features to predict in RNA folding is the pseudoknot, a structure where loops and base pairs intertwine in complex ways. These
- [Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss](https://www.rna-seqblog.com/improving-atlas-scale-single-cell-annotation-models-with-hierarchical-cross-entropy-loss/) - Single-cell RNA sequencing has transformed biology by letting scientists examine gene activity one cell at a time. A key challenge in this process is correctly identifying what type of cell each sequenced cell actually is. This step, known as cell type annotation, is essential because all downstream biological insights depend on getting these labels right.
- [RNA sequencing reveals distinct molecular subtypes of brain metastases](https://www.rna-seqblog.com/rna-sequencing-reveals-distinct-molecular-subtypes-of-brain-metastases/) - An interdisciplinary multi-centre research team led by the LKS Faculty of Medicine (HKUMed) and Faculty of Dentistry at the University of Hong Kong has constructed the world’s largest multi-omics atlas of brain metastases. This comprehensive analysis included 1,032 brain metastasis samples from diverse primary tumours, together with 82 matched primary tumours and 20 glioblastomas (a
- [omnideconv - a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data](https://www.rna-seqblog.com/omnideconv-a-unifying-framework-for-using-and-benchmarking-single-cell-informed-deconvolution-of-bulk-rna-seq-data/) - Understanding which cell types are present in a tissue is essential for interpreting gene expression data, especially when samples contain a mixture of many different cells. Bulk transcriptomics measures the average gene expression across all cells in a sample, which can hide important cell specific signals. To overcome this, scientists use cell type deconvolution methods
- [SeekGene Launches High-Throughput Single-Cell DNA Methylation + RNA Multi-Omics Solution](https://www.rna-seqblog.com/seekgene-launches-high-throughput-single-cell-dna-methylation-rna-multi-omics-solution/) - New platform integrates epigenetic and transcriptomic analysis in a unified workflow, addressing key challenges in single-cell multi-omics research. SeekGene, a biotechnology company specializing in single-cell technology platforms, announced the launch of its novel high-throughput single-cell DNA methylation and RNA multi-omics solution at the Festival of Genomics & BioData 2026. The solution aims to simplify integrated
- [Scientists find hidden diversity inside common brain parasite](https://www.rna-seqblog.com/scientists-find-hidden-diversity-inside-common-brain-parasite/) - UC Riverside study reshapes understanding of toxoplasmosis and identifies new paths for treatment A University of California, Riverside team of scientists has found that Toxoplasma gondii, a common parasite affecting up to one-third of the global population, is far more complex than previously believed. The findings, published in Nature Communications, offer new insight into how T. gondii causes disease
- [RNA sequencing reveals metabolic and synaptic changes in Alzheimer’s disease](https://www.rna-seqblog.com/rna-sequencing-reveals-metabolic-and-synaptic-changes-in-alzheimers-disease/) - Alzheimer’s disease develops slowly and involves many biological changes that begin long before clear symptoms appear. Because of this complexity, researchers are increasingly focused on finding early molecular signals that could help improve diagnosis and guide intervention. Researchers at Universidad del Valle, Colombia used RNA sequencing to study gene activity in blood samples from people
- [Mapping the hidden diversity of pediatric brain tumors](https://www.rna-seqblog.com/mapping-the-hidden-diversity-of-pediatric-brain-tumors/) - Few things are as frightening for a parent as hearing that their child has a brain tumor. Names like medulloblastoma and ependymoma are overwhelming on their own. But for some families, the diagnosis becomes even more daunting if it is followed by three letters: NOS or “not otherwise specified”. Medulloblastoma and ependymoma are among the most common pediatric brain
- [RNA sequencing reveals how low-dose THC and celecoxib may improve Alzheimer’s disease](https://www.rna-seqblog.com/rna-sequencing-reveals-how-low-dose-thc-and-celecoxib-may-improve-alzheimers-disease/) - In recent years, research into cannabis and its main psychoactive ingredient, Δ⁹-tetrahydrocannabinol (THC), has unearthed medical benefits including anti-inflammatory and neuroprotective properties. However, THC is also known to negatively affect learning and memory, limiting its potential clinical usefulness, particularly in disorders of the brain. Now, a new study led by Chu Chen, PhD, professor in the
- [scRNA-seq reveals antibody-producing immune cells that can help shape cancer immunotherapy](https://www.rna-seqblog.com/scrna-seq-reveals-antibody-producing-immune-cells-that-can-help-shape-cancer-immunotherapy/) - Scientists at the Icahn School of Medicine at Mount Sinai have identified an important immune response that helps explain why some cancer patients benefit from immunotherapy while others do not. In a study published in the January 27 online issue of Nature Medicine (DOI 10.1038/s41591-025-04177-6), the researchers found that antibody-producing immune cells called IgG1 plasma cells play a key role in helping patients respond to
- [Comparing the impact of sample multiplexing approaches for single-cell RNA-sequencing on downstream analysis](https://www.rna-seqblog.com/comparing-the-impact-of-sample-multiplexing-approaches-for-single-cell-rna-sequencing-on-downstream-analysis/) - Single cell RNA sequencing has become a powerful way to study how individual cells behave within complex tissues. One challenge, however, is throughput, running many samples and many cells can quickly become expensive and time consuming. To address this, researchers often use multiplexing, a strategy that labels cells from different samples so they can be
- [The world’s first elucidation of the immunomodulatory effects of kimchi](https://www.rna-seqblog.com/the-worlds-first-elucidation-of-the-immunomodulatory-effects-of-kimchi/) - Amid concerns about the simultaneous spread of multiple respiratory diseases, such as colds and influenza, with the change of seasons in current times, a recent clinical study has scientifically proven that kimchi, a traditional Korean fermented food, enhances the function of human immune cells and maintains the balance of the immune system. The World Institute
- [Researchers develop deep-learning tools to transform cancer diagnosis and genomic research](https://www.rna-seqblog.com/researchers-develop-deep-learning-tools-to-transform-cancer-diagnosis-and-genomic-research/) - Researchers from the Faculty of Engineering at The University of Hong Kong (HKU) have developed two innovative deep-learning algorithms, ClairS-TO and Clair3-RNA, that significantly advance genetic mutation detection in cancer diagnostics and RNA-based genomic studies. The pioneering research team, led by Professor Ruibang Luo from the School of Computing and Data Science, Faculty of Engineering,
- [Uncovering cancer's hidden oncRNA signatures - from discovery to liquid biopsy](https://www.rna-seqblog.com/uncovering-cancers-hidden-oncrna-signatures-from-discovery-to-liquid-biopsy/) - Researchers at UCSF identified something unusual with T3p, a small RNA present in breast cancer but absent from normal tissue. First described in 2018, this molecule launched a six-year effort to systematically map orphan non-coding RNAs, known as oncRNAs, across all major cancer types, determine which ones actively drive disease, and demonstrate their potential for
- [The GENCODE CLS project - massively expanding the lncRNA catalog through capture long-read RNA sequencing](https://www.rna-seqblog.com/the-gencode-cls-project-massively-expanding-the-lncrna-catalog-through-capture-long-read-rna-sequencing/) - Understanding how genomes work depends on knowing where genes are and what they produce. While protein-coding genes are relatively well annotated, long non-coding RNAs, or lncRNAs, have remained one of the least understood parts of the genome. These RNAs do not encode proteins, but they play important roles in regulating gene activity, development, and disease.
- [A dual context-aware basecaller for nanopore direct RNA sequencing](https://www.rna-seqblog.com/a-dual-context-aware-basecaller-for-nanopore-direct-rna-sequencing/) - Nanopore direct RNA sequencing (DRS) lets scientists read native RNA molecules directly, preserving important features such as chemical modifications and avoiding biases introduced by copying RNA into DNA. This makes it a powerful tool for studying the transcriptome, the full set of RNA molecules in a cell. However, one long-standing challenge has been a relatively
- [A New Method for Nanopore Direct RNA-Seq Pushes the Limits of Long Transcript Identification and Isoform Resolution](https://www.rna-seqblog.com/a-new-method-for-nanopore-direct-rna-seq-pushes-the-limits-of-long-transcript-identification-and-isoform-resolution/) - Direct RNA sequencing (DRS) on nanopore platforms promises something short-read methods cannot: native RNA molecules read end-to-end, with isoforms, long transcripts, and RNA modifications preserved. In practice, however, many labs find that conventional DRS workflows underdeliver on that promise...
- [Impact and correction of segmentation errors in spatial transcriptomics](https://www.rna-seqblog.com/impact-and-correction-of-segmentation-errors-in-spatial-transcriptomics/) - Spatial transcriptomics is a powerful approach for studying how cells behave within intact tissues. By measuring where RNA molecules are located inside a tissue, scientists can connect gene activity to specific cell types and their surrounding environment. Imaging-based spatial methods are especially attractive because they can capture molecular information at very high resolution, sometimes down
- [Research uses cutting-edge technology to map how gums become diseased](https://www.rna-seqblog.com/research-uses-cutting-edge-technology-to-map-how-gums-become-diseased/) - Millions suffer from gum disease, but how does it really begin? University of Sheffield researchers have created a detailed cellular map of periodontitis, opening the door to more targeted and transformative treatments. The research was led by Vitor C. M. Neves, Senior Clinical Lecturer at the University of Sheffield and Honorary Consultant in Periodontology, Translational and
- [Targeted long-read RNA sequencing improves diagnosis of Lynch syndrome](https://www.rna-seqblog.com/targeted-long-read-rna-sequencing-improves-diagnosis-of-lynch-syndrome/) - Many human genes produce multiple mRNA isoforms, and changes in splicing or expression can strongly influence disease risk. Yet most clinical genetic tests focus on DNA sequence alone and often miss how variants affect RNA, leaving many results uncertain. Researchers at the Medizinisch Genetisches Zentrum (MGZ) set out to close this gap by developing a
- [Comprehensive discovery of m6A sites in the human transcriptome at single-molecule resolution](https://www.rna-seqblog.com/comprehensive-discovery-of-m6a-sites-in-the-human-transcriptome-at-single-molecule-resolution/) - RNA molecules are not just simple copies of DNA, they are chemically modified in many ways that affect how genes are used by cells. One of the most common and important RNA modifications is N6-methyladenosine, or m6A, which can influence RNA stability, translation, and cell fate decisions. Despite its importance, accurately detecting and measuring RNA
- [Scientists discover a hidden RNA “aging clock” in human sperm](https://www.rna-seqblog.com/scientists-discover-a-hidden-rna-aging-clock-in-human-sperm/) - Increasing paternal age has been linked to elevated health risks for the next generation, including higher risks of obesity and stillbirth. But what drives this increased risk remains unknown. Most research into this link focuses on how the DNA inside sperm changes with age. But sperm carries other molecules as well, including a diverse array
- [TSniffer - unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data](https://www.rna-seqblog.com/tsniffer-unbiased-de-novo-identification-of-rna-editing-sites-and-quantification-of-editing-activity-in-rna-seq-data/) - RNA editing is a natural process that changes specific RNA letters after a gene has already been transcribed, helping cells fine-tune how genetic information is used. One of the most common forms of RNA editing in mammals is carried out by enzymes called ADARs, which convert adenosine bases into inosine. These edits can influence how
- [Immunai expands academic collaborations with single-cell RNA sequencing to map immune responses](https://www.rna-seqblog.com/immunai-expands-academic-collaborations-with-single-cell-rna-sequencing-to-map-immune-responses/) - Immunai Inc., a leading AI biotech company specializing in mapping the human immune system, announced the selection of four high-value academic projects to build a larger and clearer picture of how the immune system works across autoimmune disease, solid-tumor immunotherapy, and cell therapy. The selected collaborations include research proposals from the Icahn School of Medicine at
- [DBiTplus - integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section](https://www.rna-seqblog.com/dbitplus-integration-of-imaging-based-and-sequencing-based-spatial-omics-mapping-on-the-same-tissue-section/) - Researchers at Yale University have developed a new approach called DBiTplus, short for Deterministic Barcoding in Tissue sequencing plus, that overcomes this limitation. DBiTplus allows scientists to measure RNA and proteins from the same tissue section, creating a detailed spatial map of both the transcriptome and proteome. The method works by applying a grid of
- [An agentic AI framework for ingestion and standardization of single-cell RNA-seq data analysis](https://www.rna-seqblog.com/an-agentic-ai-framework-for-ingestion-and-standardization-of-single-cell-rna-seq-data-analysis/) - The rapid growth of publicly available single-cell RNA sequencing data has opened the door to answering many new biological questions. Researchers can now explore how individual cells behave in health and disease across many tissues and conditions. However, actually reusing these datasets is often slow and difficult. Scientists usually need to read the original publication,
- [iTP-seq - a scalable profiling workflow to characterize bacterial translation landscapes in vitro](https://www.rna-seqblog.com/itp-seq-a-scalable-profiling-workflow-to-characterize-bacterial-translation-landscapes-in-vitro/) - Cells do not translate all messenger RNAs at the same speed. The rate at which ribosomes move along an mRNA can change depending on the surrounding sequence, the availability of tRNAs, the growing protein chain, or external stresses like antibiotics. These pauses and slowdowns matter because they influence how much protein is made and how
- [How stressors during pregnancy impact the developing fetal brain](https://www.rna-seqblog.com/how-stressors-during-pregnancy-impact-the-developing-fetal-brain/) - The maternal microbiome and immune system have both independent and synergistic effects on fetal brain health, changes in the mother’s immune system have been linked to an increased risk of neurodevelopmental disorders in children. A new study, published today in Nature Neuroscience, expands our understanding of this “gut-immune axis” by mapping the impact of stressors
- [Evaluating whole transcriptome sequencing for clinical fusion detection](https://www.rna-seqblog.com/evaluating-whole-transcriptome-sequencing-for-clinical-fusion-detection/) - Finding gene fusions and abnormal splice variants is an important part of diagnosing and treating many cancers. Traditionally, clinical labs rely on targeted RNA panels that look for a predefined list of fusions. Whole transcriptome sequencing offers a broader alternative because it captures all RNA in a sample, but its reliability in routine diagnostics has
- [RNA sequencing reveals how viral infections boost ocean productivity](https://www.rna-seqblog.com/rna-sequencing-reveals-how-viral-infections-boost-ocean-productivity/) - A team led by researchers at the University of Tennessee, Knoxville, and University of Maryland shows viral infection of blue-green algae in the ocean stimulates productivity in the ecosystem and contributes to a rich band of oxygen in the water. “It is really a microbial planet we live on, and viruses are part of that
- [How deep is enough in single-cell RNA-seq?](https://www.rna-seqblog.com/how-deep-is-enough-in-single-cell-rna-seq/) - Guidelines for determining sequencing depth facilitate transcriptome profiling of single cells in heterogeneous populations. In recent years, single-cell RNA-seq has emerged as a powerful, new approach for characterizing the cell types present in a mixed population. These studies usually involve a trade-off between the number of samples analyzed and the number of RNA transcripts sequenced
- [ISSAAC-seq - single-nucleus chromatin accessibility and gene expression co-profiling](https://www.rna-seqblog.com/issaac-seq-single-nucleus-chromatin-accessibility-and-gene-expression-co-profiling/) - Cells with the same DNA can behave very differently, and understanding why requires looking at more than one molecular layer at a time. Traditional single-cell methods often measure either gene expression or chromatin accessibility, but not both together, which can limit insight into how genes are regulated. Researchers at Guangzhou Medical University describe a new
- [RNA sequencing reveals how OTULIN regulates tau and brain aging](https://www.rna-seqblog.com/rna-sequencing-reveals-how-otulin-regulates-tau-and-brain-aging/) - In a study published in the journal Genomic Psychiatry, the researchers reported that when they deactivated OTULIN, either by administering a custom-designed small molecule or knocking out the gene that codes for it, it halted the production of tau and removed it from neurons. The study was conducted on two different types of cells, some derived
- [Mount Sinai researchers help create largest immune cell atlas of bone marrow in multiple myeloma patients](https://www.rna-seqblog.com/mount-sinai-researchers-help-create-largest-immune-cell-atlas-of-bone-marrow-in-multiple-myeloma-patients/) - Scientists at the Icahn School of Medicine at Mount Sinai, in partnership with the Multiple Myeloma Research Foundation (MMRF) and in collaboration with leading institutions across the country, have helped generate the largest single-cell immune cell atlas of the bone marrow in patients with multiple myeloma, a blood cancer that, while treatable, remains incurable. The findings, published in Nature Cancer, provide unprecedented insight on immune
- [VISTA - bridging gene expression and spatial context](https://www.rna-seqblog.com/vista-bridging-gene-expression-and-spatial-context/) - Understanding how cells behave in the context of the tissue around them is key to figuring out how organs work, how diseases develop, and how cells interact with each other. Traditional single-cell RNA sequencing gives us a detailed picture of which genes are active in individual cells, but it does not tell us where those
- [RNA-MosaicHunter - accurate detection of somatic single-nucleotide variants from bulk RNA-seq data](https://www.rna-seqblog.com/rna-mosaichunter-accurate-detection-of-somatic-single-nucleotide-variants-from-bulk-rna-seq-data/) - Somatic variants are changes in the DNA that occur after conception, and they have been linked not only to cancer, but also to a range of developmental, aging-related, and neurological disorders. While many tools have been developed to find these mutations using DNA data, they often fall short when applied to RNA sequencing data, especially
- [Junior Research Scientist in the Center for Brain and Health](https://www.rna-seqblog.com/junior-research-scientist-in-the-center-for-brain-and-health/) - New York University: NYU – Global: Abu Dhabi: AD_Research Centers Location – Abu Dhabi Close Date – 11 Feb 2026 Description The RNA Modifications, Intellect, and NeuroDegeneration (RNA-MIND) Laboratory in collaboration with the Center of Brain and Health of New York University Abu Dhabi seeks to recruit a Research Assistant to join our laboratory focused
- [Factorial Biotechnologies and Honeycomb Biotechnologies partner to deliver high-throughput, instrument-free single-cell DNA sequencing](https://www.rna-seqblog.com/factorial-biotechnologies-and-honeycomb-biotechnologies-partner-to-deliver-high-throughput-instrument-free-single-cell-dna-sequencing/) - New partnership combines Factorial’s in-cell library preparation chemistry with Honeycomb’s HIVE™ platform to enable scalable single-cell WGS workflow with processing capacity up to 1 million cells per day. Factorial Biotechnologies, a leader in next-generation single-cell sequencing solutions, and Honeycomb Biotechnologies, a pioneer in instrument-free single-cell analysis, today announced a strategic partnership to deliver a flexible
- [ASPEN - robust detection of allelic dynamics in single cell RNA-seq](https://www.rna-seqblog.com/aspen-robust-detection-of-allelic-dynamics-in-single-cell-rna-seq-2/) - Researchers often study how genes are turned on and off in single cells to understand what makes cells different from one another. One powerful way to do this is through RNA sequencing, which tells us how much RNA, a molecule made from genes, is present in a cell. But when scientists look at RNA from
- [Temporal and spatial atlas of eosinophil specialization across tissues](https://www.rna-seqblog.com/temporal-and-spatial-atlas-of-eosinophil-specialization-across-tissues/) - Eosinophils are a type of white blood cell most people have heard of in the context of allergies or parasitic infections. But these cells actually play many roles in the body including helping control immune responses, supporting metabolism and aiding tissue repair. What hasn’t been clear until now is how eosinophils differ from one tissue
- [Mapping 10 million immune cells to decode disease mechanisms, new atlas and AI model pave way for precision immunotherapy](https://www.rna-seqblog.com/mapping-10-million-immune-cells-to-decode-disease-mechanisms-new-atlas-and-ai-model-pave-way-for-precision-immunotherapy/) - On January 8, 2026, a multi-institutional research team led by the State Key Laboratory of Genome and Multi-omics Technologies (initiated by BGI-Research), working with clinical and academic partners including Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanxi Medical University, and other collaborators, reports in Science the Chinese Immune Multi-Omics Atlas (CIMA).
- [MD Anderson and SOPHiA GENETICS announce strategic collaboration to accelerate AI-driven precision oncology](https://www.rna-seqblog.com/md-anderson-and-sophia-genetics-announce-strategic-collaboration-to-accelerate-ai-driven-precision-oncology/) - The University of Texas MD Anderson Cancer Center and SOPHiA GENETICS today announced a strategic collaboration that unites SOPHiA GENETICS’ AI-powered analytics with MD Anderson’s clinical and scientific expertise to accelerate data-driven cancer care through new tools that can accurately analyze, interpret and translate diagnostic results into clinical practice. As part of the collaboration, MD Anderson and SOPHiA GENETICS are launching a series
- [CASSIA - a multi-agent large language model for automated and interpretable cell annotation](https://www.rna-seqblog.com/cassia-a-multi-agent-large-language-model-for-automated-and-interpretable-cell-annotation/) - Cell type annotation remains one of the most critical yet time-consuming steps in single-cell RNA sequencing analysis. Researchers from the University of Wisconsin-Madison have developed CASSIA (Collaborative Agent System for Single-cell Interpretable Annotation), a novel multi-agent LLM framework that automates this process while providing interpretable, high-quality annotations without requiring reference datasets. The multi-agent LLM system
- [Single Cell Grant Available for Cancer Researchers](https://www.rna-seqblog.com/single-cell-grant-available-for-cancer-researchers/) - Join this online info session on January 15 at 8:00 AM Pacific to learn how Parse Biosciences’ combinatorial barcoding enables cancer research, what the grant includes, and how to apply...
- [ISOSCELES - predicting glioblastoma drug response using single cell transcriptional states](https://www.rna-seqblog.com/isosceles-predicting-glioblastoma-drug-response-using-single-cell-transcriptional-states/) - Glioblastoma is the most common and deadly primary brain cancer in adults, and treatment options have changed very little over the past two decades. One of the biggest challenges in treating this disease is intratumor heterogeneity. Even within a single tumor, cancer cells exist in many different transcriptional states, meaning they behave differently and respond
- [SPLISOSM - mapping isoforms and regulatory mechanisms from spatial transcriptomics data](https://www.rna-seqblog.com/splisosm-mapping-isoforms-and-regulatory-mechanisms-from-spatial-transcriptomics-data/) - Cells make many different versions of RNA from the same gene through processes like splicing and alternative 3′ end usage. This transcript diversity helps cells adapt to their environment and maintain their identity, especially in complex tissues like the brain. While RNA sequencing has shown how diverse transcripts can be, understanding how different RNA isoforms
- [CONCORD - revealing a coherent cell-state landscape across single-cell datasets](https://www.rna-seqblog.com/concord-revealing-a-coherent-cell-state-landscape-across-single-cell-datasets/) - Single-cell experiments have transformed biology by allowing researchers to measure gene activity in thousands to millions of individual cells. Techniques such as RNA sequencing reveal how cells differ from one another, but combining data from different experiments remains difficult. Technical noise, batch effects, and the sheer complexity of high-dimensional data can obscure real biological signals
- [RNA splicing and processing emerge as central features of human aging across tissues](https://www.rna-seqblog.com/rna-splicing-and-processing-emerge-as-central-features-of-human-aging-across-tissues/) - Researchers from the University of São Paulo and Kyushu University investigated how gene activity changes with age across multiple human tissues. They found that many tissues share common aging-related alterations in genes involved in RNA splicing and RNA processing. These findings are important because RNA processing is essential for accurate protein production, and disruptions in this
- [Integrating single-cell multiomics to link genetic variants with cell-type regulatory networks](https://www.rna-seqblog.com/integrating-single-cell-multiomics-to-link-genetic-variants-with-cell-type-regulatory-networks/) - Understanding how genetic differences influence disease and aging at the cellular level is one of the biggest challenges in modern biology. While large genetic studies called genome-wide association studies, or GWASs, can point to DNA variants linked to conditions like Parkinson’s disease and immune disorders, they do not explain how these variants exert their effects
- [The actionable transcriptome - a framework for incorporating RNA sequencing into precision oncology](https://www.rna-seqblog.com/the-actionable-transcriptome-a-framework-for-incorporating-rna-sequencing-into-precision-oncology/) - Comprehensive RNA sequencing is becoming an important part of how cancers are analyzed and treated. While DNA sequencing has long been used to identify mutations that drive cancer, RNA sequencing adds another layer of information by showing which genes are actually turned on or off inside tumor cells. This can reveal therapeutic opportunities that DNA-based
- [ARRP-seq - a new sequencing approach improves detection of rare and novel gene fusions in cancer](https://www.rna-seqblog.com/arrp-seq-a-new-sequencing-approach-improves-detection-of-rare-and-novel-gene-fusions-in-cancer/) - Identifying gene fusions is a cornerstone of modern cancer diagnostics. Gene fusions occur when pieces of two different genes become joined together, often creating abnormal proteins that can drive tumor growth. Some of the most effective targeted cancer therapies exist specifically because these fusion events can be identified and matched to the right drug. However,
- [Unraveling hair aging - a molecular atlas of human hair follicle senescence drawn by single-cell and spatiotemporal sequencing](https://www.rna-seqblog.com/unraveling-hair-aging-a-molecular-atlas-of-human-hair-follicle-senescence-drawn-by-single-cell-and-spatiotemporal-sequencing/) - Hair loss and graying, the earliest visible signs of skin aging, are fundamentally driven by the functional decline of the hair follicle stem cells (HFSCs) and their surrounding niche. The research, led by researchers at BGI Shenzhen, leveraging single-cell RNA sequencing of 11 human scalp samples and spatial transcriptomic sequencing of 1 sample, has created
- [CellUntangler - separating distinct biological signals in single-cell data with deep generative models](https://www.rna-seqblog.com/celluntangler-separating-distinct-biological-signals-in-single-cell-data-with-deep-generative-models/) - Single-cell RNA sequencing has transformed how scientists study biology by letting them measure gene activity in individual cells. This level of detail makes it possible to see how cells differ from one another, but it also introduces a challenge. Inside a single cell, many biological processes happen at the same time. Cell type identity, cell
- [Beyond polyA - mapping total RNA in single cells](https://www.rna-seqblog.com/beyond-polya-mapping-total-rna-in-single-cells/) -  December 16th, 2025: Dr. Alina Isakova, from Stanford University Advances in RNA sequencing are revealing that much of cellular regulation occurs beyond protein-coding mRNA, within diverse non-coding RNA populations that are largely missed by traditional single-cell methods. TotalX extends standard 10x Genomics workflows to capture both coding and non-coding RNA at scale, enabling simultaneous
- [Scorpion venom transcriptomes unlocked with optimized RNA-seq analysis](https://www.rna-seqblog.com/scorpion-venom-transcriptomes-unlocked-with-optimized-rna-seq-analysis/) - Understanding all the genes active in a complex tissue can be difficult because of technical hurdles like assembly mistakes, many versions of the same gene, and problems with how sequences are labeled. These challenges are especially true in venom glands, where many different toxin genes are expressed at varying levels. Researchers at Shahid Chamran University
- [Benchmarking single-cell RNA-seq data normalization](https://www.rna-seqblog.com/benchmarking-single-cell-rna-seq-data-normalization/) - When scientists use single-cell RNA sequencing to study thousands of individual cells, they must first correct the raw data so that meaningful biological differences aren’t obscured by technical quirks. This step, called normalization, adjusts for things like differences in sequencing depth and amplification bias so that comparisons between cells and genes are fair and accurate.
- [HAMRLNC - a comprehensive and scalable pipeline for integrated epitranscriptomic analysis](https://www.rna-seqblog.com/hamrlnc-a-comprehensive-and-scalable-pipeline-for-integrated-epitranscriptomic-analysis/) - As RNA sequencing becomes faster, cheaper, and more widely used, scientists are increasingly asking more sophisticated questions about how cells work. Traditionally, RNA sequencing has been used to measure which genes are turned on or off, helping researchers compare cell types, track changes during development, or identify genes linked to disease. However, RNA molecules carry
- [Bioinformatics Pipeline Development with Nextflow (Live Online, Jan 19–21, 2026)](https://www.rna-seqblog.com/bioinformatics-pipeline-development-with-nextflow-live-online-jan-19-21-2026/) - The purpose of the workshop is to introduce the concepts of bioinformatic pipeline development through the context of the open source Workflow Management System (WMS) Nextflow...
- [Direct RNA sequencing by Oxford Nanopore reveals epitranscriptomic changes in amphibian development and adaptation](https://www.rna-seqblog.com/direct-rna-sequencing-by-oxford-nanopore-reveals-epitranscriptomic-changes-in-amphibian-development-and-adaptation/) - Banded newts have both aquatic and terrestrial forms, going through metamorphosis and various phenotypic changes during their life. In this study, direct RNA sequencing was used to characterize m6A RNA modifications in 12 newts from the Nehalit population. We focused on genes with multiple differentially modified regions in their transcripts. Highlights: Multiple transcripts in banded
- [Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 23-25, 2026 in Berlin)](https://www.rna-seqblog.com/single-cell-rna-seq-data-analysis-a-practical-introduction-march-23-25-2026-in-berlin/) - Learn a complete, beginner-friendly single-cell workflow - from raw data processing and QC to cluster annotation, differential expression, and integration across samples. Date: March 23-25, 2026 Location: Berlin, Germany Link: Website In a nutshell Understand sequencing technologies for single-cell analysis (plate-based vs droplet-based) Process, QC and analyze scRNA-seq data with a structured, reproducible workflow Identify,
- [AlidaBio Introduces the EpiPlex™ Duo-Mod™ Service for Concurrent m6A and Inosine Mapping with Integrated RNA Expression Profiling](https://www.rna-seqblog.com/alidabio-introduces-the-epiplex-duo-mod-service-for-concurrent-m6a-and-inosine-mapping-with-integrated-rna-expression-profiling/) - SAN DIEGO, Dec. 4, 2025 /PRNewswire/ -- AlidaBio today announced the launch of the EpiPlex™ Duo-Mod™ Service, a turnkey offering that maps and quantifies m6A and inosine RNA modifications alongside RNA expression in a single integrated report. The service is designed for researchers who need sensitive RNA modification detection, relative quantitation, and high-quality RNA-seq data
- [High-fat diets make liver cells more likely to become cancerous](https://www.rna-seqblog.com/high-fat-diets-make-liver-cells-more-likely-to-become-cancerous/) - New research suggests liver cells exposed to too much fat revert to an immature state that is more susceptible to cancer-causing mutations. One of the biggest risk factors for developing liver cancer is a high-fat diet. A new study from MIT reveals how a fatty diet rewires liver cells and makes them more prone to
- [RNA-Seq reveals new clues how gestational diabetes affects offspring](https://www.rna-seqblog.com/rna-seq-reveals-new-clues-how-gestational-diabetes-affects-offspring/) - Gestational diabetes can cause a multitude of complications in the offspring, but to date, the reasons are incompletely understood. A new study, exploring a foundational step in the process of building proteins from genetic material, called splicing, reveals that this process is affected, altering how the placenta reads and processes genetic instructions. Researchers found that
- [A new way to map how cells choose their fate](https://www.rna-seqblog.com/a-new-way-to-map-how-cells-choose-their-fate/) - Researchers present an innovative computational method based on modern mathematics to shed light on cell state dynamics and development Researchers from Kyushu University have developed an innovative computational method, called ddHodge, that can reconstruct the complex dynamics of how cells decide their fate. As reported in Nature Communications, this approach paves the way for a deeper
- [ASPEN - robust detection of allelic dynamics in single cell RNA-seq](https://www.rna-seqblog.com/aspen-robust-detection-of-allelic-dynamics-in-single-cell-rna-seq/) - Scientists from the University of New South Wales, Australia, have developed a new statistical approach called ASPEN to better understand how individual copies of genes behave inside single cells using RNA sequencing data. Cells contain two copies (or alleles) of most genes, one inherited from each parent. In certain biological situations, one copy can be
- [Clair3-RNA - a deep learning-based small variant caller for long-read RNA sequencing data](https://www.rna-seqblog.com/clair3-rna-a-deep-learning-based-small-variant-caller-for-long-read-rna-sequencing-data/) - Understanding how genes vary and which RNA isoforms are produced is key to modern biology and medicine. Long-read RNA sequencing makes this possible by reading entire RNA molecules in one piece, but it also introduces a challenge, the data are noisy, with higher error rates and complex signals from RNA editing and many transcript forms.
- [Clues to Alzheimer’s disease may be hiding in our ‘junk’ DNA](https://www.rna-seqblog.com/clues-to-alzheimers-disease-may-be-hiding-in-our-junk-dna/) - UNSW scientists have uncovered the hidden switches in DNA, revealing new insights into Alzheimer’s disease. When most of us think of DNA, we have a vague idea it’s made up of genes that give us our physical features, our behavioural quirks, and keep our cells and organs running. But only a tiny percentage of our
- [Fusion of nanopores and nanofluidic devices could transform medicine and beyond](https://www.rna-seqblog.com/fusion-of-nanopores-and-nanofluidic-devices-could-transform-medicine-and-beyond/) - When disease begins forming inside the human body, something subtle happens long before symptoms appear. Individual molecules such as DNA, RNA, peptides, or proteins begin shifting in quantity or shape. Detecting these tiny molecular changes early could dramatically change how cancer, infections, and other conditions are diagnosed. For years, scientists have dreamed of reading these
- [Detailed cell map unlocks secrets of how reproductive organs form](https://www.rna-seqblog.com/detailed-cell-map-unlocks-secrets-of-how-reproductive-organs-form/) - Scientists chart a comprehensive cell atlas of the developing human reproductive system, offering new clues into congenital disorders New research has mapped the cell types that specialise to form reproductive organs in both sexes, identifying key genes and signals that drive this process. The findings offer important insights into conditions affecting the reproductive organs, and
- [Exploring the connection between gene expression and aging](https://www.rna-seqblog.com/exploring-the-connection-between-gene-expression-and-aging/) - Northwestern Medicine scientists have discovered how molecular “traffic controllers” in cells influence aging and cellular senescence, a state where cells stop dividing but remain metabolically active. The study, published in Molecular Cell, sheds light on the process of transcribing DNA into RNA, a critical step in gene expression, and how it is tightly regulated and connected to age-related changes. “Previous
- [Hummingbird Diagnostics publishes study on RNA biomarker methylation in liquid biopsies](https://www.rna-seqblog.com/hummingbird-diagnostics-publishes-study-on-rna-biomarker-methylation-in-liquid-biopsies/) - Revealing a new layer in lung cancer diagnostics using direct RNA sequencing Hummingbird Diagnostics GmbH, a pioneer in harnessing blood-based small RNAs for early disease detection and characterization, today announced the publication of a new study in Nature Communications Medicine introducing an Oxford Nanopore Technologies (ONT)-based method for detecting small RNA modifications in blood The research
- [SARS-CoV-2 infection alters RNA methylation in lung cell lncRNAs](https://www.rna-seqblog.com/sars-cov-2-infection-alters-rna-methylation-in-lung-cell-lncrnas/) - When a virus infects a cell, it does more than just hijack the machinery to make new virus particles. It can also subtly reshape how the cell regulates its own RNA. Researchers from the Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP) explored this idea by looking at how
- [RNAConnect Launches the UltraMarathonRT® Direct RNA‑Seq Kit to Advance Nanopore-based Native RNA Sequencing](https://www.rna-seqblog.com/rnaconnect-launches-the-ultramarathonrt-direct-rna-seq-kit-to-advance-nanopore-based-native-rna-sequencing/) - RNAConnect, a life science company providing next generation tools to the RNA community, today announced the commercial availability of the UltraMarathonRT® Direct RNA‑Seq (uMRT DRS) Kit, a native‑RNA library preparation solution for Oxford Nanopore Technologies® direct RNA sequencing (SQK-RNA004). The kit enables the detection of more genes, more isoforms, and longer transcripts than existing protocols. It employs a
- [RoCK and ROI - single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing](https://www.rna-seqblog.com/rock-and-roi-single-cell-transcriptomics-with-multiplexed-enrichment-of-selected-transcripts-and-region-specific-sequencing/) - Single-cell RNA sequencing is a powerful tool that helps scientists see which genes are active inside individual cells, shedding light on everything from how tissues develop to what goes wrong in disease. But traditional approaches often miss important pieces of the puzzle because they don’t capture all the parts of the RNA message for every
- [Technology advances unlock the mystery of mitochondrial DNA — our “other” genome](https://www.rna-seqblog.com/technology-advances-unlock-the-mystery-of-mitochondrial-dna-our-other-genome/) - About 1.8 billion years ago, one of our earliest ancestral cells engulfed a bacterial cell. Rather than being digested, the bacterium survived, and the two cells formed a partnership that persists to this day. Over time, that bacterium evolved into mitochondria, organelles found within cells whose role is echoed in science classrooms as being “the
- [Controlling noise in single-cell RNA sequencing with pseudobulk approaches](https://www.rna-seqblog.com/controlling-noise-in-single-cell-rna-sequencing-with-pseudobulk-approaches/) - High-throughput RNA sequencing is a powerful way to study how genes are turned on or off in cells, but it comes with a challenge. Not all differences detected in the data reflect real biological signals, some are caused by technical noise, such as variation in sample handling, sequencing machines, or other experimental factors. If this
- [scRepli-RamDA-seq - a multi-omics technology enabling the analysis of gene expression dynamics during S-phase](https://www.rna-seqblog.com/screpli-ramda-seq-a-multi-omics-technology-enabling-the-analysis-of-gene-expression-dynamics-during-s-phase/) - Understanding how cells grow and divide requires looking at both their DNA and RNA. Single-cell sequencing has given scientists a powerful way to explore differences between individual cells, but many existing methods cannot track how gene activity changes as cells progress through the S-phase of the cell cycle, when DNA is being copied. Researchers at
- [Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution](https://www.rna-seqblog.com/bioinformatics-frameworks-for-single-cell-long-read-sequencing-unlocking-isoform-level-resolution/) - Our genes are like instruction manuals for life, and the way those instructions are edited can shape how cells behave. One of the ways cells fine-tune gene activity is through alternative splicing, a process that creates different versions of RNA messages from the same gene. When splicing goes awry, it can contribute to diseases such
- [Disrupting cancer’s secret hubs: A new way to halt tumor growth](https://www.rna-seqblog.com/disrupting-cancers-secret-hubs-a-new-way-to-halt-tumor-growth-2/) - When RNA gets hijacked, cancer grows—and scientists have finally learned how to make it stop By revealing how RNA builds the “droplet hubs” that drive cancer growth—and how to dismantle them—Texas A&M Health scientists have discovered a key weakness that could help stop one of the toughest childhood cancers. In a city, coworking hubs bring
- [Researcher awarded for transformative use of genome and RNA sequencing](https://www.rna-seqblog.com/researcher-awarded-for-transformative-use-of-genome-and-rna-sequencing/) - Trailblazing geneticist Pengfei Liu, Ph.D., Associate Professor in the Department of Molecular and Human Genetics at Baylor College of Medicine, is the recipient of the 2026 Edith and Peter O’Donnell Award in Medicine from TAMEST. He was chosen for his transformative use of genome and RNA sequencing to improve the diagnosis and treatment of rare
- [Linking genes to traits using RNA sequencing and causal modeling](https://www.rna-seqblog.com/linking-genes-to-traits-using-rna-sequencing-and-causal-modeling/) - Large genetic studies have uncovered thousands of links between genes and human traits, from blood cell counts to disease risk. While these associations are powerful, they often leave a key question unanswered, how does a change in a gene actually lead to a change in biology or health? Turning statistical signals into clear biological explanations
- [RNA sequencing reveals climate-driven genetic changes in polar bears](https://www.rna-seqblog.com/rna-sequencing-reveals-climate-driven-genetic-changes-in-polar-bears/) - The study by scientists at the University of East Anglia (UEA) discovered that some genes related to heat-stress, aging and metabolism are behaving differently in polar bears living in southeastern Greenland. New research reveals a link between rising temperatures and changes in polar bear DNA, which may be helping them adapt and survive in increasingly
- [SIDISH - integrating single cell insights with bulk RNA sequencing to identify high risk cells and guide precision therapeutics](https://www.rna-seqblog.com/sidish-integrating-single-cell-insights-with-bulk-rna-sequencing-to-identify-high-risk-cells-and-guide-precision-therapeutics/) - Understanding how different cells contribute to disease is one of the biggest challenges in modern biology. Single-cell RNA sequencing gives us a close look at how individual cells behave, but it is still expensive and usually limited to small groups of patients. This means that many projects using single-cell techniques do not have the large,
- [MUTE-Seq - ultrasensitive method to detect low-frequency cancer mutations](https://www.rna-seqblog.com/mute-seq-ultrasensitive-method-to-detect-low-frequency-cancer-mutations/) - MUTE-Seq is a new liquid-biopsy method powered by an engineered ultra-precise CRISPR enzyme, FnCas9-AF2, which can distinguish single-base mismatches across all sgRNA positions with near-zero off-target activity. By selectively removing wild-type DNA before sequencing, it boosts true mutant signals up to tens of times and enables detection as low as ~0.005% VAF. The technique improves
- [Researchers develop models to help diagnose ALS earlier through blood biomarkers](https://www.rna-seqblog.com/researchers-develop-models-to-help-diagnose-als-earlier-through-blood-biomarkers/) - The models have the potential to shorten time to an ALS diagnosis, assess disease severity and identify possible treatment targets Using machine learning models, researchers at Michigan Medicine have identified a potential way to diagnose amyotrophic lateral sclerosis, or ALS, earlier from a blood sample, a study suggests. The models, which analyze blood for biomarkers
- [Pancreatic tumors plan their travels](https://www.rna-seqblog.com/pancreatic-tumors-plan-their-travels/) - Researchers uncover an intriguing characteristic of pancreatic cancer that could detect – and potentially target – metastasis earlier. Even as they develop at their primary site, pancreatic cancer cells are already expressing the genes that will determine where they will metastasize, according to new findings from Columbia researchers. The work, published in Nature Genetics, reveals a
- [Blood RNA sequencing shows overlapping gene expression across COPD phenotype domains](https://www.rna-seqblog.com/blood-rna-sequencing-shows-overlapping-gene-expression-across-copd-phenotype-domains/) - Immunotherapy has revolutionized cancer care by training the immune system to detect and destroy tumors. For many patients, it works very well in shrinking tumors and sending cancer into remission, an undetectable state of cancer. But that remission is short-lived in some cases, and the cancer can return more resistant than before. Researchers at the
- [Single cell RNA-seq uncovers breast cancer diversity](https://www.rna-seqblog.com/single-cell-rna-seq-uncovers-breast-cancer-diversity/) - Breast cancer is made up of many different types of cells, and these differences can strongly influence how a tumor grows and responds to treatment. A research team from the Henan University of Chinese Medicine used single cell RNA sequencing to look at thousands of individual cells from breast tumors. This approach allowed them to
- [Pan-cancer gene set discovery via scRNA-seq for optimal deep learning based downstream tasks](https://www.rna-seqblog.com/pan-cancer-gene-set-discovery-via-scrna-seq-for-optimal-deep-learning-based-downstream-tasks/) - Machine learning has become a powerful tool for cancer research, but it depends heavily on the quality of the data that is used to train it. RNA sequencing data can contain information on thousands of genes at once, making it difficult to decide which genes are the most meaningful for predicting cancer behavior. A research
- [Spatial Touchstone brings quality control to spatial transcriptomics](https://www.rna-seqblog.com/spatial-touchstone-brings-quality-control-to-spatial-transcriptomics/) - A collaborative project led by St. Jude Children’s Research Hospital has created a comprehensive guide to help standardize spatial transcriptomics practices. Spatial transcriptomics provides a unique perspective on the genes that cells express and where those cells are located...
- [D3Impute - dropout-aware discrimination, distribution-aware modeling, and density-guide imputation for scRNA-seq data](https://www.rna-seqblog.com/d3impute-dropout-aware-discrimination-distribution-aware-modeling-and-density-guide-imputation-for-scrna-seq-data/) - Single cell technologies have made it possible to look at gene expression in individual cells, revealing differences that were once hidden in averaged data. However, one major challenge in single cell RNA sequencing is the presence of large numbers of zeros in the data. Some of these zeros reflect true biological absence, meaning the gene
- [Isoformic - a workflow for transcript-level RNA-seq interpretation](https://www.rna-seqblog.com/isoformic-a-workflow-for-transcript-level-rna-seq-interpretation/) - Understanding the full range of RNA molecules produced by a gene is essential for grasping how cells function, yet many analyses still overlook this complexity. Researchers from the Federal University of Minas Gerais, researchers introduce Isoformic, a new R based workflow that helps scientists see beyond gene level summaries and explore transcript level information hidden
- [Deciphering cell dynamics via genetic barcoding and single-cell transcriptomics](https://www.rna-seqblog.com/deciphering-cell-dynamics-via-genetic-barcoding-and-single-cell-transcriptomics/) - Even when cells look normal under a microscope, they can carry subtle genetic changes that may eventually lead to cancer. Researchers at the University of Texas MD Anderson Cancer Center set out to understand how these early changes in esophageal cells develop and evolve over time, which could help identify the earliest steps in esophageal
- [PERlncDB - new platform developed to explore epigenetic regulation of plant long non-coding RNAs](https://www.rna-seqblog.com/perlncdb-new-platform-developed-to-explore-epigenetic-regulation-of-plant-long-non-coding-rnas/) - Long non-coding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. Once considered mere transcriptional noise, lncRNAs are now known to play vital roles in plant growth, development, and responses to environmental stress. However, few studies have used epigenomic data to investigate functions of lncRNAs in plants.In a study by
- [Human gene maps are biased towards European ancestries](https://www.rna-seqblog.com/human-gene-maps-are-biased-towards-european-ancestries/) - A study published today in Nature Communications by researchers from CRG and BSC-CNS shows that human gene maps lack global representation because they were built mainly using data from individuals of European ancestry. Human gene maps contain major blind spots because they were built largely from the DNA sequences of people with European ancestry. Researchers
- [New RNA class discovered that helps keep cells organized](https://www.rna-seqblog.com/new-rna-class-discovered-that-helps-keep-cells-organized/) - Discovery of smOOPs sheds light on why certain RNAs cluster into condensates – a breakthrough that opens new avenues for disease research Inside cells, RNAs and proteins form tiny, liquid-like droplets called biomolecular condensates. These droplets are essential for organizing cellular life, yet why some RNAs cluster more readily than others has remained unclear. Disruptions
- [VarRNA - variant calling from RNA-Seq data](https://www.rna-seqblog.com/varrna-variant-calling-from-rna-seq-data-2/) - Understanding how genetic variants influence cancer is one of the major challenges in modern biomedical research. These variants can drive tumor growth, affect how a cancer behaves, and even determine how well a patient responds to treatment. In a new investigation led by researchers from Nationwide Children’s Hospital, researchers explored how looking at RNA, rather
- [scPER - a computational method to identify tumor cell subtypes from total RNA sequencing](https://www.rna-seqblog.com/scper-a-computational-method-to-identify-tumor-cell-subtypes-from-total-rna-sequencing/) - Understanding what makes one patient respond to cancer treatment while another does not often comes down to the cells inside a tumor. But tumors are complex communities with many different cell types, and figuring out that mix can be difficult, especially across large groups of patients. Researchers from the University of Texas MD Anderson Cancer
- [Multiple overlapping binding sites determine transcription factor occupancy](https://www.rna-seqblog.com/multiple-overlapping-binding-sites-determine-transcription-factor-occupancy/) - Transcription factors are proteins that turn genes on or off by attaching to specific DNA sequences. For years, researchers have used high-throughput lab methods to figure out which DNA sequences these proteins prefer. However, many of these methods miss weaker binding sites, even though those sites play an important role in fine-tuning when and where
- [Understanding tumor heterogeneity through RNA expression](https://www.rna-seqblog.com/understanding-tumor-heterogeneity-through-rna-expression/) - Intratumoral genomic heterogeneity, or ITGH, refers to the genetic and functional differences that can exist within different regions of a single tumor. These differences often explain why some cancers resist therapy. A team led by researchers at the Roswell Park Comprehensive Cancer Center and the University of Buffalo explored whether a tool called the DEPTH2
- [scKGBERT - a knowledge-enhanced foundation model for single-cell transcriptomics](https://www.rna-seqblog.com/sckgbert-a-knowledge-enhanced-foundation-model-for-single-cell-transcriptomics/) - Understanding how individual cells behave is essential for advancing modern biology and medicine. Scientists often turn to single-cell transcriptomics, a technique that measures gene activity one cell at a time, to uncover hidden differences between cells that look similar on the surface. However, many existing computational tools only examine gene expression levels and miss deeper
- [Lexogen and Ochre Bio advance large-scale RNA sequencing to accelerate functional genomics and RNA therapy discovery](https://www.rna-seqblog.com/lexogen-and-ochre-bio-advance-large-scale-rna-sequencing-to-accelerate-functional-genomics-and-rna-therapy-discovery/) - Lexogen, a Vienna-based biotech company specialized in RNA transcriptomics technologies and services announces the completion of a large-scale data generation project producing comprehensive functional genomics datasets from primary human hepatocytes with Ochre Bio. The project included over 120,000 samples assessed with Lexogen’s proprietary extraction-free, high-resolution gene expression profiling platform and NGS Services. Ochre Bio is a biotechnology company developing RNA medicines for
- [RNA-Seq reveals how brain protein OTULIN controls tau expression and could transform Alzheimer's treatment](https://www.rna-seqblog.com/rna-seq-reveals-how-brain-protein-otulin-controls-tau-expression-and-could-transform-alzheimers-treatment/) - Groundbreaking research identifies unexpected role for deubiquitinase enzyme in regulating toxic tau protein accumulation Scientists have uncovered a surprising mechanism by which a brain enzyme called OTULIN controls the expression of tau, the protein that forms toxic tangles in Alzheimer’s disease. The findings, published today in Genomic Psychiatry, reveal that OTULIN functions not only as expected
- [Helixer: ab initio prediction of primary eukaryotic gene models](https://www.rna-seqblog.com/helixer-ab-initio-prediction-of-primary-eukaryotic-gene-models/) - Understanding where genes are located within a genome is a critical part of biology, because genes act as the instruction manual for how organisms grow, function, and adapt. Yet as scientists sequence more species, especially those that have not been studied deeply, identifying genes accurately remains a major challenge. Many organisms have complex genomes, and
- [The Festival of Genomics & Biodata in London](https://www.rna-seqblog.com/the-festival-of-genomics-biodata-in-london/) - Registration for The Festival of Genomics & Biodata in London is now open! Join us on Wednesday 28th January – Thursday 29th January 2026 in London for inspirational speakers, the latest research and clinical breakthroughs, cutting-edge technology and unbeatable networking opportunities. Free for 90% of attendees, the Festival is designed to help you return to
- [A DNA search engine](https://www.rna-seqblog.com/a-dna-search-engine/) - Computer scientists at ETH Zurich have developed a digital tool capable of searching through millions of published DNA records in a matter of seconds. This can significantly accelerate research into antibiotic resistance and unknown pathogens. DNA datasets can be searched quickly using a simple search function in the “MetaGraph” tool. (Image generated with AI: Adobe Stock
- [G4mer - An RNA language model for transcriptome-wide identification of G-quadruplexes](https://www.rna-seqblog.com/g4mer-an-rna-language-model-for-transcriptome-wide-identification-of-g-quadruplexes/) - RNA does much more than simply carry genetic information from DNA to protein. Its ability to fold into complex three-dimensional shapes allows it to act as a regulator of gene expression. Among these structures, RNA G-quadruplexes, or rG4s, stand out for their stability and influence on how genes are turned on or off. These structures
- [Study uncovers and predicts widespread molecular changes in ALS brain cells](https://www.rna-seqblog.com/study-uncovers-and-predicts-widespread-molecular-changes-in-als-brain-cells/) - Researchers at the University of Toronto’s Temerty Faculty of Medicine have found widespread genetic and protein changes in the brain cells of people with amyotrophic lateral sclerosis (ALS), which may help shed light on mechanisms of the disease. The study, recently published in Cell Genomics, also describes development of a deep-learning tool to help predict whether the changes
- [Benchmarking deep learning methods for biologically conserved single-cell integration](https://www.rna-seqblog.com/benchmarking-deep-learning-methods-for-biologically-conserved-single-cell-integration/) - Researchers at Sun Yat-sen University set out to solve a growing challenge in single-cell biology. As single-cell RNA sequencing generates data from millions of cells, scientists often need to combine information from different labs, instruments or techniques. However, technical differences between datasets, known as batch effects, can hide the real biological patterns that researchers care
- [ERNIE-RNA - an RNA language model with structure-enhanced representations](https://www.rna-seqblog.com/ernie-rna-an-rna-language-model-with-structure-enhanced-representations/) - A team led by researchers from Tsinghua University has developed a novel tool for understanding RNA sequences. The team recognised that most existing computational models treat an RNA molecule simply as a string of letters (A, U, G, C), but they often ignore the way the molecule folds and forms base-pairs, and yet structure is
- [scSpecies - enhancement of network architecture alignment in comparative single-cell studies](https://www.rna-seqblog.com/scspecies-enhancement-of-network-architecture-alignment-in-comparative-single-cell-studies/) - Comparing human and animal cells can reveal powerful insights about health and disease, but the data from each species often look very different. Researchers at the University of Freiburg have developed a deep learning method designed to bridge this gap and make cross species comparisons more reliable. The researchers developed a computational tool called scSpecies
- [Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues](https://www.rna-seqblog.com/systematic-benchmarking-of-imaging-spatial-transcriptomics-platforms-in-ffpe-tissues/) - Imaging spatial transcriptomics is reshaping how scientists study tissues because it reveals not only which genes are active, but also where in the tissue those genes are expressed. This spatial context helps researchers understand how cells communicate, how diseases progress, and how tumors interact with their surrounding microenvironment. A new benchmarking paper led by researchers
- [Upcoming Webinar - Everything you need to know about RNA sequencing](https://www.rna-seqblog.com/upcoming-webinar-everything-you-need-to-know-about-rna-sequencing/) - REGISTER FOR THE JULY 17TH WEBINARRNA sequencing unlocks the mysteries hidden in the transcriptome. Whether your goal is gene expression analysis, gene fusion analysis, SNP analysis or miRNA expression analysis, achieving high-performance library preparation can prove essential to maximizing your discoveries. In this webinar, you will learn about best practices, considerations and tips for library
- [RNA sequencing reveals how muscle stem cells guide macrophages to drive tadpole tail regeneration](https://www.rna-seqblog.com/rna-sequencing-reveals-how-muscle-stem-cells-guide-macrophages-to-drive-tadpole-tail-regeneration/) - Researchers discover how muscle stem cells shift the role of macrophages, normally responsible for immune function, to promote regeneration of tadpole tails. Researchers Sumika Kato, Takeo Kubo, and Taro Fukazawa of the University of Tokyo have discovered that c1qtnf3, a secreting factor, namely a protein molecule that is secreted by a cell and influence functions of
- [Single-cell insights into leaf development in Brassica rapa](https://www.rna-seqblog.com/single-cell-insights-into-leaf-development-in-brassica-rapa/) - Leaf vasculature plays a pivotal role in nutrient transport and leaf morphology. A new study in Brassica rapa reveals the developmental trajectories of vascular tissues in Chinese cabbage using single-cell RNA sequencing (scRNA-seq). This comprehensive transcriptome map identifies seven distinct vascular cell types and traces the differentiation processes of xylem and phloem tissues. The study
- [Parse Biosciences Announces FFPE-compatible Barcoding Technology for Whole Transcriptome Single Cell Analysis](https://www.rna-seqblog.com/parse-biosciences-announces-ffpe-compatible-barcoding-technology-for-whole-transcriptome-single-cell-analysis/) - New method enables single cell discovery from archived tissue samples, expanding access to translational and clinical research Parse Biosciences, the leading provider of scalable and accessible single cell sequencing solutions, today announced a breakthrough technology that unlocks the full potential of formalin-fixed, paraffin-embedded (FFPE) samples. By enabling whole transcriptome capture from archived tissues at single
- [RNA sequencing provides functional insights and diagnostic resolution in previously unsolved rare disease cases](https://www.rna-seqblog.com/rna-sequencing-provides-functional-insights-and-diagnostic-resolution-in-previously-unsolved-rare-disease-cases/) - Understanding genetic disorders can be challenging, especially when standard DNA tests do not provide clear answers. A team led by researchers from ARUP Laboratories examined how RNA sequencing can fill these gaps and help solve difficult medical cases involving rare diseases. Traditional genetic testing usually focuses on DNA, but DNA alone cannot always show how
- [Uli-epic - profiling RNA modifications from ultra-low input samples](https://www.rna-seqblog.com/uli-epic-profiling-rna-modifications-from-ultra-low-input-samples/) - Understanding RNA modifications is essential for learning how cells control which genes turn on and off. Until recently, however, scientists needed large amounts of RNA to study these chemical changes. This made it difficult to analyze rare cell types or very small samples. A team led by at the Fudan University Shanghai Cancer Center has
- [Foli-seq - fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut](https://www.rna-seqblog.com/foli-seq-fecal-exfoliome-sequencing-captures-immune-dynamics-of-the-healthy-and-inflamed-gut/) - Scientists have long used gut microbiome sequencing to understand how microbes affect health. But feces contain more than bacteria. They also carry tiny amounts of human cells that have naturally shed from the lining of the digestive system. These cells can reveal important information about immunity and intestinal health, but their RNA breaks down quickly,
- [The world’s oldest RNA extracted from woolly mammoth](https://www.rna-seqblog.com/the-worlds-oldest-rna-extracted-from-woolly-mammoth/) - Researchers from Stockholm University have for the first time ever managed to successfully isolate and sequence RNA molecules from Ice Age woolly mammoths. These RNA sequences are the oldest ever recovered and come from mammoth tissue preserved in the Siberian permafrost for nearly 40,000 years. The study, published in the journal Cell, shows that not
- [New England Biolabs® launches the NEBNext® Flu A Integrated Indexing Primer Module to advance Influenza A surveillance and sequencing](https://www.rna-seqblog.com/new-england-biolabs-launches-the-nebnext-flu-a-integrated-indexing-primer-module-to-advance-influenza-a-surveillance-and-sequencing/) - Streamlined, high-throughput sequencing of Influenza A virus with integrated indexing for Oxford Nanopore Technologies® platforms New England Biolabs (NEB®) today announces the release of the NEBNext Flu A Integrated Indexing Primer Module (NEB #E3436), designed to streamline and scale the sequencing of Influenza A virus from a range of species and sample types using Oxford
- [The new era of single-molecule RNA modification detection through nanopore base-calling models](https://www.rna-seqblog.com/the-new-era-of-single-molecule-rna-modification-detection-through-nanopore-base-calling-models/) - Researchers from the Centre for Genomic Regulation (CRG) in Barcelona explore how scientists are using advanced sequencing tools to study chemical changes on RNA. These RNA modifications can affect how cells function, but detecting them accurately has been a major challenge. Nanopore direct RNA sequencing has opened new doors by allowing researchers to read RNA
- [Reversing fibrosis - new research provides insight for novel therapies](https://www.rna-seqblog.com/reversing-fibrosis-new-research-provides-insight-for-novel-therapies/) - Yale School of Medicine (YSM) researchers have made key breakthroughs in understanding how to treat fibrotic diseases such as scleroderma and graft-versus-host disease. Fibrotic diseases are a group of conditions, often autoimmune, characterized by excessive tissue scarring. They can drastically hinder patients’ quality of life, and in some cases, they can be life-threatening—fibrosis contributes to
- [Leading genomics research powers innovation and direct human impact](https://www.rna-seqblog.com/leading-genomics-research-powers-innovation-and-direct-human-impact/) - Every cell in the body holds a story written in three billion letters. For decades, scientists struggled to translate that code into something they understood and could use. On a sunny Santa Cruz rooftop on October 28th, the emerging rewards of that struggle were on full display. At the Genomics Rooftop Mixer, hosted by Santa
- [GREGoR - accelerating genomics for rare diseases](https://www.rna-seqblog.com/gregor-accelerating-genomics-for-rare-diseases/) - Researchers from a group of universities are advancing our understanding of rare diseases through the Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium. While individual rare diseases may each affect only a small number of people, collectively they impact about one in twenty individuals worldwide. For many patients and families, finding a
- [Long-read sequencing disentangles isoform complexity at allele-specific loci](https://www.rna-seqblog.com/long-read-sequencing-disentangles-isoform-complexity-at-allele-specific-loci/) - Researchers from the Technical University of Munich have made important progress in understanding how genetic information differs between alleles, the two versions of each gene we inherit from our parents. By using advanced long-read RNA sequencing, the team was able to see how these genetic variations influence which RNA transcripts are produced. Traditional short-read sequencing
- [Personalized cancer insights, grounded in biology, DNA/RNA & AI delivered in an average of 10 days](https://www.rna-seqblog.com/personalized-cancer-insights-grounded-in-biology-dna-rna-ai-delivered-in-an-average-of-10-days/) - In cancer care, every day that passes can cost a life. First Ascent Biomedical is racing against that clock. By testing a patient’s live cancer cells outside the body, the company reveals how their unique biology responds to FDA-approved drugs and combinations before treatment begins, delivering personalized options in an average of ten days before
- [With new donation and NIH grant, Brown aims to capitalize on potential of RNA research](https://www.rna-seqblog.com/with-new-donation-and-nih-grant-brown-aims-to-capitalize-on-potential-of-rna-research/) - Following a gift from Brown trustee Giammaria Giuliani P’28 and Sabrina Giuliani P’28, Brown’s RNA center will be named the Giuliani RNA Center. Established in 2024, the RNA center aims to advance scientific growth and advancements in the field of RNA. With the support of two new funding sources — including a gift from a
- [CellWhisperer - multimodal learning enables chat-based exploration of single-cell data](https://www.rna-seqblog.com/cellwhisperer-multimodal-learning-enables-chat-based-exploration-of-single-cell-data/) - Researchers from the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences have introduced a powerful new tool called CellWhisperer that changes how scientists can explore complex single-cell data. Single-cell sequencing has transformed the life sciences by allowing researchers to study gene expression in individual cells rather than in bulk populations. This level
- [HydraRNA - a hybrid architecture based full-length RNA language model](https://www.rna-seqblog.com/hydrarna-a-hybrid-architecture-based-full-length-rna-language-model/) - Researchers from the Southern University of Science and Technology, Shenzhen have developed an innovative artificial intelligence model called HydraRNA that can interpret the complex biological “language” of RNA. RNA, a key molecule that helps convert genetic information from DNA into proteins, is central to almost every cellular process. Understanding how RNA functions and regulates itself
- [RNA sequencing reveals immune biomarkers for improved diagnosis of extrapulmonary tuberculosis](https://www.rna-seqblog.com/rna-sequencing-reveals-immune-biomarkers-for-improved-diagnosis-of-extrapulmonary-tuberculosis/) - A research team involving the University of Bonn has identified specific biomarkers, thus taking an important step toward quicker diagnoses and personalized treatment. Researchers from the LIMES Institute at the University of Bonn, the German Center for Infection Research (DZIF), the German Center for Neurodegenerative Diseases (DZNE) and the University Hospital Cologne have decoded the
- [Virome profiling of Culex tarsalis through small RNA-seq](https://www.rna-seqblog.com/virome-profiling-of-culex-tarsalis-through-small-rna-seq/) - Exploring the Hidden Viruses in Mosquitoes with RNA Sequencing Researchers from Pennsylvania State University have uncovered new insights into the viral world living inside Culex tarsalis mosquitoes. These mosquitoes are common across North America and are well known for transmitting West Nile virus (WNV), a disease that can infect birds, humans, and other mammals. However,
- [MntJULiP and Jutils - differential splicing analysis of RNA-seq data with covariates](https://www.rna-seqblog.com/mntjulip-and-jutils-differential-splicing-analysis-of-rna-seq-data-with-covariates/) - As RNA sequencing technology continues to advance, scientists are generating massive datasets that capture how genes are expressed in different tissues and disease conditions. However, these datasets often include variables such as age, sex, ethnicity, and clinical history, all of which can influence results and make data interpretation challenging. Researchers from Johns Hopkins University have
- [Elucidation of a novel mechanism regulating bone growth](https://www.rna-seqblog.com/elucidation-of-a-novel-mechanism-regulating-bone-growth/) - Chondrocytes play a crucial role in skeletal development. Many bones, such as those in the arms and legs, are formed through endochondral ossification, in which chondrocytes assemble to create a cartilage scaffold that is later replaced by bone. The maturation of chondrocytes, required for their diverse functions, is regulated by epigenetic mechanisms that modulate gene
- [Women are three times more likely than men to get severe long COVID: Here’s why](https://www.rna-seqblog.com/women-are-three-times-more-likely-than-men-to-get-severe-long-covid-heres-why/) - New U of A research reveals underlying mechanisms of how long COVID affects women and men differently. Research published today in Cell Reports Medicine reveals key biological differences that may explain why women with long COVID — especially those who develop chronic fatigue syndrome — tend to experience more severe and persistent symptoms than men do. Post COVID-19
- [RNA sequencing data analysis using R and Bioconductor - 3–14 November](https://www.rna-seqblog.com/rna-sequencing-data-analysis-using-r-and-bioconductor-3-14-november/) - We are excited to announce this excellent training opportunity for anyone looking to gain hands-on experience with RNA sequencing data analysis using R and Bioconductor! Course website: https://www.physalia-courses.org/courses-workshops/course19/ Instructor: Ludwig Geistlinger, Director of Computational Biology, Core for Computational Biomedicine (Harvard Medical School) This online course on “RNA Sequencing Data Analysis with R/Bioconductor”, from 3–14
- [QIAGEN to acquire Parse Biosciences, expanding its Sample technologies portfolio into highly scalable single-cell solutions](https://www.rna-seqblog.com/qiagen-to-acquire-parse-biosciences-expanding-its-sample-technologies-portfolio-into-highly-scalable-single-cell-solutions/) - Parse Biosciences is a fast-growing innovator in single-cell sample preparation, with technologies used in more than 3,000 labs across over 40 countries Acquisition strengthens QIAGEN’s presence in the rapidly growing single-cell market, accelerating growth across its industry-leading Sample technologies portfolio Parse provides Evercode, a highly differentiated instrument-free platform built for analyzing millions and billions of
- [Enhanced adipogenesis and fatty acid transport in Tibetan pigs revealed by single-cell RNA sequencing](https://www.rna-seqblog.com/enhanced-adipogenesis-and-fatty-acid-transport-in-tibetan-pigs-revealed-by-single-cell-rna-sequencing/) - Adipose tissue is a crucial energy-regulating organ in mammals, responsible not only for storing excess energy but also participating in body temperature maintenance and metabolic balance. Adipocyte development is a complex dynamic process, starting from mesenchymal stem cells with differentiation potential, which gradually proliferate and differentiate into preadipocytes, and ultimately form mature adipocytes capable of
- [Alithea Genomics Introduces MERCURIUS™ Spheroid DRUG-seq: Extraction-Free, RNA-seq for 3D Drug Screening and Toxicology](https://www.rna-seqblog.com/alithea-genomics-introduces-mercurius-spheroid-drug-seq-extraction-free-rna-seq-for-3d-drug-screening-and-toxicology/) - Lausanne, Switzerland and Frederick, MD – October 09, 2025 – Life Science Newswire – Alithea Genomics, a leader in next-generation transcriptomic solutions, today announced the commercial launch of MERCURIUS™ Spheroid DRUG-seq, a novel, extraction-free RNA sequencing library preparation kit built for 3D spheroid models. This advancement extends Alithea’s MERCURIUS DRUG-seq technology into physiologically relevant 3D systems, bringing simplicity, sensitivity, and throughput
- [Live Webinar: Cellular Time Travel. Determine Today’s Transcriptome, Study Tomorrow’s Response](https://www.rna-seqblog.com/live-webinar-cellular-time-travel-determine-todays-transcriptome-study-tomorrows-response/) - Hi! Following last month’s Cytosurge × Lexogen announcement, we’re presenting the first end‑to‑end commercial Live‑seq (live‑cell sequencing) workflow, FluidFM OMNIUM sampling + LUTHOR HD library prep, plus sequencing and analysis support. Why join: > Capture full transcriptomes from living cells via subcellular biopsies > Follow the same cell over time to reveal cause‑and‑effect responses > Hear
- [BreastSubtypeR: a unified R toolkit for breast-cancer subtyping](https://www.rna-seqblog.com/breastsubtyper-a-unified-r-toolkit-for-breast-cancer-subtyping/) - What is BreastSubtypeR? BreastSubtypeR is an R/Bioconductor package for intrinsic molecular subtyping of breast cancer. It brings widely used predictors—PAM50 variants (e.g., ssBC/ssBC.v2), AIMS, and others—into one reproducible workflow with harmonized inputs/outputs and clear defaults, enabling consistent reporting across datasets in research and translational studies. Why it matters Subtype calls often differ across methods and
- [Clustering Assessment in OmicsBox 3.5](https://www.rna-seqblog.com/clustering-assessment-in-omicsbox-3-5/) - Accurate cell type prediction is a key step in single-cell RNA-seq (scRNA-seq) analysis, as downstream biological interpretations strongly depend on the quality of these predictions. However, most cell annotation strategies start with an unsupervised clustering step, where parameter choices can substantially affect the resulting cell groupings. Different clustering configurations may reveal distinct biological insights, making
- [Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites](https://www.rna-seqblog.com/riboswitch-discovery-by-combining-rna-seq-and-genome-wide-identification-of-transcriptional-start-sites/) - Researchers at the Institut Pasteur in Paris have developed an innovative approach to uncover hidden layers of gene regulation within bacterial genomes. Their work focuses on identifying riboswitches, small segments of RNA that act like molecular “on-off” switches, controlling gene activity in response to specific cellular signals. These regulatory elements help bacteria fine-tune processes such
- [SPT Labtech and Alithea Genomics collaborate to automate ultra sensitive single-cell transcriptomic workflows](https://www.rna-seqblog.com/spt-labtech-and-alithea-genomics-collaborate-to-automate-ultra-sensitive-single-cell-transcriptomic-workflows/) - SPT Labtech, a global leader in the design and development of laboratory automation and liquid handling solutions, and Alithea Genomics, a pioneer in the field of large-scale RNA sequencing and transcriptomics, today announced a collaboration to provide an automated solution for single-cell transcriptomics. The collaboration integrates Alithea Genomics’ ultra-sensitive single-cell RNA-seq technology, MERCURIUS™ FLASH-seq, with
- [Researchers introduce a new tool for more accurate RNA modification detection from nanopore signals](https://www.rna-seqblog.com/researchers-introduce-a-new-tool-for-more-accurate-rna-modification-detection-from-nanopore-signals/) - Researchers from the University of Eastern Finland and Aalto University have developed a computational framework called SegPore, which enhances the accuracy of RNA modification detection from direct RNA nanopore sequencing data. RNA modifications are essential epigenetic regulators of gene expression and are involved in diverse biological processes, including cell differentiation, stress response and disease progression.
- [Scientific Director of Clinical NGS](https://www.rna-seqblog.com/scientific-director-of-clinical-ngs-2/) - About Us: The people of Memorial Sloan Kettering Cancer Center (MSK) are united by a singular mission: ending cancer for life. Our specialized care teams provide personalized, compassionate, expert care to patients of all ages. Informed by basic research done at our Sloan Kettering Institute, scientists across MSK collaborate to conduct innovative translational and clinical
- [DirectRM - integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing](https://www.rna-seqblog.com/directrm-integrated-detection-of-landscape-and-crosstalk-between-multiple-rna-modifications-using-direct-rna-sequencing/) - Researchers at Fujian Medical University have developed a powerful new method for studying chemical modifications on RNA molecules, offering a clearer view of the epitranscriptome. The team’s new platform, called DirectRM, takes advantage of Nanopore direct RNA sequencing to identify six common RNA modifications at once, including N4-acetylcytidine, 1-methyladenosine, 5-methylcytidine, N7-methylguanosine, N6-methyladenosine, and pseudouridine. Overall
- [Stress hormones silence key brain genes through chromatin-bound RNAs, study reveals](https://www.rna-seqblog.com/stress-hormones-silence-key-brain-genes-through-chromatin-bound-rnas-study-reveals/) - New research led by Professor Yogesh Dwivedi at the University of Alabama at Birmingham uncovers how long noncoding RNAs engage chromatin-silencing machinery under glucocorticoid receptor activation, linking stress biology to potential biomarkers for depression. What if the brain’s response to stress could be read not in fleeting neurotransmitter bursts, but in the quieting of genes
- [Nicheformer - a new foundation model that reveals how cells are organized in tissues](https://www.rna-seqblog.com/nicheformer-a-new-foundation-model-that-reveals-how-cells-are-organized-in-tissues/) - Missing Context in Single-Cell Data Single-cell RNA sequencing has transformed biology by showing which genes are active in individual cells. However, this approach requires cells to be removed from their natural environment, erasing information about their position and neighbors. Spatial transcriptomics preserves this context but is technically more limited and harder to scale. Researchers have
- [Answer ALS completes release of full dataset and integrates ALS TDI ARC study data into Neuromine](https://www.rna-seqblog.com/answer-als-completes-release-of-full-dataset-and-integrates-als-tdi-arc-study-data-into-neuromine/) - Answer ALS today announced the full release of its comprehensive ALS clinical and multi-omics dataset, marking the culmination of a multi-year research program and a groundbreaking collaboration with the ALS Therapy Development Institute (ALS TDI). For the first time, the complete data from over 1,100 individuals who participated in the Answer ALS study, along with
- [KATMAP infers splicing factor activity and regulatory targets from knockdown data](https://www.rna-seqblog.com/katmap-infers-splicing-factor-activity-and-regulatory-targets-from-knockdown-data/) - Researchers at the Massachusetts Institute of Technology have introduced a new computational framework called KATMAP that helps scientists uncover how specific proteins known as splicing factors control the way genes are expressed. Splicing factors play a key role in a process called RNA splicing, where sections of RNA, called exons and introns, are rearranged or
- [From bench to bioinformatics: networking the next generation in genetic sequencing](https://www.rna-seqblog.com/from-bench-to-bioinformatics-networking-the-next-generation-in-genetic-sequencing/) - Thanks to a unique pair of symposia, animal health diagnosticians who protect agriculture and public health are now more familiar with progressive technologies to respond to infectious disease outbreaks, using next-generation sequencing (NGS) and a purpose-built network of colleagues across the country. In May and July 2025, the National Animal Health Laboratory Network (NAHLN) hosted Next-Generation Sequencing Symposia at Michigan State
- [isoLASER -long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing](https://www.rna-seqblog.com/isolaser-long-read-rna-seq-demarcates-cis-and-trans-directed-alternative-rna-splicing/) - Researchers at UCLA have made a significant advance in understanding how genes influence RNA splicing, a fundamental process that determines how genetic information is used to make proteins. RNA splicing occurs after DNA is transcribed into RNA, trimming out non-coding regions (introns) and joining together the coding parts (exons). However, this process isn’t one-size-fits-all. Different
- [Decoding interferon signaling in kidney cancer with single-cell RNA sequencing](https://www.rna-seqblog.com/decoding-interferon-signaling-in-kidney-cancer-with-single-cell-rna-sequencing/) - Single-cell RNA sequencing reveals how interferon signaling in macrophages drives resistance to immunotherapy in renal cell carcinoma, offering new insights for biomarker discovery and treatment strategies...
- [Single-Cell Splicing EStimation - deciphering splicing heterogeneity at single-cell resolution](https://www.rna-seqblog.com/single-cell-splicing-estimation-deciphering-splicing-heterogeneity-at-single-cell-resolution/) - Researchers from the Beijing Institute of Genomics have created a new computational framework called SCSES (Single-Cell Splicing EStimation) that improves how scientists study alternative splicing using RNA sequencing data from individual cells. Alternative splicing is a process that allows a single gene to produce multiple different RNA transcripts, which helps explain the vast diversity of
- [RNA sequencing reveals age-related changes in T cells that weaken vaccine responses](https://www.rna-seqblog.com/how-rna-sequencing-reveals-age-related-changes-in-t-cells-that-weaken-vaccine-responses/) - As flu season approaches and public health officials roll out their annual push for vaccination, Allen Institute scientists are learning why vaccines can trigger a weaker response in older adults, around age 65, and what can be done to improve them. These insights open the door to designing more effective vaccines. In the largest study
- [Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses](https://www.rna-seqblog.com/bioinformatics-perspectives-on-transcriptomics-a-comprehensive-review-of-bulk-and-single-cell-rna-sequencing-analyses/) - Researchers from the Yucatan Scientific Research Center have published an insightful review examining how advances in RNA sequencing (RNA-seq) technologies are revolutionizing the field of transcriptomics, the study of all RNA molecules produced in a cell. The transcriptome provides a detailed snapshot of cellular activity, showing which genes are active, how strongly they are expressed,
- [sysVI - integrating single-cell RNA-seq datasets with substantial batch effects](https://www.rna-seqblog.com/sysvi-integrating-single-cell-rna-seq-datasets-with-substantial-batch-effects/) - Researchers at Helmholtz Munich developed sysVI, a machine learning method that improves integration of RNA sequencing data across diverse systems while preserving vital...
- [Matching gene expression to metabolite production in single plant cells](https://www.rna-seqblog.com/matching-gene-expression-to-metabolite-production-in-single-plant-cells/) - A pioneering method enables simultaneous RNA and metabolite analysis To the point Gene activity and plant metabolites analyzed together in the same plant cell for the first time: Researchers have combined two techniques, single-cell RNA sequencing (scRNA-seq) and single-cell mass spectrometry (scMS), to measure gene expression and the metabolite profile in the same cell. A direct
- [MultiGATE - integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning](https://www.rna-seqblog.com/multigate-integrative-analysis-and-regulatory-inference-in-spatial-multi-omics-data-via-graph-representation-learning/) - Researchers from the Chinese University of Hong Kong have introduced an innovative approach called MultiGATE, designed to integrate complex spatial multi-omics data. Spatial multi-omics combines information about where specific molecules are located in tissues with what genes or proteins they represent. By linking transcriptomics (RNA sequencing data) with other molecular features like proteins and epigenetic
- [New Single cell Methods Guide 2025](https://www.rna-seqblog.com/new-single-cell-methods-guide-2025/) - New guide for emerging single cell methods: Methyl-Seq, CRISPR-Cas9 Screening, Gene Expression, ATAC-Seq, Multiomics, and more! Single cell sequencing is changing rapidly, with new methods that enable as many as 2.6 million cells to be sequenced at once at 62% lower cost*. Download the NEW Single Cell Methods Guide to learn about emerging techniques for
- [P-body-seq permits comprehensive profiling of P-body contents](https://www.rna-seqblog.com/p-body-seq-permits-comprehensive-profiling-of-p-body-contents/) - A team led by researchers at Baylor College of Medicine has uncovered a surprising mechanism that helps determine how stem cells decide what type of cell they will become. Their work focuses on RNA condensates, tiny, droplet-like structures inside cells that organize and store RNA molecules. One type of RNA condensate, known as a P-body,
- [OpenPedCan expands access to pediatric cancer data for researchers worldwide](https://www.rna-seqblog.com/openpedcan-expands-access-to-pediatric-cancer-data-for-researchers-worldwide/) - The OpenPedCan Project harmonizes genomic and clinical data from over 6,000 pediatric tumors across 100 cancer types, creating an open-access resource to advance collaboration and accelerate childhood cancer research. Modern cancer breakthroughs depend on collaboration and open data. The Open Pediatric Cancer (OpenPedCan) Project, published last month in GigaScience, is opening new doors for discovery
- [CytoTRACE 2 - improved reconstruction of single-cell developmental potential](https://www.rna-seqblog.com/cytotrace-2-improved-reconstruction-of-single-cell-developmental-potential/) - Researchers at Stanford University, have introduced a powerful new computational framework called CytoTRACE 2 that improves our ability to predict how individual cells develop and specialize. This innovation represents a major advance in single-cell biology and data-driven research. Understanding how cells transition from one type to another, such as how stem cells mature into specialized
- [Twist Bioscience and Element Biosciences Advance Collaboration with Launch of New Trinity Freestyle™ Sequencing Workflow for the AVITI™ System](https://www.rna-seqblog.com/twist-bioscience-and-element-biosciences-advance-collaboration-with-launch-of-new-trinity-freestyle-sequencing-workflow-for-the-aviti-system/) - Launch of End-to-End Workflow for AVITI and AVITI24™ Enabling Sample to Sequencer in as Little as Five Hours Twist Gains Exclusive Access to the new, co-developed Trinity Freestyle™ Sequencing Workflow Twist Bioscience Corporation (NASDAQ: TWST), a mid-cap growth and value biotech company, and Element Biosciences, Inc., a company democratizing access to advanced life science solutions, today announced
- [Glial diversity revealed through RNA sequencing across brain regions and species](https://www.rna-seqblog.com/glial-diversity-revealed-through-rna-sequencing-across-brain-regions-and-species/) - Salk Institute study suggests glia may play a larger role in shaping neural circuit function than was previously appreciated Histology reveals the organization of neurons (white), astrocytes (red), and oligodendrocytes (green) in the mammalian anterior piriform cortex. Background: Neurons have dominated neuroscience research for decades, but a growing body of evidence suggests that a group of non-neuronal brain
- [Unlocking the regulatory code of RNA: launching the Human RNome Project](https://www.rna-seqblog.com/unlocking-the-regulatory-code-of-rna-launching-the-human-rnome-project/) - Researchers around the world are embarking on an ambitious global effort known as the Human RNome Project, a groundbreaking initiative led by the International Human RNome Project Consortium, which includes scientists from top institutions such as the European Molecular Biology Laboratory. Just as the Human Genome Project revolutionized our understanding of DNA, this new project
- [Algorithm maps genetic connection between Alzheimer’s and specific neurons](https://www.rna-seqblog.com/algorithm-maps-genetic-connection-between-alzheimers-and-specific-neurons/) - Tool can pinpoint disease-relevant cell types across many complex conditions The number of people living with dementia worldwide was estimated at 57 million in 2021 with nearly 10 million new cases recorded each year. In the U.S., dementia impacts more than 6 million lives, and the number of new cases is expected to double over the next
- [Nanostraw electroporation for temporal RNA sampling from living 2D and 3D cell culture systems](https://www.rna-seqblog.com/nanostraw-electroporation-for-temporal-rna-sampling-from-living-2d-and-3d-cell-culture-systems/) - Scientists have long faced a major challenge when studying how genes behave inside living cells: to measure gene activity, they usually have to destroy the cells. Traditional methods of RNA extraction rely on cell lysis, a process that breaks open the cell membrane to release its contents. While this allows scientists to analyze RNA, the
- [GraphComm - predicting cell cell communication using a graph based deep learning method in single cell RNA sequencing data](https://www.rna-seqblog.com/graphcomm-predicting-cell-cell-communication-using-a-graph-based-deep-learning-method-in-single-cell-rna-sequencing-data/) - A team led by researchers at the Princess Margaret Cancer Centre in Toronto have introduced a powerful new approach to studying how cells communicate with one another. Their deep learning framework, called GraphComm, uses single-cell RNA sequencing (RNA-seq) data to uncover the intricate web of molecular signals that allow cells to “talk” and coordinate their
- [tcga-data-nf - reproducible processing of TCGA regulatory networks](https://www.rna-seqblog.com/tcga-data-nf-reproducible-processing-of-tcga-regulatory-networks/) - Researchers at the Harvard T.H. Chan School of Public Health have created a powerful new computational workflow that could help scientists make better use of one of the world’s largest cancer data resources, The Cancer Genome Atlas (TCGA). TCGA contains massive amounts of genomic information, including RNA sequencing, DNA methylation, and other molecular data from
- [Emixed - probabilistic multi-omics cellular deconvolution of bulk omics data](https://www.rna-seqblog.com/emixed-probabilistic-multi-omics-cellular-deconvolution-of-bulk-omics-data/) - Researchers at the University of Pittsburgh have developed a powerful new computational method called EMixed that can more precisely uncover the cellular composition of complex tissues. Understanding which cell types make up a tissue is essential for studying how organs function, how diseases progress, and how treatments might work at the cellular level. Traditionally, scientists
- [Disrupting cancer’s secret hubs: A new way to halt tumor growth](https://www.rna-seqblog.com/disrupting-cancers-secret-hubs-a-new-way-to-halt-tumor-growth/) - When RNA gets hijacked, cancer grows, and scientists have finally learned how to make it stop By revealing how RNA builds the “droplet hubs” that drive cancer growth, and how to dismantle them, Texas A&M Health scientists have discovered a key weakness that could help stop one of the toughest childhood cancers. (Adobe Stock) In
- [RNA sequencing uncovers and predicts widespread molecular changes in ALS brain cells](https://www.rna-seqblog.com/rna-sequencing-uncovers-and-predicts-widespread-molecular-changes-in-als-brain-cells/) - Researchers at the University of Toronto’s Temerty Faculty of Medicine have found widespread genetic and protein changes in the brain cells of people with amyotrophic lateral sclerosis (ALS), which may help shed light on mechanisms of the disease. The study, recently published in Cell Genomics, also describes development of a deep-learning tool to help predict whether the changes
- [Benchmarking scRNA-seq copy number variation callers](https://www.rna-seqblog.com/benchmarking-scrna-seq-copy-number-variation-callers/) - Researchers at LMU Munich have conducted a comprehensive evaluation of computational tools used to detect copy number variations (CNVs) from single-cell RNA sequencing (scRNA-seq) data. CNVs, which are gains or losses of sections of DNA, play a significant role in diseases such as cancer, where they can drive tumor growth and influence how a patient
- [LnCeVar 2.0 - an updated resource and web tools for genomic variations disrupting ceRNA networks](https://www.rna-seqblog.com/lncevar-2-0-an-updated-resource-and-web-tools-for-genomic-variations-disrupting-cerna-networks-from-single-cell-spatial-transcriptomics-data/) - Researchers Harbin Medical University have released LnCeVar 2.0, a powerful database designed to help scientists explore how small genetic variations affect cellular communication in diseases such as cancer. The update integrates RNA sequencing and single-cell transcriptomics data to reveal how specific mutations can disrupt complex gene regulatory networks known as competing endogenous RNA (ceRNA) networks.
- [Decoding the genetic regulation of RNA splicing with artificial intelligence](https://www.rna-seqblog.com/decoding-the-genetic-regulation-of-rna-splicing-with-artificial-intelligence/) - Researchers from the Center for Genomic Regulation in Barcelona have developed a new way to study how splicing factors control gene expression in cancer. Splicing factors determine how genes are pieced together into different RNA isoforms, shaping the diversity of proteins in our cells. When these factors malfunction, they can drive diseases such as cancer
- [Lexogen Launches miRVEL Profiling Small RNA-Seq Kit for Streamlined and Cost-Efficient sRNA Expression Analysis](https://www.rna-seqblog.com/lexogen-launches-mirvel-profiling-small-rna-seq-kit-for-streamlined-and-cost-efficient-srna-expression-analysis/) - Lexogen, a leader in RNA sequencing technologies, announces the launch of the miRVEL Profiling Small RNA-Seq Library Prep Kit, designed to facilitate small RNA research. The innovative kit integrates seamlessly in the miRVEL small RNA sequencing line and helps scientists achieve reliable results faster and with less hands-on work. The miRVEL Profiling Kit will be officially revealed at
- [Understanding gene expression in pancreatic islet cells through RNA sequencing](https://www.rna-seqblog.com/understanding-gene-expression-in-pancreatic-islet-cells-through-rna-sequencing/) - Researchers from Lund University compared two powerful RNA sequencing methods, single-cell (scRNA-seq) and single-nuclei (snRNA-seq), to understand how human pancreatic islet cells express their genes. These cells, which include insulin-producing beta cells, are key to understanding diabetes and metabolic health. Study design and donor characteristics (a) A schematic picture of the study design, including four
- [Plasmidsaurus launches ultrafast RNA-seq service with unprecedented speed, affordability, and convenience](https://www.rna-seqblog.com/plasmidsaurus-launches-ultrafast-rna-seq-service-with-unprecedented-speed-affordability-and-convenience/) - Plasmidsaurus, the leading global Sequencing as a Service company, today announced the launch of its new RNA-Seq service. Applying Plasmidsaurus’s innovative approach to sequencing as a service to Illumina short read applications, Plasmidsaurus is bringing the same speed, convenience, and insights they pioneered for plasmid sequencing to gene expression analysis. Attendees at this week’s American Society
- [Carolina Molecular selected as certified service provider for CS Genetics' single-cell sequencing platform](https://www.rna-seqblog.com/carolina-molecular-selected-as-certified-service-provider-for-cs-genetics-single-cell-sequencing-platform/) - Carolina Molecular, a clinical sequencing lab and NGS foundry, and CS Genetics, an emerging leader in single-cell RNA sequencing (scRNA-Seq) technology, today announced that Carolina Molecular has been named one of the first Certified Service Providers (CSPs) for CS Genetics’ SimpleCell™ platform. “Our clients have a ton of interest around scRNA-Seq,” said Trent Carrier, President
- [Baylor Genetics presents new data on clinical and diagnostic utility of RNA sequencing for rare disease at the ASHG 2025 annual meeting](https://www.rna-seqblog.com/baylor-genetics-presents-new-data-on-clinical-and-diagnostic-utility-of-rna-sequencing-for-rare-disease-at-the-ashg-2025-annual-meeting/) - Research underscores clinical utility of RNA sequencing in providing critical insights to drive diagnoses and medical management Baylor Genetics, a clinical diagnostic laboratory at the forefront of genetic testing, today showcased new research in RNA sequencing (RNA-seq) to uncover critical information leading to rare disease diagnoses at the American Society of Human Genetics 2025 Annual Meeting,
- [Understanding Gene-LLMs: how large language models are learning the language of life](https://www.rna-seqblog.com/understanding-gene-llms-how-large-language-models-are-learning-the-language-of-life/) - Researchers at the Vellore Institute of Technology have explored an exciting intersection between artificial intelligence and biology, where language models originally developed for text, like ChatGPT, are now being used to interpret DNA. These new systems, called Genome Large Language Models (Gene-LLMs), are trained to read and understand the genetic code in much the same
- [RNA sequencing reveals early photoreceptor development and retinoblastoma vulnerability](https://www.rna-seqblog.com/rna-sequencing-reveals-early-photoreceptor-development-and-retinoblastoma-vulnerability/) - The retina is a light-sensitive neural tissue that lines the back of the eye, comprised of retinal cells that are essential for vision. All human retinal cells, subclassed as cone or rod photoreceptors, are generated in the womb. Abnormalities in retinal cell development can cause vision-threating disorders, such as retinal dystrophies and retinoblastoma, an early
- [A review of technical considerations for planning an RNA-Sequencing experiment](https://www.rna-seqblog.com/a-review-of-technical-considerations-for-planning-an-rna-sequencing-experiment/) - Planning an RNA sequencing (RNA-Seq) experiment is one of the most crucial steps in any genomics research project. While RNA-Seq has become a standard method for studying gene expression, designing a successful experiment requires thoughtful planning, technical understanding, and clear analysis goals. In a recent commentary researchers from the Morehouse School of Medicine shared practical
- [SMART-RNA-Metavirome - a practical RNA metavirome platform compatible with high-throughput sequencing of both short and long reads](https://www.rna-seqblog.com/smart-rna-metavirome-a-practical-rna-metavirome-platform-compatible-with-high-throughput-sequencing-of-both-short-and-long-reads/) - Researchers from Southern Medical University have developed an innovative tool called the SMART-RNA-Metavirome platform that enhances scientists’ ability to detect and analyze RNA viruses in complex samples. RNA viruses, such as dengue, Zika, and Japanese encephalitis viruses, are often difficult to identify when present in low quantities, especially in samples from mosquitoes or patient blood.
- [The utility of ultra-deep RNA sequencing in Mendelian disorder diagnostics](https://www.rna-seqblog.com/the-utility-of-ultra-deep-rna-sequencing-in-mendelian-disorder-diagnostics/) - Researchers from Baylor College of Medicine have demonstrated that using ultra-deep RNA sequencing can dramatically improve the diagnosis of genetic diseases. Traditional RNA sequencing typically captures about 50 to 150 million reads per sample, which is often enough to study common gene expression patterns. However, this level of coverage can miss important but rare signals,
- [New tool offers single-cell study of specific genetic variants](https://www.rna-seqblog.com/new-tool-offers-single-cell-study-of-specific-genetic-variants/) - With a closer look at genomic variation, scientists now have a faster, more precise way to uncover new links to disease EMBL scientists created SDR-seq, a tool for single-cell DNA-RNA-sequencing that studies both DNA and RNA simultaneously, linking coding and non-coding genetic variants to gene expression in the same single cell. Credit: Daniela Velasco/EMBL Summary
- [Alithea Genomics introduces extraction-free, RNA-seq for 3D drug screening and toxicology](https://www.rna-seqblog.com/alithea-genomics-introduces-extraction-free-rna-seq-for-3d-drug-screening-and-toxicology/) - The MERCURIUS™ Spheroid DRUG-seq is a novel, extraction-free RNA sequencing library preparation kit built for 3D spheroid models Alithea Genomics has launched its MERCURIUS™ Spheroid DRUG-seq, a novel, extraction-free RNA sequencing library preparation kit built for 3D spheroid models. This advancement extends Alithea’s MERCURIUS DRUG-seq technology into physiologically relevant 3D systems, bringing simplicity, sensitivity, and
- [So3D - a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease](https://www.rna-seqblog.com/so3d-a-comprehensive-three-dimensional-spatial-omics-resource-for-decoding-tissue-architecture-in-physiology-and-disease/) - Researchers from Harbin Medical University have developed a powerful new resource called So3D that helps scientists explore how cells are organized and interact within three-dimensional tissues. Traditional biological studies often rely on two-dimensional data, which can overlook the complex structures that make up real tissues and organs. Understanding how cells function in 3D space is
- [PCsRNAdb: a comprehensive resource of small noncoding RNAs across cancers](https://www.rna-seqblog.com/pcsrnadb-a-comprehensive-resource-of-small-noncoding-rnas-across-cancers/) - Researchers from Sun Yat-sen University have developed an extensive new database that could deepen our understanding of small noncoding RNAs, or sncRNAs, in cancer. These tiny RNA molecules, which include miRNAs, piRNAs, and tRNA- and rRNA-derived fragments, play important roles in regulating how genes behave in cells. While miRNAs have long been known as key
- [BestopCloud: an integrated one-stop solution for single-cell RNA sequencing data analysis](https://www.rna-seqblog.com/bestopcloud-an-integrated-one-stop-solution-for-single-cell-rna-sequencing-data-analysis/) - Researchers from Beijing BestopCell Co have introduced BestopCloud, an advanced cloud-based platform that makes the analysis of single-cell RNA sequencing (scRNA-seq) data more accessible and efficient. Single-cell RNA sequencing has transformed how scientists study biological systems by enabling the measurement of gene expression in individual cells rather than in bulk populations. This allows researchers to
- [Takara Bio USA, Inc. announces a series of updates to its spatial biology product portfolio, extending its innovation with a new class of spatial technology](https://www.rna-seqblog.com/takara-bio-usa-inc-announces-a-series-of-updates-to-its-spatial-biology-product-portfolio-extending-its-innovation-with-a-new-class-of-spatial-technology/) - Takara Bio USA, Inc. (“Takara Bio USA”), a wholly owned subsidiary of Takara Bio Inc. (“Takara Bio”), today announced a series of updates to its spatial biology product portfolio, extending its innovation with a new class of spatial technology. Takara Bio USA has expanded its instrument-free Trekker™ Single-Cell Spatial Mapping Kits for compatibility with formalin-fixed
- [Unlocking cellular complexity with Cell2Text](https://www.rna-seqblog.com/unlocking-cellular-complexity-with-cell2text/) - Single-cell RNA sequencing has changed how scientists explore the inner workings of cells by measuring gene activity in individual cells. This technology helps identify different cell types and states, especially in diseases like cancer or immune disorders. However, even the most advanced computational models tend to simplify cells into fixed categories that overlook their complex
- [MetaGraph - efficient and accurate search in petabase-scale sequence repositories](https://www.rna-seqblog.com/metagraph-efficient-and-accurate-search-in-petabase-scale-sequence-repositories/) - The amount of biological sequencing data available in public databases is growing at an astonishing rate. Researchers now have access to millions of DNA and RNA sequences collected from across all forms of life, including viruses, bacteria, plants, animals, and humans. While this wealth of information is incredibly valuable, finding specific sequences within such massive
- [DeepScence - single-cell and spatial detection of senescent cells](https://www.rna-seqblog.com/deepscence-single-cell-and-spatial-detection-of-senescent-cells/) - Researchers at the Duke University School of Medicine have developed a powerful new method called DeepScence to accurately identify senescent cells, which are cells that have stopped dividing and can contribute to aging, tissue dysfunction, and disease progression. Senescent cells play a critical role in processes like inflammation, cancer development, and age-related disorders, but detecting
- [The ‘DART’ side of transcription: New role for NSUN2 in the RNA-dependent DNA damage response](https://www.rna-seqblog.com/the-dart-side-of-transcription-new-role-for-nsun2-in-the-rna-dependent-dna-damage-response/) - A recent study from the Gullerova lab at the Sir William Dunn School of Pathology, led by Dr Alagia reveals an important mechanism by which cells repair DNA damage. Published in Nature Communications, the work highlights the importance of RNA modifications and how the NSUN2 protein is involved in the cellular response to DNA damage.
- [HALO - hierarchical causal modeling for single cell multi-omics data](https://www.rna-seqblog.com/halo-hierarchical-causal-modeling-for-single-cell-multi-omics-data/) - Researchers at the University of Pittsburgh have developed an innovative framework called HALO that reveals how changes in gene activity and chromatin structure interact over time. While open chromatin often signals active transcription, these two processes don’t always move in lockstep. HALO helps scientists understand when and how they do. The main framework of HALO
- [Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution](https://www.rna-seqblog.com/cisformer-a-scalable-cross-modality-generation-framework-for-decoding-transcriptional-regulation-at-single-cell-resolution/) - Understanding how genes are turned on or off inside individual cells is a key challenge in modern biology. Researchers from Tongji University have developed a powerful new computational model called Cisformer to help solve this problem. In single-cell biology, scientists often study different “modalities” or types of information from the same cell, such as RNA
- [Uppsala set to power a new excellence cluster for RNA–protein interaction research](https://www.rna-seqblog.com/uppsala-set-to-power-a-new-excellence-cluster-for-rna-protein-interaction-research/) - “Our goal is to pave the way for research that contributes to a new generation of medical innovations,” say Erik Jansson and Lindon Moodie, who with a SEK 1.2 million grant from the Swedish Research Council are mapping the conditions to establish a Swedish cluster of excellence for large-scale mapping and analysis of RNA-protein interactions.”
- [Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples](https://www.rna-seqblog.com/comparison-of-imaging-based-single-cell-resolution-spatial-transcriptomics-profiling-platforms-using-formalin-fixed-paraffin-embedded-tumor-samples/) - A research team led by researchers at The University of Texas MD Anderson Cancer Center has taken a closer look at some of the most advanced tools used in spatial transcriptomics, a field that allows scientists to visualize where genes are active within tissues. Understanding how genes are expressed in specific parts of a tumor
- [PRIM-seq - protein-RNA interaction mapping by sequencing](https://www.rna-seqblog.com/prim-seq-protein-rna-interaction-mapping-by-sequencing/) - Bioengineers at the University of California San Diego have developed a powerful new technology that can map the entire network of RNA-protein interactions inside human cells — an achievement that could offer new strategies for treating diseases ranging from cancer to Alzheimer’s. RNA-protein interactions regulate many essential processes in cells, from turning genes on and
- [PaRPI predicts RNA-Protein interactions from cross-protocol and cross-batch RNA-binding protein datasets](https://www.rna-seqblog.com/parpi-predicts-rna-protein-interactions-from-cross-protocol-and-cross-batch-rna-binding-protein-datasets/) - Understanding how proteins interact with RNA is crucial for uncovering how genes are regulated and how diseases develop. RNA-binding proteins (RBPs) control many essential biological processes, including how RNA is processed, transported, and translated into proteins. However, existing computational tools often focus on specific proteins and rely heavily on the experimental setup used to collect
- [Identification of the post-transcriptional regulation reveals complexity in peanut pod development by Direct RNA sequencing](https://www.rna-seqblog.com/identification-of-the-post-transcriptional-regulation-reveals-complexity-in-peanut-pod-development-by-direct-rna-sequencing/) - Researchers from the Peking University Institute of Advanced Agricultural Sciences authors explored post-transcriptional regulation, including polyadenylation, alternative splicing, and RNA adenosine methylation (m6A), in peanut pods across four developmental stages by performing direct RNA sequencing. A total of 14,627 newly identified transcripts and 6,769 new genes were generated from 12 samples at four developmental stages
- [Webinar: Experimental Design and Sample Prep for Single Cell Sequencing](https://www.rna-seqblog.com/upcoming-webinar-experimental-design-and-sample-prep-for-single-cell-sequencing/) - Single cell RNA sequencing offers deeper biological insights than bulk RNA sequencing. This webinar guides researchers through experimental design, sample preparation, and quality control for successful scRNA-seq projects...
- [Webinar: Why Single Cell RNA Sequencing?](https://www.rna-seqblog.com/upcoming-webinar-why-single-cell-rna-sequencing/) - Single Cell RNA Sequencing (scRNA-seq) is helping researchers uncover new insights in ways not possible with traditional bulk RNA sequencing methods. For researchers interested in learning more or just getting started, we’ve developed a series of four educational webinars focused on demystifying scRNA-seq...
- [MOADE - a multimodal autoencoder for dissociating bulk multi-omics data](https://www.rna-seqblog.com/moade-a-multimodal-autoencoder-for-dissociating-bulk-multi-omics-data/) - Understanding complex tissues and tumors is a major challenge in biology, especially when different types of cells are mixed together in bulk samples. Traditional methods often rely only on RNA sequencing data to separate these cell types, which can limit accuracy when looking at other types of biological information, such as proteins or DNA modifications.
- [BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration](https://www.rna-seqblog.com/blend-probabilistic-cellular-deconvolution-with-individualized-single-cell-reference-integration/) - Understanding the makeup of tissues is one of the toughest challenges in biology, especially when studying diseases like Alzheimer’s. Traditional methods use bulk RNA data to estimate what types of cells are present, but these methods often miss key details because they treat all samples the same and struggle to integrate data from different sources.
- [RNA Isoform Atlas May Improve Understanding of Cardiovascular Disease](https://www.rna-seqblog.com/rna-isoform-atlas-may-improve-understanding-of-cardiovascular-disease/) - Northwestern Medicine scientists have developed a comprehensive atlas of genetic coding sequences in both healthy adult hearts and those with heart failure, a resource that has the potential to improve the understanding of heart health and inform the development of new therapeutic targets for cardiovascular disease, as detailed in a recent study published in Circulation. “Our study offers
- [Unlocking gill health: biomarkers and management of disease in farmed Atlantic salmon](https://www.rna-seqblog.com/unlocking-gill-health-biomarkers-and-management-of-disease-in-farmed-atlantic-salmon/) - This project investigated the drivers of complex gill disease (CGD) in farmed Atlantic salmon, identified molecular biomarkers and microbial signatures of gill health, and evaluated whether functional feeds could mitigate disease progression. BACKGROUND Gill health is critical to fish welfare and the efficiency of aquaculture production, yet it is highly vulnerable to pathogens and environmental
- [Fair Rules for Sharing Sequence Data](https://www.rna-seqblog.com/fair-rules-for-sharing-sequence-data/) - DNA and RNA datasets in public repositories are expanding at an unprecedented pace, creating a global atlas of microbial diversity. While open access continues to drive research forward, it also presents a dilemma: painstakingly collected data are often made available worldwide before the researchers who generated them can publish their own findings. In response, an
- [Aging-TCA - a cross-species single-cell transcriptomic atlas for studying testicular aging](https://www.rna-seqblog.com/aging-tca-a-cross-species-single-cell-transcriptomic-atlas-for-studying-testicular-aging/) - The testis is one of the most transcriptionally active tissues in the human body, meaning it expresses more genes than any other organ. Because of this, it provides a valuable way to study how aging impacts gene regulation. Thanks to single-cell RNA sequencing, scientists can now look at how individual cells in the testis change
- [KAIST team links early life epigenetic memory to adult brain inflammation​](https://www.rna-seqblog.com/kaist-team-links-early-life-epigenetic-memory-to-adult-brain-inflammation/) - Why do some people remain healthy through childhood yet become more vulnerable to brain disorders such as dementia later in life? A KAIST (President Kwang Hyung Lee) -led team has uncovered a key part of the answer: a developmental ‘switch’ in astrocytes—the brain’s most abundant support cells that shapes how strongly the brain’s immune system
- [Hybrid BAG-seq - DNA and RNA from the same single nucleus](https://www.rna-seqblog.com/hybrid-bag-seq-dna-and-rna-from-the-same-single-nucleus/) - Researchers from Cold Spring Harbor Laboratory have developed a powerful new technique called hybrid BAG-seq that can analyze DNA and RNA from the same single cell. This breakthrough allows scientists to look at both the genetic code and how it is being expressed, giving a more complete picture of what is happening inside tumors. Overview
- [How clinical RNA sequencing at SickKids is accelerating Precision Child Health](https://www.rna-seqblog.com/how-clinical-rna-sequencing-at-sickkids-is-accelerating-precision-child-health/) - At The Hospital for Sick Children (SickKids), new research is highlighting a powerful tool to support clinical care: RNA sequencing. While researchers have used RNA sequencing for years to better understand human genetics, its integration into clinical care is much newer. In 2023, SickKids became the first hospital in Canada to validate an RNA sequencing
- [RNA sequencing reveals gene program for antigen archiving by lymphatic endothelial cells](https://www.rna-seqblog.com/rna-sequencing-reveals-gene-program-for-antigen-archiving-by-lymphatic-endothelial-cells/) - A study published today in Nature Communications describes how lymphatic endothelial cells assist in generating robust immune memory, offering new insights into how the immune system functions. Specifically, the researchers found there is a particular genetic program within the lymphatic endothelial cells that enables storage and archival of portions of an immunization or pathogen (antigens) for future
- [Gene expression may help predict treatment response in thyroid cancer](https://www.rna-seqblog.com/gene-expression-may-help-predict-treatment-response-in-thyroid-cancer/) - Histological image of papillary thyroid carcinoma. Photo: Christofer Juhlin A study led by Vincenzo Condello and Christofer Juhlin at the Karolinska Institutet, has been published in Endocrine Pathology. The researchers explored why some papillary thyroid cancers don’t respond well to radioactive iodine (RAI) therapy – a key treatment used after surgery to eliminate remaining thyroid
- [scEssentials - assessing tissue-specific gene expression of essential genes from human and mouse](https://www.rna-seqblog.com/scessentials-assessing-tissue-specific-gene-expression-of-essential-genes-from-human-and-mouse/) - A gene is called essential when an organism cannot survive if it is lost or damaged. Finding these genes is important because they reveal the core machinery that keeps cells and tissues alive. Traditionally, scientists have used tools like CRISPR to turn genes on or off in cell cultures to see which ones are essential.
- [Understanding and mitigating the impact of ambient mRNA contamination in single-cell RNA-sequencing analysis](https://www.rna-seqblog.com/understanding-and-mitigating-the-impact-of-ambient-mrna-contamination-in-single-cell-rna-sequencing-analysis/) - Single-cell RNA sequencing, or scRNA-seq, is a powerful method that allows scientists to study the activity of individual cells. By looking at which genes are turned on or off in single cells, researchers can learn more about how the body responds to infection, disease, and development. But one major challenge with this technique is contamination
- [KEGNI - knowledge graph enhanced framework for gene regulatory network inference](https://www.rna-seqblog.com/kegni-knowledge-graph-enhanced-framework-for-gene-regulatory-network-inference/) - Mapping out how genes are controlled inside cells is one of the most important tasks in modern biology. Genes rarely work in isolation. Instead, they operate within large regulatory networks, where certain genes act like “switches” that turn others on or off depending on the needs of the cell. Understanding these networks is essential for
- [RCANE - whole-genome pan-cancer somatic copy number aberration prediction using RNA-seq data](https://www.rna-seqblog.com/rcane-whole-genome-pan-cancer-somatic-copy-number-aberration-prediction-using-rna-seq-data/) - Researchers are finding smarter ways to get more information from the data scientists already collect. In cancer research, transcriptome sequencing, or RNA sequencing, is commonly used to measure gene activity and understand how tumors grow and change. But what if the same data could also reveal structural changes in the genome that drive cancer? That
- [The Biodiversity Cell Atlas - mapping the tree of life at cellular resolution](https://www.rna-seqblog.com/the-biodiversity-cell-atlas-mapping-the-tree-of-life-at-cellular-resolution/) - Cells are the building blocks of life, but scientists still know surprisingly little about how diverse cell types are across the many branches of the tree of life. Advances in single-cell technologies and genome sequencing are opening the door to a much clearer picture. An international team led by researchers from the Centre for Genomic
- [Seeking to understand RNA better and to contribute to new therapies](https://www.rna-seqblog.com/seeking-to-understand-rna-better-and-to-contribute-to-new-therapies/) - RNA is central to how cells function. Through the detailed study of RNA that combines molecular biology with advanced bioinformatics, Vicente Pelechano Garcia hopes to contribute to the development of a new generation of RNA-based treatment and diagnosis. Meet one of the new professors of Karolinska Institutet who will participate in this year's installation ceremony
- [RNA sequencing uncovers COL6A3 as a therapeutic target in recurrent meningiomas](https://www.rna-seqblog.com/chatgpt-said-rna-sequencing-uncovers-col6a3-as-a-therapeutic-target-in-recurrent-meningiomas/) - Korea University College of Medicine Research Team Identifies New Therapeutic Target by Tracing Meningioma Recurrence Mechanism A research team led by Professor Jason Kyungha Sa from the Department of Biomedical Informatics at Korea University College of Medicine has identified a novel therapeutic target for recurrent meningioma through precision genomic analysis. By performing single-cell RNA profiling
- [RNA sequencing of urine biomarkers enables accurate noninvasive detection of prostate cancer](https://www.rna-seqblog.com/rna-sequencing-of-urine-biomarkers-enables-accurate-noninvasive-detection-of-prostate-cancer/) - Researchers at the Johns Hopkins Kimmel Cancer Center, Johns Hopkins All Children’s Hospital and four other institutions have devised a novel method to test for prostate cancer using biomarkers present in urine, funded in part by the National Institutes of Health. This approach could significantly reduce the need for invasive, often painful biopsies, they say. By analyzing urine
- [Single-Cell RNA-Seq Data Analysis: A Practical Introduction (October 6-8 in Berlin)](https://www.rna-seqblog.com/single-cell-rna-seq-data-analysis-a-practical-introduction-october-6-8-in-berlin/) - Master the tools and techniques to confidently analyze single-cell RNA-seq data and gain new insights into complex biological systems The Single-Cell RNA-Seq Workshop is designed to provide a thorough introduction to the analysis of single-cell RNA sequencing data. Through a combination of lectures and hands-on exercises, participants will learn how to process, analyze and integrate
- [Associate/Full Staff Scientist - Lessard Lab](https://www.rna-seqblog.com/associate-full-staff-scientist-lessard-lab/) - Associate/Full Staff Scientist - Lessard Lab Department: Genes & Human Disease Location: Oklahoma City, OK Position Overview and Responsibilities The https://omrf.org/research-faculty/scientists/christopher-j-lessard-ph-d/ seeking an Associate or Full Staff Scientist with specific training and expertise related to the fields of human immunology, rheumatology, and/or autoimmunity to join our research team. Our research investigates the regulatory functions that
- [RNA sequencing study ties contact sports head hits to brain damage](https://www.rna-seqblog.com/rna-sequencing-study-ties-contact-sports-head-hits-to-brain-damage/) - Repetitive head impacts can cause cell loss, inflammation, and vascular damage—even without CTE Lacing up cleats, dusting down pads, pumping up soccer balls: for many young athletes and weekend warriors, fall is the time to get back on the sports field. And while most accept the outside risk of a twisted ankle, strained hamstring, or
- [scHSC - enhancing single-cell RNA-seq clustering via hard sample contrastive learning](https://www.rna-seqblog.com/schsc-enhancing-single-cell-rna-seq-clustering-via-hard-sample-contrastive-learning/) - Single-cell RNA sequencing allows scientists to study the activity of genes in individual cells, providing a detailed picture of how cells function. This powerful technology has helped uncover new cell types and given researchers insight into diseases at a level never seen before. However, analyzing this kind of data is not simple. One of the
- [RNA sequencing reveals how ants control odorant receptor expression through transcriptional interference](https://www.rna-seqblog.com/rna-sequencing-reveals-how-ants-control-odorant-receptor-expression-through-transcriptional-interference/) - Details of an ant’s antenna stained for two different odorant receptors (in cyan and yellow). The antenna contains specialized hairs that house the dendrites of olfactory sensory neurons. (Kronauer lab) Ant societies are built on scent. Pheromones guide the insects to food, warn them of predators, and regulate the rhythms of their colonies. This chemical communication
- [iRECODE - A new computational method that brings clarity to single-cell analysis](https://www.rna-seqblog.com/irecode-a-new-computational-method-that-brings-clarity-to-single-cell-analysis/) - The world of cells is surprisingly noisy. Each cell carries unique genetic information, but when we try to measure cellular activity, signals can be lost or blurred, and differences between experiments can further obscure the data. These challenges have made it difficult for researchers to capture the true behavior of cells, especially when studying rare
- [A comparison of single-cell RNA-seq methods to enable transcriptome profiling of neutrophils in clinical samples](https://www.rna-seqblog.com/a-comparison-of-single-cell-rna-seq-methods-to-enable-transcriptome-profiling-of-neutrophils-in-clinical-samples/) - Neutrophils, a type of white blood cell, are the body’s first responders in fighting infections and play a critical role in inflammation and immunity. Understanding how their genes are expressed can provide valuable insights for developing diagnostics, designing therapies, and improving clinical trials. However, neutrophils are fragile cells. Their gene activity can be altered during
- [Integrated single-cell atlas of human atherosclerotic plaques](https://www.rna-seqblog.com/integrated-single-cell-atlas-of-human-atherosclerotic-plaques/) - Atherosclerosis, the buildup of fatty deposits and inflammation in the arteries, is the main driver of many cardiovascular diseases. These plaques can grow, rupture, and block blood flow, leading to life-threatening conditions like heart attacks and strokes. Understanding which cells are involved in plaque development is critical for finding better ways to prevent and treat
- [Decoding the selfish gene, from evolutionary cheaters to disease control](https://www.rna-seqblog.com/decoding-the-selfish-gene-from-evolutionary-cheaters-to-disease-control/) - New research is shining a light on one of genetics’ enduring puzzles – how the workings of the so-called “selfish gene” could be harnessed to control harmful insect populations. Malaysian stalk-eyed fly (Teleopsis dalmanni). Credit: Paul Richards By understanding the molecular basis of a selfish gene and the way it operates, scientists believe they could
- [Uncovering the limits of single-cell chromatin studies](https://www.rna-seqblog.com/uncovering-the-limits-of-single-cell-chromatin-studies/) - Researchers are constantly developing new tools to understand how our genes are regulated. One such tool is single-cell ATAC-seq, short for Assay for Transposase Accessible Chromatin with Sequencing, which helps identify which regions of DNA are open and active in individual cells. This is important because open chromatin regions often indicate where genes can be
- [NAP-seq for full-length noncapped RNA sequencing](https://www.rna-seqblog.com/nap-seq-for-full-length-noncapped-rna-sequencing/) - Researchers from Sun Yat-sen University have developed a new method called NAP-seq that shines light on the hidden world of “dark matter” RNAs. These RNAs, which make up nearly 80% of the human genome, often go unnoticed because they lack the chemical cap usually found at the start of RNA molecules. Despite this, they play
- [Mapping plant stem cell regulators with single cell RNA sequencing for crop improvement](https://www.rna-seqblog.com/mapping-plant-stem-cell-regulators-with-single-cell-rna-sequencing-for-crop-improvement/) - A thin section of a maize ear at a very early stage of development (about 3 millimeters long). Each color represents the expression of a different gene in stem cells and associated cells. Plant stem cells are crucial for the world’s food supply, animal feed, and fuel production. They lay the foundation for how plants
- [Spotting stealth multiplets for better single-cell experiment design](https://www.rna-seqblog.com/spotting-stealth-multiplets-for-better-single-cell-experiment-design/) - Researchers at EMBL Barcelona have quantitatively evaluated the risk of undetected artefacts in single-cell RNA sequencing experiments Fumio Nakaki combined theoretical modelling with experimental benchmarking and used publicly available single-cell datasets to assess how sample multiplexing influences multiplet detection. Credit: Fumio Nakaki/EMBL Single-cell RNA sequencing (scRNA-seq) has revolutionised modern biology, allowing scientists to study the
- [M&M - an RNA-seq based pan-cancer classifier for paediatric tumours](https://www.rna-seqblog.com/mm-an-rna-seq-based-pan-cancer-classifier-for-paediatric-tumours/) - Diagnosing childhood cancers is one of the most difficult challenges in modern medicine. While many cancers can be identified by looking at tumor cells under a microscope, rare tumors are much harder to classify. An incorrect or delayed diagnosis can lead to less effective treatment, which is especially concerning for children whose health and survival
- [Single Cell Discoveries partners with Immunewatch to enhance TCR insights](https://www.rna-seqblog.com/single-cell-discoveries-partners-with-immunewatch-to-enhance-tcr-insights/) - Single Cell Discoveries is excited to announce a new partnership with the Belgian company ImmuneWatch, aimed at expanding our TCR single-cell sequencing services. As part of this collaboration, they are integrating ImmuneWatch’s DETECT tool into their data consulting services, giving researchers the ability to predict epitopes directly from TCR sequencing data. Combined with their end-to-end TCR
- [scSiameseClu - a Siamese clustering framework for interpreting single-cell RNA sequencing data](https://www.rna-seqblog.com/scsiameseclu-a-siamese-clustering-framework-for-interpreting-single-cell-rna-sequencing-data/) - Single-cell RNA sequencing, or scRNA-seq, has given scientists an unprecedented ability to look at gene expression in individual cells. Instead of seeing an average across millions of cells, researchers can now explore the unique patterns that make each cell type distinct. This has opened exciting possibilities in areas like cancer research, immunology, and developmental biology.
- [Korea University study reveals hidden complexity in recurrent brain tumors](https://www.rna-seqblog.com/korea-university-study-reveals-hidden-complexity-in-recurrent-brain-tumors/) - Meningiomas are the most common primary brain tumors, accounting for nearly one-third of all central nervous system (CNS) tumors. While most are benign and manageable, 20–30% progress to high-grade forms that behave aggressively, recur frequently, and resist standard treatments. Recurrence remains a major clinical challenge, as these tumors often return stronger, leaving patients with limited
- [Long-term alcohol use suspends liver cells in limbo, preventing regeneration](https://www.rna-seqblog.com/long-term-alcohol-use-suspends-liver-cells-in-limbo-preventing-regeneration/) - Long-term alcohol consumption causes a breakdown in the liver’s regenerative abilities, thanks to inflammation disrupting the protein-making process, Illinois researchers and collaborators found in a new study. Illustration by Deyasini Roy Excessive alcohol consumption can disrupt the liver’s unique regenerative abilities by trapping cells in limbo between their functional and regenerative states, even after a
- [How evolution explains autism rates in humans](https://www.rna-seqblog.com/how-evolution-explains-autism-rates-in-humans/) - About one in 31 (3.2%) children in the United States has been identified with Autism Spectrum Disorder. Globally, the World Health Organization estimates that around one in 100 children have autism. From an evolutionary perspective, many scientist believe that autism and schizophrenia may be unique to humans. It is very rare to find behaviors associated
- [New tool automates cell identification in complex datasets](https://www.rna-seqblog.com/new-tool-automates-cell-identification-in-complex-datasets/) - Analyzing single-cell RNA sequencing (scRNA-seq) data is crucial for understanding complex biological processes and disease development, but identifying individual cell types within these vast datasets has been a significant bottleneck. An international research group led by The University of Osaka has developed a new computational tool, scODIN (Optimized Detection and Inference of Names in scRNA-seq
- [Genome-wide mapping of RNA-protein associations through sequencing](https://www.rna-seqblog.com/genome-wide-mapping-of-rna-protein-associations-through-sequencing/) - Proteins and RNAs are constantly interacting inside our cells, shaping how genes are expressed and how cellular processes are carried out. Mapping these interactions is difficult because of the wide variety of RNA-protein structures, but a new tool offers an innovative way forward. Researchers from the University of California San Diego have developed PRIM-seq, short
- [SLRanger - an integrated approach for spliced leader detection and operon prediction using long RNA reads](https://www.rna-seqblog.com/slranger-an-integrated-approach-for-spliced-leader-detection-and-operon-prediction-using-long-rna-reads/) - In many organisms, including simple animals like worms, genes are often arranged in clusters called operons. When these genes are copied into RNA, they need an extra step of processing called spliced leader (SL) trans-splicing. This process attaches a short piece of RNA, known as the spliced leader, to the beginning of the message. SL
- [Rare immune cells offer new hope for treating acute respiratory distress syndrome](https://www.rna-seqblog.com/rare-immune-cells-offer-new-hope-for-treating-acute-respiratory-distress-syndrome/) - Basophils are found to suppress lung inflammation during the recovery stage of ARDS, revealing potential treatment strategies for this life-threatening condition Basophils, a type of white blood cell, promote recovery from acute respiratory distress syndrome (ARDS) in mice, according to researchers at Science Tokyo. In a mouse model of ARDS, basophils were found to release
- [Beckman Coulter Life Sciences and 10x Genomics Partner to Enable Single Cell Workflow Automation](https://www.rna-seqblog.com/beckman-coulter-life-sciences-and-10x-genomics-partner-to-enable-single-cell-workflow-automation/) - Beckman Coulter Life Sciences, a global leader in laboratory automation and innovation, and 10x Genomics, a leader in single cell and spatial biology, today announced a new partnership to expand automation solutions for single cell assay workflows. As part of the agreement, 10x Genomics plans to develop dedicated Chromium Single Cell kits to be used
- [Tiny fish open new horizons for autism research](https://www.rna-seqblog.com/tiny-fish-open-new-horizons-for-autism-research/) - Researchers from Brain Research Institute, Niigata University, Japan have revealed that environment influences social behaviours in autism. By using zebrafish that have a mutation in ube3a, a gene linked to Angelman Syndrome (AS) and autism spectrum disorders (ASD), they demonstrated that sensory processing of environmental information is determinant in the outcome of socializing or not. The
- [Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data](https://www.rna-seqblog.com/bayesian-inference-for-copy-number-intra-tumoral-heterogeneity-from-single-cell-rna-sequencing-data/) - Researchers from St. Vincent’s Institute of Medical Research have introduced a new computational tool called Chloris that helps scientists better understand the complex structure of tumors at the single-cell level. Tumors are not uniform; they are composed of different groups of cells, called clones, each carrying distinct genetic changes known as copy number alterations, or
- [New method calculates rate of gene expression to understand cell fate](https://www.rna-seqblog.com/new-method-calculates-rate-of-gene-expression-to-understand-cell-fate/) - Essentially all cells in an organism’s body have the same genetic blueprint, or genome, but the set of genes that are actively expressed at any given time in a cell determines what type of cell it will be and its function. How rapidly gene expression in a single cell changes over time can provide insight
- [Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing](https://www.rna-seqblog.com/using-synthetic-rna-to-benchmark-polya-length-inference-from-direct-rna-sequencing/) - Poly(A) tails are stretches of adenine nucleotides added to the end of messenger RNA (mRNA) molecules. These tails play a crucial role in determining how long RNA molecules survive in the cell, how efficiently they are translated into proteins, and which specific RNA isoforms are expressed. Because of their central role in RNA biology, accurately
- [Sweetwater - an interpretable and adaptive autoencoder for efficient tissue deconvolution](https://www.rna-seqblog.com/sweetwater-an-interpretable-and-adaptive-autoencoder-for-efficient-tissue-deconvolution/) - Understanding the genetic activity of different cell types is crucial for studying diseases and developing treatments. However, most RNA sequencing experiments measure gene activity from a mixture of many cells, making it difficult to know which signals come from which cell type. To solve this problem, scientists use computational methods called deconvolution models, which estimate
- [Scientific Director of Clinical NGS](https://www.rna-seqblog.com/scientific-director-of-clinical-ngs/) - About Us: The people of Memorial Sloan Kettering Cancer Center (MSK) are united by a singular mission: ending cancer for life. Our specialized care teams provide personalized, compassionate, expert care to patients of all ages. Informed by basic research done at our Sloan Kettering Institute, scientists across MSK collaborate to conduct innovative translational and clinical
- [Alzheimer’s erodes brain cells’ control of gene expression, undermining function, cognition](https://www.rna-seqblog.com/alzheimers-erodes-brain-cells-control-of-gene-expression-undermining-function-cognition/) - Study of 3.5 million cells from more than 100 human brains finds that Alzheimer’s progression, but also resilience to disease, depends on preserving epigenomic stability. Most people recognize Alzheimer’s from its devastating symptoms such as memory loss, while new drugs target pathological aspects of disease manifestations, such as plaques of amyloid proteins. Now a sweeping
- [Multiomic single-cell DNA–RNA sequencing - functional phenotyping of genomic variants using](https://www.rna-seqblog.com/multiomic-single-cell-dna-rna-sequencing-functional-phenotyping-of-genomic-variants-using/) - Understanding how genetic variants affect our cells is one of the biggest challenges in biology. Some changes in DNA can disrupt how genes function, which may lead to diseases such as cancer. But connecting specific DNA variants to their effects on gene activity has been difficult because the tools available have been limited. Researchers from
- [Novel sequencing technology links DNA and RNA to provide molecular insights into breast cancer progression](https://www.rna-seqblog.com/novel-sequencing-technology-links-dna-and-rna-to-provide-molecular-insights-into-breast-cancer-progression/) - Breast cancer is one of the most complex diseases to study because tumors are not made up of identical cells. Instead, they contain different subpopulations of cells that can change over time. Understanding how these differences arise and how they affect cancer progression is critical for developing better treatments. A team led by researchers from
- [T-CellAnnoTator - reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions](https://www.rna-seqblog.com/t-cellannotator-reproducible-single-cell-annotation-of-programs-underlying-t-cell-subsets-activation-states-and-functions/) - Researchers are gaining a clearer picture of how T cells, the body’s key defenders in the immune system, actually work. T cells are known for recognizing threats like viruses or cancer cells and then turning on specific genetic programs that allow them to multiply, attack, and send signals to other immune cells. Traditionally, scientists believed
- [Why male embryos grow faster: RNA-seq reveals genetic clues](https://www.rna-seqblog.com/why-male-embryos-grow-faster-rna-seq-reveals-genetic-clues/) - Cornell researchers have uncovered the genetic triggers that cause male and female bovine embryos to develop differently, as early as seven to eight days after fertilization. The breakthrough in basic science has implications for human health, such as drug development and in vitro fertilization, and for bovine health and dairy industry sustainability. Scientists have known
- [Slide-tags enables single-nucleus barcoding for multimodal spatial genomics](https://www.rna-seqblog.com/slide-tags-enables-single-nucleus-barcoding-for-multimodal-spatial-genomics/) - Understanding how cells are arranged in tissues is just as important as knowing what genes they are expressing. Traditional single-cell and single-nucleus RNA sequencing has given researchers valuable insights into gene activity, but until now, it has not been easy to pinpoint exactly where those cells are located in tissue. To solve this problem, researchers
- [Study identifies key features of cancer cell response and resistance to treatment](https://www.rna-seqblog.com/study-identifies-key-features-of-cancer-cell-response-and-resistance-to-treatment/) - Researchers develop a cellular atlas of prostate cancer using mouse models. Their findings reveal why some prostate tumors respond to therapy while others become resistant Prostate cancer is one of the leading causes of cancer-related death in men. Most patients who are diagnosed during earlier stages usually respond well to treatment. In some, however, the
- [Sniffing out how neurons are made](https://www.rna-seqblog.com/sniffing-out-how-neurons-are-made/) - Cellular differentiation of stem cells into specialized cells requires many steps, including division, to create more cells; fate determination, which is a commitment to a specific lineage or developmental path; and migration, to integrate the cell into its final location. Previous in vitro work has shown that stem cells can spontaneously self-organize into groups of
- [Researchers develop AI tool to unravel secrets of the dark genome](https://www.rna-seqblog.com/researchers-develop-ai-tool-to-unravel-secrets-of-the-dark-genome/) - We mapped the human genome decades ago, but most of it is still a black box. Now, UNSW scientists have developed a tool to peer inside and what they find could reshape how we think about disease. Your genome is the genetic map of you, and we understand almost none of it. Our handle on
- [RNAConnect® Announces Commercial Launch of UltraMarathonRT® cDNA Synthesis and Amplification Kit for Enhanced Short-Read RNA Sequencing](https://www.rna-seqblog.com/rnaconnect-announces-commercial-launch-of-ultramarathonrt-cdna-synthesis-and-amplification-kit-for-enhanced-short-read-rna-sequencing/) - RNAConnect, a leader in next-generation molecular biology tools, today announced the commercial launch of the UltraMarathonRT cDNA Synthesis and Amplification Kit, designed to elevate short-read RNA sequencing workflows. This kit unleashes the power of UltraMarathonRT (uMRT) to deliver unprecedented sensitivity and breadth of transcript detection and quantification, even for the most challenging transcripts. “UltraMarathonRT represents
- [Roswell Park leads largest-ever genomic study of triple-negative breast cancer in african american women](https://www.rna-seqblog.com/roswell-park-leads-largest-ever-genomic-study-of-triple-negative-breast-cancer-in-african-american-women/) - African American women have highest incidence of deadliest type of breast cancer Study included 462 African American women with TNBC across the US Findings appear today in Nature Genetics Triple-negative breast cancer (TNBC), the deadliest breast cancer subtype, disproportionately affects African American women – but until now, they were underrepresented in genomic studies aimed at
- [Uncovering phenotypic inheritance from single cells with Microcolony-seq](https://www.rna-seqblog.com/uncovering-phenotypic-inheritance-from-single-cells-with-microcolony-seq/) - Bacteria aren’t just mindless microbes. New research from the Hebrew University of Jerusalem reveals that single bacterial cells can carry a “memory” of their past environments, passing it down through generations, before eventually forgetting. Using a new technique called Microcolony-seq, scientists uncovered hidden subpopulations inside infections, each with different survival strategies. The finding could explain
- [Optimal sequencing depth for measuring the concentrations of molecular barcodes](https://www.rna-seqblog.com/optimal-sequencing-depth-for-measuring-the-concentrations-of-molecular-barcodes/) - When researchers use combinatorial genetic engineering, they often rely on next-generation sequencing (NGS) to track and measure barcoded or mutated genes. Choosing how deep to sequence, meaning how many times each piece of DNA is read, is a critical step because it affects accuracy, cost, and data quality. A team led by researchers from Sorbonne
- [Picking brains with new single-cell techniques](https://www.rna-seqblog.com/picking-brains-with-new-single-cell-techniques/) - The brain is an extraordinarily complex organ, controlling physiological functions ranging from movement to thought. When it comes to brain biology, neurons are often the stars of the show. In fact, decades of research have characterized the genetic and functional diversity of neurons, giving scientists important insights into neurological mechanisms underlying normal and disease-associated brain
- [SpaIM: single-cell spatial transcriptomics imputation via style transfer](https://www.rna-seqblog.com/spaim-single-cell-spatial-transcriptomics-imputation-via-style-transfer/) - Understanding how cells are organized within tissues is a major focus in biology, but the tools scientists use often come with limitations. Spatial transcriptomics is a powerful method that shows where genes are active in tissue samples, yet it usually captures only a fraction of gene activity, leaving many details unknown. To address this challenge,
- [Liquid biopsy diagnostics for non-small cell lung cancer via elucidation of tRNA signatures](https://www.rna-seqblog.com/liquid-biopsy-diagnostics-for-non-small-cell-lung-cancer-via-elucidation-of-trna-signatures/) - Lung cancer is one of the most common and deadly cancers worldwide, with non-small cell lung cancer (NSCLC) making up about 85 percent of cases. Detecting it early is critical, but current methods like CT scans and biopsies can be invasive, carry risks, and sometimes produce false positives. A research team from the University of
- [single-cell RNA sequencing reveals cells from the spleen play surprising role after heart attack](https://www.rna-seqblog.com/single-cell-rna-sequencing-reveals-cells-from-the-spleen-play-surprising-role-after-heart-attack/) - After a person survives a heart attack, the heart has a brief window of time in which it can heal if the right circumstances exist. But most of the time, scar tissue forms in the areas that lacked oxygen during the heart attack. This scar tissue impairs heart function, which can worsen into heart failure,
- [A study of gene expression in the living human brain](https://www.rna-seqblog.com/a-study-of-gene-expression-in-the-living-human-brain/) - One of the biggest challenges in psychiatric and neurological research is figuring out what is happening in the living human brain at the molecular level. Traditionally, most studies have relied on postmortem brain tissue because collecting brain samples from living people is not possible in most cases. But is gene expression in postmortem tissue really
- [Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics](https://www.rna-seqblog.com/mapping-early-human-blood-cell-differentiation-using-single-cell-proteomics-and-transcriptomics/)
- [Exposure-inducible genes may contribute to missingness in RNAseq-based gene expression analyses](https://www.rna-seqblog.com/exposure-inducible-genes-may-contribute-to-missingness-in-rnaseq-based-gene-expression-analyses/) - When scientists study gene activity using RNA sequencing, they often encounter missing data points, where certain genes appear to have no measurable expression. Understanding why this happens is important because missing values can skew analyses, leading to incorrect conclusions about how genes behave in health and disease. A recent study led by researchers from Baylor
- [RnaXtract - a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing](https://www.rna-seqblog.com/rnaxtract-a-tool-for-extracting-gene-expression-variants-and-cell-type-composition-from-bulk-rna-sequencing/) - RNA sequencing has transformed the way scientists study gene activity, but many current tools are limited in the kinds of information they can provide. A new pipeline called RnaXtract has been developed to overcome these challenges. Researchers from the Université Laval, Québec designed RnaXtract as an all-in-one solution for bulk RNA sequencing data. What makes
- [RNA sequencing maps spatial and temporal gene expression in mouse brain development](https://www.rna-seqblog.com/rna-sequencing-maps-spatial-and-temporal-gene-expression-in-mouse-brain-development/) - During early brain development, cells perform a complicated dance to determine their eventual locations and function. NC State scientist Eric Brooks and colleagues have worked to create a new cellular atlas to study this delicate part of development. Studying the process of brain formation illuminates just how much of development is a series of tiny miracles.
- [rescueSim - simulating paired and longitudinal single-cell RNA sequencing data](https://www.rna-seqblog.com/rescuesim-simulating-paired-and-longitudinal-single-cell-rna-sequencing-data/) - Scientists are constantly searching for better ways to understand how cells change over time. Single-cell RNA sequencing allows researchers to look at which genes are active in individual cells, but analyzing data from experiments that track the same subjects across time has been a challenge. A research team led by researchers from National Jewish Health
- [CRISPR screening by AAV episome-sequencing (CrAAVe-seq): a scalable cell-type-specific in vivo platform uncovers neuronal essential genes](https://www.rna-seqblog.com/crispr-screening-by-aav-episome-sequencing-craave-seq-a-scalable-cell-type-specific-in-vivo-platform-uncovers-neuronal-essential-genes/) - Understanding which genes keep brain cells alive is one of the biggest challenges in neuroscience. When neurons, the cells of the brain, die or lose function, it can lead to devastating conditions such as Alzheimer’s or Parkinson’s disease. Scientists have long searched for effective ways to identify which genes are most critical for neuron survival,
- [HybriSeq - probe-based device-free single-cell RNA profiling](https://www.rna-seqblog.com/hybriseq-probe-based-device-free-single-cell-rna-profiling/) - A research team led by researchers at University of California San Francisco has developed a new technique called HybriSeq for studying RNA inside individual cells. Unlike traditional methods that rely heavily on physical devices to capture and sequence RNA, HybriSeq uses a clever combination of probes and barcoding to track specific transcripts. The process begins with
- [Scientists debut a new foundational atlas of the plant life cycle](https://www.rna-seqblog.com/scientists-debut-a-new-foundational-atlas-of-the-plant-life-cycle/) - Salk Institute researchers map every cell type and developmental state across the entire life cycle of model plant Arabidopsis Nearly everything you know about plants was first discovered in a plant you’ve likely never heard of. Arabidopsis thaliana, also known as thale cress, is a small, flowering weed that has shaped much of plant biology as
- [consHLA - a next generation sequencing consensus-based HLA typing workflow](https://www.rna-seqblog.com/conshla-a-next-generation-sequencing-consensus-based-hla-typing-workflow/) - Researchers from the Children’s Cancer Institute in Australia have developed a powerful new tool called consHLA to improve how doctors analyze HLA genes. HLA, or human leukocyte antigens, are proteins that help the immune system recognize what belongs in the body and what does not. Accurate HLA typing is essential in medicine, especially for organ
- [Gene sequencing uncovers differences in wild and domesticated crops](https://www.rna-seqblog.com/gene-sequencing-uncovers-differences-in-wild-and-domesticated-crops/) - Can understanding these differences help researchers breed better crops suited for a changing climate? This diagram illustrates the methodology of a meta-analysis comparing gene expression data between wild relatives and domesticated species. Using public gene expression databases and computer-based methods, researchers analyzed data from rice, tomato, and soybean to identify differentially expressed genes and common
- [Axelyf closes seed financing to advance next-generation RNA-LNP therapeutics](https://www.rna-seqblog.com/axelyf-closes-seed-financing-to-advance-next-generation-rna-lnp-therapeutics/) - Icelandic venture capital firm Brunnur Ventures leads funding round to support development of breakthrough lipid nanoparticle delivery technologies Axelyf, Inc., a biotechnology company developing next-generation lipid nanoparticle (LNP) delivery systems for RNA therapeutics, today announced the closing of $2.6 million in seed funding, with the potential to reach a total of $4.1 million this fall.
- [Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks](https://www.rna-seqblog.com/evolution-of-comparative-transcriptomics-biological-scales-phylogenetic-spans-and-modeling-frameworks/) - Comparative transcriptomics is a field that explores how gene activity changes across different organisms and tissues, helping scientists understand how evolution shapes the diversity of life. Researchers at the Universitat Pompeu Fabra discuss how new technologies are pushing this field forward. The authors describe how RNA sequencing initially focused on bulk tissue and organ samples,
- [Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis](https://www.rna-seqblog.com/uncovering-the-multi-layer-cis-regulatory-landscape-of-rice-via-integrative-nascent-rna-analysis/) - Researchers at the Université du Québec À Montréal have uncovered new insights into the regulatory elements of the rice genome by integrating multiple genomic approaches. In juvenile leaf tissues of the Azucena rice variety, the team combined analyses of conserved noncoding sequences, intergenic bi-directional nascent transcripts, and chromatin accessibility to identify regions that control gene
- [Ensuring appropriate allocation to minimize batch effects](https://www.rna-seqblog.com/ensuring-appropriate-allocation-to-minimize-batch-effects/) - Avoiding the formation of unwanted clusters of similar elements when dividing data into groups is of great importance for the analysis of medical data. Psychologists and computer scientists from Heinrich Heine University Düsseldorf (HHU) developed a new method to solve this “anticlustering” problem in 2020. Together with researchers from the University of California, San Francisco
- [Molecular characterization of Kawasaki disease subgroups using cell-free RNA profiling](https://www.rna-seqblog.com/molecular-characterization-of-kawasaki-disease-subgroups-using-cell-free-rna-profiling/) - Kawasaki disease is a serious condition in children that causes inflammation of blood vessels and is the leading cause of acquired heart disease in pediatric patients. Diagnosing Kawasaki disease can be challenging because children present with different symptoms, making it difficult to classify the severity and type of disease. Researchers at Cornell University used cell-free
- [Blood test predicts immunotherapy efficacy in triple-negative breast cancer](https://www.rna-seqblog.com/blood-test-predicts-immunotherapy-efficacy-in-triple-negative-breast-cancer/) - A new study has identified a set of plasma proteins that can predict whether patients with triple-negative breast cancer (TNBC) will respond to immunotherapy. By analyzing blood samples from 195 TNBC patients, researchers discovered that proteins like ARG1, NOS3 and CD28 are strongly linked to treatment outcomes. The team also developed a predictive model, the
- [Researchers find that missing messenger RNA fragments could be key to new immunotherapy for hard-to-treat tumors](https://www.rna-seqblog.com/researchers-find-that-missing-messenger-rna-fragments-could-be-key-to-new-immunotherapy-for-hard-to-treat-tumors/) - The researchers identified a potential therapeutic vulnerability in pediatric high-grade gliomas A new study, led by researchers at Children’s Hospital of Philadelphia (CHOP), identified tiny pieces of messenger RNA that are missing in pediatric high-grade glioma tumors but not in normal brain tissues. Preclinical research indicates that these missing RNA fragments can make difficult-to-treat tumors more responsive
- [Mubadala Health Dubai Invests in Precision Diagnostics with Qlucore Transcriptomics Insights for Lung Cancer and Pediatric Leukemia](https://www.rna-seqblog.com/mubadala-health-dubai-invests-in-precision-diagnostics-with-qlucore-transcriptomics-insights-for-lung-cancer-and-pediatric-leukemia/) - Qlucore, a driving force in software development for precision diagnostics, has signed an agreement with Mubadala Health Dubai. They will use Qlucore Insights software for the analysis of cancer samples. Cancer diagnostics are changing rapidly, and Qlucore is at the forefront of this development. The Qlucore software, unique in its field, combines advanced visualization, AI-based
- [Rapid multi-omics test offers breakthrough in diagnosing pediatric joint infections](https://www.rna-seqblog.com/rapid-multi-omics-test-offers-breakthrough-in-diagnosing-pediatric-joint-infections/) - UTSW study shows advanced genetic and immune profiling can swiftly distinguish septic arthritis from autoimmune conditions, potentially sparing children unnecessary antibiotics A small-scale clinical study from UT Southwestern found that a combination of tests can quickly and accurately diagnose septic arthritis in children with joint pain. This approach, called multi-omics, looks for bacterial DNA, inflammatory
- [Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation](https://www.rna-seqblog.com/computational-methods-for-alternative-polyadenylation-and-splicing-in-post-transcriptional-gene-regulation/) - When we think about genes, we often imagine a straightforward process where DNA is copied into RNA, and RNA is used to make proteins. But in reality, our cells have a set of clever editing tricks that can create many different messages from the same gene, and these tricks dramatically influence how our bodies function.
- [InnoSIGN launches first-in-class portal to identify disease drivers from gene expression data](https://www.rna-seqblog.com/innosign-launches-first-in-class-portal-to-identify-disease-drivers-from-gene-expression-data/) - InnoSIGN, a leader in diagnostic-ready computational biology, today announced the launch of the InnoSIGN Portal, a powerful, first-in-class platform designed to uncover the drivers and mechanisms of disease through advanced pathway analysis of RNA sequencing (RNA-seq) data. The secure, cloud-based portal enables researchers, bioinformatics teams, and clinicians to confidentially upload gene expression data and receive quantifiable, interpretable, and actionable
- [Flu fighters - Mizzou researchers getting a closer look at immune response to influenza](https://www.rna-seqblog.com/flu-fighters-mizzou-researchers-getting-a-closer-look-at-immune-response-to-influenza/) - Findings can help scientists develop better flu therapies, vaccines for pigs and humans A team of researchers at the University of Missouri is on a mission to better understand which immune cells in pigs are most responsive to an influenza infection. Because swine and humans share genetic similarities, their research may one day lay the
- [UTSW researchers gain powerful new tools to explore gene expression cell by cell and in the spatial context of the tissue](https://www.rna-seqblog.com/utsw-researchers-gain-powerful-new-tools-to-explore-gene-expression-cell-by-cell-and-in-the-spatial-context-of-the-tissue/) - During transcription, the information encoded within the DNA sequence of a gene is copied into a strand of RNA, called an RNA transcript. The transcriptome, the population of RNA transcripts within a cell, provides a picture of active gene expression and biological pathways within a cell. Bulk RNA sequencing is a commonly used method to
- [SLAMseq reveals potential transfer of RNA from liver to kidney in the mouse](https://www.rna-seqblog.com/slamseq-reveals-potential-transfer-of-rna-from-liver-to-kidney-in-the-mouse/) - Scientists at the University of Edinburgh have been investigating an intriguing question: can RNA molecules, the messengers inside our cells, travel between organs in mammals and help them communicate? While it is well-known that extracellular RNA (exRNA) plays important signalling roles in simpler animals, whether this happens naturally in mammals has remained uncertain. To explore
- [Researchers identify key biomarkers for chronic fatigue syndrome](https://www.rna-seqblog.com/researchers-identify-key-biomarkers-for-chronic-fatigue-syndrome/) - When cells expire, they leave behind an activity log of sorts: RNA expelled into blood plasma that reveal changes in gene expression, cellular signaling, tissue injury and other biological processes. Cornell researchers developed machine-learning models that can sift through this cell-free RNA and identify key biomarkers for myalgic encephalomyelitis, also known as chronic fatigue syndrome
- [Researchers develop a bioinformatics tool to boost omics data analysis in precision medicine](https://www.rna-seqblog.com/researchers-develop-a-bioinformatics-tool-to-boost-omics-data-analysis-in-precision-medicine/) - The Barcelona Institute for Global Health (ISGlobal), a centre supported by the ”la Caixa” Foundation, has launched HTGAnalyzer, a new, easy-to-use, fast and reproducible bioinformatics tool for advanced transcriptomic data analysis. Designed within the R statistical environment, this package simplifies complex analytical processes, making them accessible to professionals without specific expertise in bioinformatics. Transcriptomic analysis:
- [RNA-Seq reveals targeted therapy for aggressive liver cancer](https://www.rna-seqblog.com/rna-seq-reveals-targeted-therapy-for-aggressive-liver-cancer/) - Combining angiogenesis inhibitors with immune checkpoint inhibitors shows promise in treating aggressive liver tumors Hepatocellular carcinoma (HCC), the most common liver cancer, includes aggressive subtypes resistant to treatment. Researchers from Institute of Science Tokyo (Science Tokyo), Japan, identified a key mechanism behind one such subtype and developed a mouse model replicating its characteristics. Their study
- [RNA-Seq uncovers molecular drivers of cellular differentiation](https://www.rna-seqblog.com/rna-seq-uncovers-molecular-drivers-of-cellular-differentiation/) - In two published papers, researchers at Sylvester Comprehensive Cancer Center, part of the University of Miami Miller School of Medicine, documented their use of a new RNA sequencing technology to uncover molecular drivers of cellular differentiation that could lead to better regenerative therapies. In addition to being used in the lab, the technique, Rapid Precision
- [MAPIT-seq - co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues](https://www.rna-seqblog.com/mapit-seq-co-profiling-of-in-situ-rna-protein-interactions-and-transcriptome-in-single-cells-and-tissues/) - Researchers from Peking University have developed an innovative technique called MAPIT-seq that offers scientists a powerful new way to study how proteins interact with RNA inside cells. These proteins, known as RNA-binding proteins (RBPs), play a crucial role in controlling the fate of RNA molecules, from how they are processed to how long they survive,
- [scTail - precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data](https://www.rna-seqblog.com/sctail-precise-polyadenylation-site-detection-and-its-alternative-usage-analysis-from-reads-1-preserved-3-scrna-seq-data/) - Researchers at the University of Hong Kong have developed a powerful new tool that reveals overlooked features in RNA sequencing data. The method, called scTail, was developed to improve our understanding of how genes are regulated at the RNA level, particularly the ends of RNA molecules where polyadenylation sites (PAS) are located. Polyadenylation sites are
- [scCOSMiX - a mixed-effects framework for differential coexpression and transcriptional interactions modeling in single-cell RNA-seq](https://www.rna-seqblog.com/sccosmix-a-mixed-effects-framework-for-differential-coexpression-and-transcriptional-interactions-modeling-in-single-cell-rna-seq/) - Single-cell RNA sequencing (scRNA-seq) is revolutionizing how scientists study individual cells, especially how genes interact with each other under different conditions. But understanding those interactions isn’t always straightforward, especially when cells come from multiple individuals and experiments use different methods. To tackle this challenge, researchers at the University of South Carolina have developed a powerful
- [UMass Chan postdoc receives competitive award from Quebec research foundation](https://www.rna-seqblog.com/umass-chan-postdoc-receives-competitive-award-from-quebec-research-foundation/) - A UMass Chan Medical School postdoctoral fellow is one of 14 researchers from Quebec working in the United States to receive a prestigious award from the Fonds de recherche du Québec-Santé. Tara Delorme, PhD, a postdoc in the lab of Ryan W. Logan, PhD, professor of psychiatry & behavioral sciences, received the award for advanced
- [A new method allows genes in plants to be silenced to improve crop yields](https://www.rna-seqblog.com/a-new-method-allows-genes-in-plants-to-be-silenced-to-improve-crop-yields/) - A team of researchers from the Spanish National Research Council, an entity attached to the Spanish Ministry of Science, Innovation, and Universities, has made a significant advance in plant biotechnology by developing a new method for silencing genes. The novel technique uses ultra-short ribonucleic acid (RNA) sequences carried by genetically modified viruses to achieve genetic
- [CytoAnalyst web platform facilitates comprehensive single cell RNA sequencing analysis](https://www.rna-seqblog.com/cytoanalyst-web-platform-facilitates-comprehensive-single-cell-rna-sequencing-analysis/) - Studying individual cells is one of the most powerful ways scientists are learning about how life works on the smallest scale. Single-cell technologies, especially single-cell RNA sequencing, let researchers explore how different cells express genes, respond to their environment, and change over time. But as exciting as this field is, analyzing the massive amount of
- [Optimized summary-statistic-based single-cell eQTL meta-analysis](https://www.rna-seqblog.com/optimized-summary-statistic-based-single-cell-eqtl-meta-analysis/) - Researchers are constantly trying to understand how small differences in our DNA can increase the risk of diseases. One powerful tool in this effort is identifying expression quantitative trait loci, or eQTLs, which are spots in the genome that affect how much a gene is turned on or off. However, many of these genetic effects
- [Vivo-seq - integration of phospho-signaling and transcriptomics in single cells](https://www.rna-seqblog.com/vivo-seq-integration-of-phospho-signaling-and-transcriptomics-in-single-cells/) - Understanding how immune cells behave and change over time is crucial for treating diseases ranging from infections to cancer. However, while single-cell RNA sequencing (scRNA-seq) has helped scientists map gene activity in individual cells, it misses key pieces of the puzzle, like protein activity, needed to fully understand how cells respond to signals. A research
- [Conducting RNA reconnaissance](https://www.rna-seqblog.com/conducting-rna-reconnaissance/) - Fred Hutch researchers invent a CRISPR screening method to understand RNA-binding proteins often mutated in cancer and other diseases In biology’s standard tale of two acids — deoxyribonucleic (DNA) and ribonucleic (RNA) — RNA is merely the messenger. Its better-known cousin DNA plays the lead role, issuing genetic instructions for the construction of complex molecules called proteins that
- [Prediction of the risk of transplant rejection based on RNA sequencing data of PBMCs](https://www.rna-seqblog.com/prediction-of-the-risk-of-transplant-rejection-based-on-rna-sequencing-data-of-pbmcs/) - Researchers are working hard to find better ways to predict whether a transplanted organ will be rejected by a patient’s immune system. Currently, doctors often detect rejection only after it has started, and sometimes the damage is already permanent. But what if we could spot signs of rejection before the transplant even happens? A team
- [Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing](https://www.rna-seqblog.com/nuclei-isolation-from-adult-mouse-kidney-for-single-nucleus-rna-sequencing/) - Understanding how the kidney works at the level of individual cells is essential for studying health and disease. However, traditional methods for single-cell RNA sequencing (scRNA-seq) in kidney research come with major drawbacks. They typically require fresh tissue and can stress the cells during processing. This often leads to data that mostly reflects the outer
- [Programmable RNA nanostructures enable nanopore detection of cotranscriptionally introduced RNA modifications](https://www.rna-seqblog.com/programmable-rna-nanostructures-enable-nanopore-detection-of-cotranscriptionally-introduced-rna-modifications/) - Researchers at the University of Cambridge have developed a new way to detect chemical modifications in RNA as it is being made. The researchers used tiny pores and special DNA:RNA nanostructures to sense whether certain modified building blocks were added to RNA during transcription. This advancement makes it easier to analyze even short strands of
- [RNA sequencing reveals hidden drivers of asthma flare-ups in children](https://www.rna-seqblog.com/rna-sequencing-reveals-hidden-drivers-of-asthma-flare-ups-in-children/) - A recent multicenter clinical trial has uncovered inflammatory pathways that contribute to asthma flare-ups in children that occur despite treatment, according to findings published in JAMA Pediatrics. Eosinophilic asthma is characterized by high levels of eosinophils, a type of white blood cell involved in the body’s immune response. While eosinophils typically help fight infections, in eosinophilic asthma, they
- [RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation](https://www.rna-seqblog.com/rna-sequencing-and-immunohistochemistry-jointly-improve-tumor-biomarker-interpretation/) - Understanding which biomarkers are present in a tumor is critical for diagnosing cancer and deciding which treatment may be most effective. Traditionally, doctors use a method called immunohistochemistry, or IHC, to identify these biomarkers. However, IHC can sometimes be subjective, depending on how the results are interpreted under a microscope. A team led by researchers
- [OpDetect - a convolutional and recurrent neural network classifier for precise and sensitive operon detection from RNA-seq data](https://www.rna-seqblog.com/opdetect-a-convolutional-and-recurrent-neural-network-classifier-for-precise-and-sensitive-operon-detection-from-rna-seq-data/) - Understanding how genes are organized and regulated is a big part of studying how organisms function. In bacteria, many genes are grouped together into units called operons, which are transcribed as a single unit. These gene clusters often control related biological processes, and figuring out which genes belong to the same operon can provide important
- [Unlocking the mystery of purple leaves: the genetic secrets of tea plants](https://www.rna-seqblog.com/unlocking-the-mystery-of-purple-leaves-the-genetic-secrets-of-tea-plants/) - Purple tea, known for its vivid color and health benefits, is gaining global attention, but the genetic mechanism behind its purple leaves remained unclear. This study combined bulked segregant analysis (BSA-seq), bulked segregant RNA sequencing (BSR-seq), and transcriptome analysis (RNA-seq) on a segregating F1 tea population to uncover the molecular basis of anthocyanin accumulation. Researchers
- [IC2Bert - an AI-powered model that improves prediction of cancer immunotherapy success using RNA sequencing](https://www.rna-seqblog.com/ic2bert-an-ai-powered-model-that-improves-prediction-of-cancer-immunotherapy-success-using-rna-sequencing/) - Predicting which cancer patients will respond to immunotherapy is a major goal in precision medicine. While RNA sequencing has become a powerful tool to help with this, results can vary a lot between studies because of differences in patient groups and data collection methods. These inconsistencies make it hard to build a single model that
- [New protocol unlocks degradome sequencing for damaged RNA samples](https://www.rna-seqblog.com/new-protocol-unlocks-degradome-sequencing-for-damaged-rna-samples/) - Researchers from the Plant Breeding and Acclimatization Institute-National Research Institute in Poland have developed an innovative protocol that makes it possible to study gene regulation using even badly degraded RNA samples. Their work focuses on degradome sequencing, a powerful method used to identify how small molecules called microRNAs (miRNAs) control gene expression by cutting RNA
- [RNA editing characterized in the aging brain with Alzheimer’s disease](https://www.rna-seqblog.com/rna-editing-characterized-in-the-aging-brain-with-alzheimers-disease/) - Genomic study lays groundwork for insights into potential biomarkers and therapeutic strategies New Cleveland Clinic-led research published in Alzheimer’s and Dementia (2025 Jul;21[7]:e70452) describes how a range of post-transcriptional modifications known as RNA editing may serve as an understudied link between aging and neurodegeneration. These modifications, which change the molecules in RNA, may serve as new targets
- [RNA sequencing sheds light on why some CAR T therapies work better than others](https://www.rna-seqblog.com/rna-sequencing-sheds-light-on-why-some-car-t-therapies-work-better-than-others/) - CAR T-cell therapy has revolutionized treatment for patients with hard-to-treat large B-cell lymphoma, but not all CAR T products are created equal. Two of the most widely used therapies, axicabtagene ciloleucel (axi-cel) and tisagenlecleucel (tisa-cel), both target CD19, but they perform differently in patients. Axi-cel often shows stronger responses, but it also causes more side
- [RNA sequencing powers new machine learning tool to discover hidden microproteins](https://www.rna-seqblog.com/rna-sequencing-powers-new-machine-learning-tool-to-discover-hidden-microproteins/) - Salk Institute researchers launch ShortStop, a machine learning framework that explores overlooked DNA regions in search of microproteins that may play roles in disease Proteins sustain life as we know it, serving many important structural and functional roles throughout the body. But these large molecules have cast a long shadow over a smaller subclass of
- [In-Person Workshop - A Practical Introduction to NGS Data Analysis (September 10-12, 2025 in Berlin)](https://www.rna-seqblog.com/in-person-workshop-a-practical-introduction-to-ngs-data-analysis-september-10-12-2025-in-berlin/) - The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally
- [mLLMCelltype: A Multi-Model Framework for Cell Type Annotation in Single-Cell RNA-seq Data](https://www.rna-seqblog.com/mllmcelltype-a-multi-model-framework-for-cell-type-annotation-in-single-cell-rna-seq-data/) - ### mLLMCelltype: A Multi-Model Framework for Cell Type Annotation in Single-Cell RNA-seq Data We present mLLMCelltype, a computational framework that employs multiple large language models (LLMs) to perform automated cell type annotation in single-cell RNA sequencing (scRNA-seq) data. The tool is available as both a web application (https://www.mllmcelltype.com) and a Python package. #### Methodology mLLMCelltype
- [Alithea Genomics Announces the Launch of MERCURIUS™ FLASH-seq: A Plate-Based, Full-Length Single Cell RNA-seq Kit Delivering Exceptional Sensitivity and Simplicity](https://www.rna-seqblog.com/alithea-genomics-announces-the-launch-of-mercurius-flash-seq-a-plate-based-full-length-single-cell-rna-seq-kit-delivering-exceptional-sensitivity-and-simplicity/) - Lausanne, Switzerland and Frederick, MD – June 24, 2025 – Life Science Newswire – Alithea Genomics, a pioneering biotech company based in Switzerland and the USA specializing in high-throughput RNA sequencing solutions, today announced the commercial launch of MERCURIUS™ FLASH-seq, a next-generation library preparation kit for full-length single-cell RNA sequencing. MERCURIUS™ FLASH-seq is based on
- [TrAMA - New RNA-based measure predicts mortality risk and tracks aging](https://www.rna-seqblog.com/trama-new-rna-based-measure-predicts-mortality-risk-and-tracks-aging/) - “TraMA is likely to be of particular value to researchers interested in understanding the biological processes underlying health and aging, and for social, psychological, epidemiological, and demographic studies of health and aging.” In this study, led by Eric T. Klopack from the University of Southern California, researchers created a new RNA-based aging measure that predicts health
- [Cell by cell, petal by petal - mei blossoms reveal secrets of floral fragrance](https://www.rna-seqblog.com/cell-by-cell-petal-by-petal-mei-blossoms-reveal-secrets-of-floral-fragrance/) - Fragrance gives flowers their identity, yet the specific cells orchestrating this scent symphony have remained elusive, until now. Scientists have generated the first single-cell map of petal tissues in Prunus mume (mei), a classic ornamental tree known for its floral aroma. By integrating single-cell RNA sequencing with volatile compound profiling, researchers identified six major petal
- [Enabling scalable single-cell transcriptomic analysis through distributed computing with Apache spark](https://www.rna-seqblog.com/enabling-scalable-single-cell-transcriptomic-analysis-through-distributed-computing-with-apache-spark/) - Researchers at Indiana University have developed an innovative computational tool called scSPARKL to help scientists manage and analyze the massive amounts of data generated by single-cell RNA sequencing (scRNA-seq) experiments. As more labs adopt scRNA-seq to explore gene expression in individual cells, the datasets have grown exponentially in size, creating new challenges in data processing,
- [Protocol to distinguish pre-mRNA from mRNA in RNA-protein interaction studies](https://www.rna-seqblog.com/protocol-to-distinguish-pre-mrna-from-mrna-in-rna-protein-interaction-studies/) - Researchers at the University of Vienna have developed a new method to better understand how a specific RNA-binding protein, called tristetraprolin (TTP), interacts with RNA inside cells. RNA-binding proteins (RBPs) play important roles in controlling how genes are expressed by attaching to RNA molecules. However, many RBPs can bind to different types of RNA, including
- [Senior Computational Biologist, Single Cell Genomics](https://www.rna-seqblog.com/senior-computational-biologist-single-cell-genomics/) - The Satija lab at the New York Genome Center is looking for an enthusiastic and highly motivated senior computational biologist. We encourage applications from talented scientists who are interested in gaining experience in a multidisciplinary, international, and dynamic research environment. The successful candidate will supervise and work closely to PhD students, postdoctoral fellows, and computational
- [PacBio joins the 1000 Genomes long read project to add isoform sequencing with Kinnex and Revio](https://www.rna-seqblog.com/pacbio-joins-the-1000-genomes-long-read-project-to-add-isoform-sequencing-with-kinnex-and-revio/) - New Iso-Seq data from ~1,000 samples to expand transcriptomic insights using highly accurate HiFi sequencing PacBio, a leading developer of high-quality, highly accurate sequencing solutions, today announced it has joined the 1000 Genomes Long Read Sequencing Project, which will involve contributing long-read transcriptome data to one of the world’s most expansive human genomics initiatives. In
- [New approach maps nearly 10,000 disease genes to 93 complex diseases, creating 54,240 gene-disease-cell links for precision medicine](https://www.rna-seqblog.com/new-approach-maps-nearly-10000-disease-genes-to-93-complex-diseases-creating-54240-gene-disease-cell-links-for-precision-medicine/) - Researchers have released TripletDGC, a publicly available resource that links nearly 10,000 disease-associated genes to the specific cell types they most strongly affect, filling a critical gap in our understanding of how genetic risk drives disease at the cellular level. “By linking each disease gene to its most affected cell type, we can finally see
- [IMMCG researchers develop tool to sharpen accuracy of personalized medicine](https://www.rna-seqblog.com/immcg-researchers-develop-tool-to-sharpen-accuracy-of-personalized-medicine/) - When scientists study individual cells, the tiniest unwanted signals can blur their results, much like trying to paint fine details with a spray can that is anything but accurate. Now, a new tool developed by researchers at the Immunology Center of Georgia at Augusta University is helping pinpoint cell markers, revealing clearer answers about how the immune
- [scComplete-seq - automated high-throughput profiling of single-cell total transcriptome](https://www.rna-seqblog.com/sccomplete-seq-automated-high-throughput-profiling-of-single-cell-total-transcriptome/) - Understanding all the RNA molecules in a cell is essential for discovering how genes are regulated and how cells respond to their environment. Most single-cell RNA sequencing methods only capture polyadenylated RNAs, which represent just a portion of the transcriptome. That means many important RNA molecules, such as histone RNAs and enhancer RNAs, are often
- [DiffCoRank - a comprehensive framework for discovering hub genes and differential gene co-expression in brain implant-associated tissue responses](https://www.rna-seqblog.com/diffcorank-a-comprehensive-framework-for-discovering-hub-genes-and-differential-gene-co-expression-in-brain-implant-associated-tissue-responses/) - Brain implants hold promise for treating neurological disorders and expanding our understanding of the brain. However, their long-term effectiveness is often limited by the brain’s response to these foreign objects. Understanding what drives this tissue reaction is critical for developing more stable and biocompatible implants. To explore this, researchers from Michigan State University have created
- [New England Biolabs® launches NEBNext® Low-bias Small RNA Library Prep Kit, presenting a new method for capturing the true diversity of RNA samples](https://www.rna-seqblog.com/new-england-biolabs-launches-nebnext-low-bias-small-rna-library-prep-kit-presenting-a-new-method-for-capturing-the-true-diversity-of-rna-samples/) - Original research by NEB scientists contributes to the kit's unprecedented low bias, peed, shelf life, and input range New England Biolabs (NEB®) today announced the launch of the NEBNext Low-bias Small RNA Library Prep Kit, designed to minimize biased representation of small RNA species in sequencing data. This next generation small RNA preparation method is
- [How trees heal themselves - mapping root regeneration in poplar](https://www.rna-seqblog.com/how-trees-heal-themselves-mapping-root-regeneration-in-poplar/) - How do trees regrow roots after being cut? A new study sheds light on this question using cutting-edge spatial transcriptomics to track how poplar stems regenerate roots. Researchers mapped gene activity during the regeneration process and discovered a sophisticated hormonal interplay between auxin and cytokinin. They identified two genes, SAC56 and LOS1, as spatial markers critical to root
- [Longcell - single cell and spatial alternative splicing analysis with Nanopore long read sequencing](https://www.rna-seqblog.com/longcell-single-cell-and-spatial-alternative-splicing-analysis-with-nanopore-long-read-sequencing/) - A team led by researchers at the Perelman School of Medicine, University of Pennsylvania, have developed a powerful new tool called Longcell to improve the analysis of alternative splicing using Nanopore RNA sequencing. Alternative splicing is a biological process that allows a single gene to produce multiple RNA variants or “isoforms,” which can have different
- [ModiDeC - a multi-RNA modification classifier for direct nanopore sequencing](https://www.rna-seqblog.com/modidec-a-multi-rna-modification-classifier-for-direct-nanopore-sequencing/) - RNA molecules aren’t just messengers carrying genetic information, they’re also finely tuned with chemical modifications that affect how cells function. Understanding these modifications, often called the “epitranscriptome,” can reveal important insights into gene regulation, disease processes, and potential new therapies. Researchers from the University of Mainz in Germany have developed a powerful new tool called
- [FedscGen - privacy-preserving federated batch effect correction of single-cell RNA sequencing data](https://www.rna-seqblog.com/fedscgen-privacy-preserving-federated-batch-effect-correction-of-single-cell-rna-sequencing-data/) - Understanding gene activity at the single-cell level is a powerful tool in modern biology, but comparing data across different studies can be challenging. One major issue is “batch effects,” which are technical differences introduced when samples are processed or sequenced at different times or in different labs. These variations can make it hard to tell
- [Exploring how spaceflight affects tiny rotifers using RNA sequencing](https://www.rna-seqblog.com/exploring-how-spaceflight-affects-tiny-rotifers-using-rna-sequencing/) - Researchers at the University of Namur have taken a close look at how spaceflight affects a tiny aquatic animal called the bdelloid rotifer Adineta vaga. These microscopic creatures were sent to the International Space Station (ISS) to explore how life responds to the unique conditions of space, such as microgravity and increased radiation. To do
- [ScISOr-ATAC - combined single-cell profiling of chromatin–transcriptome and splicing](https://www.rna-seqblog.com/scisor-atac-combined-single-cell-profiling-of-chromatin-transcriptome-and-splicing/) - Understanding how our genes behave in the brain is a huge step toward uncovering the mysteries of neurological diseases like Alzheimer’s. Scientists from Weill Cornell Medicine have taken that step by developing a powerful method that allows them to look at both RNA splicing and chromatin accessibility in the same single cell, even in frozen
- [RNA extraction and RNA-sequencing method for transcriptomic analysis of <i>Mycobacterium tuberculosis</i>](https://www.rna-seqblog.com/rna-extraction-and-rna-sequencing-method-for-transcriptomic-analysis-of-mycobacterium-tuberculosis-2/) - Understanding how Mycobacterium tuberculosis, the bacterium responsible for tuberculosis (TB), responds to drugs at the molecular level is key to developing better treatments. A new research protocol developed by researchers from the National Microbiology Laboratory at the Public Health Agency of Canada offers a valuable solution for scientists studying the transcriptome of this difficult-to-work-with pathogen.
- [LMD - cluster-independent multiscale marker identification in single-cell RNA-seq data](https://www.rna-seqblog.com/lmd-cluster-independent-multiscale-marker-identification-in-single-cell-rna-seq-data/) - With the help of single-cell RNA sequencing (scRNA-seq), scientists try to understand what makes individual cells unique. This is important in everything from tracking immune cell behavior to identifying early disease markers or monitoring how cells respond to treatment. A key step in this process is identifying cell markers, genes that are highly active in
- [CompasSeq - epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution](https://www.rna-seqblog.com/compasseq-epitranscriptome-wide-percentage-assessment-of-metabolite-capped-rna-at-the-transcript-resolution/) - Understanding the many layers of RNA biology is key to unraveling how our genes are regulated, especially as we age. A recent paper by researchers at the Chinese Academy of Sciences, introduces a powerful new tool called CompasSeq that does just that. This analytical platform offers a novel way to examine and quantify special chemical
- [One Biosciences secures €15M to advance its AI-powered transcriptomic platform](https://www.rna-seqblog.com/one-biosciences-secures-e15m-to-advance-its-ai-powered-transcriptomic-platform/) - Funding will be used to establish the clinical utility of OneMap™, a proprietary artificial intelligence (AI) driven single cell transcriptomic oncology platform, to guide treatment decisions, patient selection, therapy development, and optimize clinical trials Proceeds will also help scale strategic partnerships with pharmaceutical and biotechnology companies Financing led by Redmile Group and Blast, with participation
- [Sceptic - pseudotime analysis for time-series single-cell sequencing and imaging data](https://www.rna-seqblog.com/sceptic-pseudotime-analysis-for-time-series-single-cell-sequencing-and-imaging-data/) - A team of researchers from the University of Washington has introduced a new way to better understand how cells change over time. When scientists study individual cells using RNA sequencing, they often want to track how these cells develop or respond to treatments. This process, called pseudotime analysis, helps reconstruct the timeline of changes happening
- [scGPT - end-to-end protocol for fine-tuned retinal cell type annotation](https://www.rna-seqblog.com/scgpt-end-to-end-protocol-for-fine-tuned-retinal-cell-type-annotation/) - Single-cell RNA sequencing (scRNA-seq) has changed the way researchers study cells by allowing them to examine gene expression at the level of individual cells. This technology helps uncover subtle differences between cell types, identify rare cells, and track how cells change over time. However, the growing scale of scRNA-seq datasets makes it increasingly difficult to
- [Clinical utility of targeted RNA sequencing in cancer molecular diagnostics](https://www.rna-seqblog.com/clinical-utility-of-targeted-rna-sequencing-in-cancer-molecular-diagnostics/) - Researchers at The Hospital for Sick Children in Toronto have demonstrated the significant benefits of using RNA sequencing (RNA-seq) for cancer diagnosis and treatment decisions. While most cancer diagnostics traditionally focus on DNA sequencing to identify mutations, RNA sequencing offers unique advantages by analyzing gene expression and detecting fusion genes and splice variants that DNA
- [CELLO-seq - long-read RNA sequencing of transposable elements from single cells](https://www.rna-seqblog.com/cello-seq-long-read-rna-sequencing-of-transposable-elements-from-single-cells/) - Transposable elements, or TEs, are fragments of DNA that can move around the genome. Once thought to be genomic “junk,” scientists now understand that these mobile genetic elements influence everything from embryonic development to neurological disorders and cancer. Surprisingly, TEs account for nearly half of the mammalian genome, yet studying their function has remained a
- [T-DNAreader - fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data](https://www.rna-seqblog.com/t-dnareader-fast-and-precise-identification-of-t-dna-insertion-sites-in-plant-genomes-using-rna-sequencing-data/) - Researchers at Seoul National University have developed a powerful new computational tool called T-DNAreader that significantly advances the study of genetically modified plants. In plant research, one of the most common methods to introduce new genes into plants is through Agrobacterium-mediated transformation. This process uses a natural soil bacterium, Agrobacterium tumefaciens, which transfers a piece
- [A pluripotent stem cell atlas of multilineage differentiation](https://www.rna-seqblog.com/a-pluripotent-stem-cell-atlas-of-multilineage-differentiation/) - Researchers from the University of Queensland have created a detailed atlas showing how human pluripotent stem cells develop into many different cell types. Using single-cell RNA sequencing, the team followed more than 60,000 individual cells over time as they transitioned from a pluripotent state (where cells can become any type of cell in the body)
- [Viome and Scripps Research partner to develop first at-home RNA screening test to prevent colon cancer before it strikes](https://www.rna-seqblog.com/viome-and-scripps-research-partner-to-develop-first-at-home-rna-screening-test-to-prevent-colon-cancer-before-it-strikes/) - First-of-its-kind 1,000-patient clinical study will use RNA-based stool and saliva tests to detect colon polyps — early warning signs of colorectal cancer — before they become cancerous. Study aims to enhance colorectal cancer prevention by identifying polyp molecular signals, offering improved sensitivity over at-home DNA tests, which have limited ability to detect precancerous lesions. Viome Life Sciences,
- [Director, R&D (NGS/Genomics)](https://www.rna-seqblog.com/director-rd-ngs-genomics/) - This role is 100% on-site at our South San Francisco headquarters. The R&D team at Twist is seeking a curious, thoughtful, and driven leader in genomics and NGS to help us develop and enhance products and applications in the Genomics space. Leveraging our silicon-based, massively parallel DNA synthesis platform, you will lead a team to
- [ENEO - efficient and effective identification of cancer neoantigens from tumor only RNA-seq](https://www.rna-seqblog.com/eneo-efficient-and-effective-identification-of-cancer-neoantigens-from-tumor-only-rna-seq/) - Researchers from the National Research Council (CNR), Italy have introduced a new computational tool called ENEO that could simplify and speed up the process of identifying cancer neoantigens, small mutated proteins that the immune system can recognize as a threat. Neoantigen detection is crucial for creating personalized immunotherapies, such as cancer vaccines, but current methods
- [ExpressRM - multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data](https://www.rna-seqblog.com/expressrm-multimodal-zero-shot-learning-of-previously-unseen-epitranscriptomes-from-rna-seq-data/) - When scientists want to understand how genes are regulated beyond just the sequence of RNA, they look to the epitranscriptome—the collection of chemical modifications on RNA molecules that influence their stability, translation, and function. One of the most common and well-studied modifications is N6-methyladenosine (m6A), which plays key roles in brain development, immune responses, and
- [CS Genetics launches 96-sample SimpleCell™ kit, delivering same-day single cell RNA-seq at population scale](https://www.rna-seqblog.com/cs-genetics-launches-96-sample-simplecell-kit-delivering-same-day-single-cell-rna-seq-at-population-scale/) - New high-throughput format expands the SimpleCell product line, empowering researchers to run larger, more complex studies with unprecedented ease and efficiency. CS Genetics, a privately held genomics technology company, today announced the commercial launch of its 96-sample SimpleCell 3′ Gene Expression Kit, further expanding the capabilities of its SimpleCell platform for scalable, cost-efficient single cell
- [Which tool tells the truth? A head-to-head benchmarking of scRNA-seq CNV methods](https://www.rna-seqblog.com/which-tool-tells-the-truth-a-head-to-head-benchmarking-of-scrna-seq-cnv-methods/) - Tumors are often genetic mosaics, harboring diverse cell populations shaped by mutations like copy number variations (CNVs). These genomic alterations drive cancer evolution, but detecting them at single-cell resolution remains challenging. In this study, scientists systematically evaluated five widely used tools that infer CNVs from single-cell RNA sequencing (scRNA-seq) data. The analysis uncovered dramatic differences
- [IT-scC&T-seq streamlines scalable, parallel profiling of protein–DNA interactions in single cells](https://www.rna-seqblog.com/it-scct-seq-streamlines-scalable-parallel-profiling-of-protein-dna-interactions-in-single-cells/) - Understanding how DNA is regulated inside individual cells is essential for decoding the complexity of tissues and diseases. One major part of that regulation involves chromatin, the structure that packages DNA and controls which genes are turned on or off. However, studying chromatin in single cells has been challenging, especially when trying to track how
- [Direct RNA Oxford Nanopore sequencing distinguishes between modifications in tRNA at the U34 position](https://www.rna-seqblog.com/direct-rna-oxford-nanopore-sequencing-distinguishes-between-modifications-in-trna-at-the-u34-position/) - A team led by researchers at the Warsaw University of Technology have developed a promising new approach to studying tRNA modifications using Oxford Nanopore Sequencing (ONS). While ONS has been widely used to study mRNA, its application to transfer RNA (tRNA), which carries amino acids during protein synthesis, has been limited due to the complexity
- [Nano3P-seq - charting the coding and noncoding transcriptome at single-molecule resolution](https://www.rna-seqblog.com/nano3p-seq-charting-the-coding-and-noncoding-transcriptome-at-single-molecule-resolution/) - Understanding RNA and how it functions in the body is essential for studying gene expression and disease. One critical aspect of RNA biology is polyadenylation, the process of adding a string of adenine nucleotides, called a poly(A) tail, to the end of RNA molecules. These tails help determine how long RNAs last and how efficiently
- [A novel preservation method enables field-based single-cell RNA sequencing of malaria infections](https://www.rna-seqblog.com/a-novel-preservation-method-enables-field-based-single-cell-rna-sequencing-of-malaria-infections/) - Researchers are making a major leap in malaria research thanks to new advances in single-cell RNA sequencing. Led by researchers at the Institute of Tropical Medicine in Belgium, scientists have validated a way to study individual malaria parasites from real human infections, not just lab models. Malaria parasites, like Plasmodium knowlesi, pass through several stages
- [DiscMycoVir - a user-friendly platform for discovering mycoviruses in fungal transcriptomes](https://www.rna-seqblog.com/discmycovir-a-user-friendly-platform-for-discovering-mycoviruses-in-fungal-transcriptomes/) - A team led by researchers from the University of Patras in Greece have developed an accessible new tool that simplifies the discovery of viruses in fungi using RNA sequencing data. Led by first author Alexandros Bompotas, the team created DiscMycoVir, an easy-to-use platform designed to detect mycoviruses, viruses that infect fungi, in transcriptome data, even
- [Novogene Europe expands sequencing capabilities with fifth NovaSeq X Plus system in Europe](https://www.rna-seqblog.com/novogene-europe-expands-sequencing-capabilities-with-fifth-novaseq-x-plus-system-in-europe/) - Novogene Europe announces the installation of its fifth Illumina NovaSeq X Plus sequencing system, expanding high-throughput sequencing capacity to meet surging European demand. This strategic enhancement solidifies Novogene's position as Europe's trusted genomics partner, delivering unprecedented speed, data quality, and scalability for large-scale research. "Investing in the NovaSeq X Plus allows us to meet the increasing
- [Innovative liquid biopsy test uses RNA to detect early-stage cancer](https://www.rna-seqblog.com/innovative-liquid-biopsy-test-uses-rna-to-detect-early-stage-cancer/) - UChicago researchers have developed a new liquid biopsy test that uses RNA modifications to detect early-stage colorectal cancer with 95% accuracy. Liquid biopsies are tests that detect signs of cancer through a simple blood draw. Unlike traditional biopsies, which require removing a piece of tissue, a liquid biopsy typically looks for mutations or modification changes
- [eNRSA - a faster and more powerful approach for nascent transcriptome analysis](https://www.rna-seqblog.com/enrsa-a-faster-and-more-powerful-approach-for-nascent-transcriptome-analysis/) - Understanding how genes are regulated in real time is critical for studying everything from development and disease to environmental responses and drug effects. One powerful method for doing this is nascent RNA sequencing, which captures RNA molecules as they are being made by RNA polymerase, before they are processed or degraded. This allows researchers to
- [Essential RNA-seq Metrics: Part 1](https://www.rna-seqblog.com/essential-rna-seq-metrics-part-1/) - The NGS world is full of metrics—both pre-sequencing metrics, such as yield and library size, and post-sequencing metrics, such as coverage, duplicate rates, and mapping rates. And while many of these metrics apply to both DNA sequencing and RNA sequencing, some are unique to RNA-seq, or have different implications in this context. In this two-part
- [Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis](https://www.rna-seqblog.com/tracing-the-evolutionary-pathway-of-sars-cov-2-through-rna-sequencing-analysis/) - Researchers continue to uncover how SARS-CoV-2, the virus responsible for COVID-19, has changed over time to better understand how it affects the human body. Researchers at Wake Forest University School of Medicine used RNA sequencing to examine how different variants of the virus influence gene expression in infected individuals. The team analyzed RNA sequencing data
- [Single-nucleus RNA sequencing confirms that neurons form in the adult brain](https://www.rna-seqblog.com/single-nucleus-rna-sequencing-confirms-that-neurons-form-in-the-adult-brain/) - A study in the journal Science presents compelling new evidence that neurons in the brain’s memory centre, the hippocampus, continue to form well into late adulthood. The research from Karolinska Institutet provides answers to a fundamental and long-debated question about the human brain’s adaptability. The hippocampus is a brain region that is essential for learning
- [Negativeome characterization and decontamination in early-life virome studies](https://www.rna-seqblog.com/negativeome-characterization-and-decontamination-in-early-life-virome-studies/) - Virome studies aim to explore all viruses present in a particular environment, such as the human gut. However, one major obstacle in analyzing gut viromes, especially in infants, is contamination from external sources during sample preparation. A recent study led by researchers from the University of Groningen highlights the extent and impact of such contamination
- [scICE - enhancing clustering reliability and efficiency of scRNA-seq data with multi-cluster label consistency evaluation](https://www.rna-seqblog.com/scice-enhancing-clustering-reliability-and-efficiency-of-scrna-seq-data-with-multi-cluster-label-consistency-evaluation/) - Single-cell RNA sequencing (scRNA-seq) has opened new doors in biology, allowing researchers to study gene expression in individual cells rather than averaging data across thousands or millions of them. This detailed view helps scientists uncover rare cell types, track cell development, and understand diseases at a deeper level. But there’s a catch, analyzing the data
- [scTsI - an effective two-stage imputation method for single-cell RNA-seq data](https://www.rna-seqblog.com/sctsi-an-effective-two-stage-imputation-method-for-single-cell-rna-seq-data/) - Single-cell RNA sequencing (scRNA-seq) has become an essential tool for understanding the diversity of cells in development, disease, and tissue organization. It lets researchers examine gene expression in individual cells rather than looking at average signals from bulk tissue. However, a major challenge in scRNA-seq is the occurrence of “dropouts”, instances where genes appear to
- [RNA sequencing reveals how lncRNA LINC01235 regulates gene expression in triple negative breast cancer](https://www.rna-seqblog.com/rna-sequencing-reveals-how-lncrna-linc01235-regulates-gene-expression-in-triple-negative-breast-cancer/) - Breast cancer is one of the most common cancers among women in the United States. Thanks to decades of fundamental research, it’s also one of the most curable. The exception is a particularly aggressive variant known as triple-negative breast cancer (TNBC). It accounts for 10 to 15 percent of all breast cancer cases. It disproportionately
- [RNA sequencing reveals how ocrelizumab reshapes immune responses in multiple sclerosis](https://www.rna-seqblog.com/rna-sequencing-reveals-how-ocrelizumab-reshapes-immune-responses-in-multiple-sclerosis/) - When ocrelizumab became the first FDA-approved treatment for early forms of multiple sclerosis (MS) in 2017, it offered patients immense hope. The long-awaited drug is a monoclonal antibody that depletes B cells, the immune cells that drive MS progression. Exactly how ocrelizumab does this, however, remains unclear. In a new study published in The Journal of
- [Introduction to Metagenomics: Tools, Workflows & Insights](https://www.rna-seqblog.com/introduction-to-metagenomics-tools-workflows-insights/) - Metagenomics, first conceptualized by Handelsman et al. (1998) through their pioneering work on soil microbial communities, has fundamentally transformed microbial ecology by enabling culture-independent analysis of complex microbial assemblages...
- [MGI announces partnership with Negedia: enhance genomic sequencing technologies at the service of scientific research and precision medicine in Italy](https://www.rna-seqblog.com/mgi-announces-partnership-with-negedia-enhance-genomic-sequencing-technologies-at-the-service-of-scientific-research-and-precision-medicine-in-italy/) - In the study of rare diseases and precision medicine, understanding gene expression in the spatial context of tissues is essential. High-throughput sequencing and STOmics technology will enhance biological and molecular understanding of various pathologies. MGI Tech Co., Ltd. (MGI), a company dedicated to developing core tools and technologies that drive innovation in life sciences, today
- [New statistical method identifies hidden gene programs linked to poor survival in aggressive pancreatic cancer](https://www.rna-seqblog.com/new-statistical-method-identifies-hidden-gene-programs-linked-to-poor-survival-in-aggressive-pancreatic-cancer/) - Researchers from UChicago built a statistical method to better understand the complexity of pancreatic cancer. Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer, known for its aggressive behavior and resistance to treatment. Treating PDAC is challenging because the tumors are extraordinarily complex, with a chaotic mix of cells with different behaviors,
- [Kapa Biosystems](https://www.rna-seqblog.com/kapa-biosystems/) - KAPA RNA HyperPrep Kits are a comprehensive, modular solution for a variety of RNA sequencing applications, from mRNA capture and rRNA depletion to whole transcriptome sequencing (WTS) and custom transcript depletion. Each kit includes KAPA Pure Beads and KAPA HiFi Polymerase ReadyMix, ensuring optimal performance and high-quality results.
- [MEBOCOST - mapping metabolite-mediated intercellular communications using single-cell RNA-seq](https://www.rna-seqblog.com/mebocost-mapping-metabolite-mediated-intercellular-communications-using-single-cell-rna-seq/) - Cell-to-cell communication is vital for our bodies to function properly. While scientists have long studied how proteins help cells communicate, they’ve had a much harder time understanding how metabolites, the small molecules involved in metabolism, carry messages between cells. A new tool called MEBOCOST, developed by researchers at Boston Children’s Hospital, offers a solution by
- [Total RNA Sequencing Breakthroughs Transform Research Accessibility](https://www.rna-seqblog.com/total-rna-sequencing-breakthroughs-transform-research-accessibility/) - (From Broad Clinical Labs) RNA Research for All: How Advances in Total RNA Sequencing are Transforming Accessibility The study of the transcriptome has revolutionized our understanding of gene expression and regulation across biological systems. RNA sequencing (RNA-Seq) has emerged as a fundamental approach to this analysis, providing unprecedented insights into cellular function in both health
- [DSRNAFold - enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis](https://www.rna-seqblog.com/dsrnafold-enhanced-rna-secondary-structure-prediction-through-integrative-deep-learning-and-structural-context-analysis/) - RNA molecules are essential players in our cells, involved in many crucial processes such as carrying genetic information, regulating genes, and catalyzing chemical reactions. To perform these functions, RNA folds into specific shapes, known as secondary structures, formed by the way its building blocks, nucleotides, pair up and interact. Understanding these folded shapes helps scientists
- [RNA-SCAN - RNA single-nucleotide characterization and analysis nanolatch system](https://www.rna-seqblog.com/rna-scan-rna-single-nucleotide-characterization-and-analysis-nanolatch-system/) - Understanding the smallest changes in RNA is key to uncovering the root causes of many diseases. However, detecting these subtle mutations and chemical modifications has long been a challenge due to the limitations of traditional techniques. Now, scientists at the University of Cambridge have introduced an innovative approach called RNA-SCAN that offers a precise, simple,
- [Parse Biosciences GigaLab to Support Mount Sinai Researchers in Generating One of the Largest Alzheimer’s and Parkinson’s Single Cell Datasets](https://www.rna-seqblog.com/parse-biosciences-gigalab-to-support-mount-sinai-researchers-in-generating-one-of-the-largest-alzheimers-and-parkinsons-single-cell-datasets/) - RNA sequencing of over 10 million single cells will uncover alternative splicing events in neurodegenerative diseases, providing insights into Alzheimer’s and Parkinson’s beyond traditional genomic studies...
- [High quality whole transcriptome RNA-sequencing from challenging clinical samples](https://www.rna-seqblog.com/high-quality-whole-transcriptome-rna-sequencing-from-challenging-clinical-samples/) - This poster by CellCarta and Watchmaker Genomics presents a comparison of RNA sequencing (RNA-seq) workflows designed for challenging clinical samples such as formalin-fixed, paraffin-embedded (FFPE) tissues and whole blood. The study evaluates three approaches: Polaris Depletion alone, exome capture alone, and a combination of both, comparing them to a standard reference method.
- [Improving beta cell transplant survival with RNA sequencing and small molecule screening](https://www.rna-seqblog.com/improving-beta-cell-transplant-survival-with-rna-sequencing-and-small-molecule-screening/) - A pretreatment step could help transplanted pancreatic islets survive longer in patients with type 1 diabetes, according to a new preclinical study from Weill Cornell Medicine investigators. One combination of small molecules extended the cells’ lives in female mice, and adding two molecules to the mixture boosted cell survival in male mice. The findings, published on
- [Scientists discover network of cells and genes involved in Crohn’s disease complication](https://www.rna-seqblog.com/scientists-discover-network-of-cells-and-genes-involved-in-crohns-disease-complication/) - RNA sequencing and spatial mapping revealed distinct fibroblast populations and genetic risk factors driving fibrosis in Crohn’s disease, offering new insight into potential personalized treatments....
- [UIC Spatial and Genome Technologies Core opens new research pathways](https://www.rna-seqblog.com/uic-spatial-and-genome-technologies-core-opens-new-research-pathways/) - Speakers at the SGT Core launch event included Melissa Leone, Olga Karginova, George Chlipala, Yue Huang, Gayatry Mohapatra, Maria Sverdlov, Alvaro Hernandez, Claire White, Dan Moline, Ameen Salahudeen, Don Vander Griend. Understanding the makeup of cells and their interactions is essential for interpreting biological processes in organs and tissues. Single-cell sequencing allows researchers to determine
- [Avance Biosciences Launches NGS Center of Excellence in Houston](https://www.rna-seqblog.com/avance-biosciences-launches-ngs-center-of-excellence-in-houston/) - Purpose-Built Facility Expands Sequencing Capabilities for Biologics and Cell and Gene Therapy Development Houston, Texas – June 25, 2025 – Avance Biosciences is proud to announce the launch of its Next-Generation Sequencing (NGS) Center of Excellence, a purpose-built facility designed to unify and enhance the company’s sequencing capabilities across all phases of drug development. Located in Houston,
- [Comparison of whole transcriptome and targeted RNA sequencing for ecological high-throughput transcriptomics](https://www.rna-seqblog.com/comparison-of-whole-transcriptome-and-targeted-rna-sequencing-for-ecological-high-throughput-transcriptomics/) - In an effort to make environmental monitoring more efficient and affordable, the U.S. Environmental Protection Agency (EPA) launched a federal challenge in 2019 to evaluate low-cost, high-throughput RNA sequencing technologies. The goal was to support a new initiative in ecological high-throughput transcriptomics, a field that uses gene expression data to understand how organisms respond to
- [scDown - a pipeline for single-cell RNA-seq downstream analysis](https://www.rna-seqblog.com/scdown-a-pipeline-for-single-cell-rna-seq-downstream-analysis/) - A research team led by researchers at Boston Children’s Hospital has developed a powerful new tool for analyzing single-cell RNA sequencing data. The tool, called scDown, is designed to help scientists better understand how cells behave, communicate, and change over time, especially in the context of rare diseases. Single-cell RNA sequencing (scRNA-seq) allows researchers to
- [Alithea Genomics Launches MERCURIUS™ Total DRUG-seq: A Next-Generation Full-Length Transcriptome Profiling Platform for High-Throughput Compound Screening and Target Validation](https://www.rna-seqblog.com/alithea-genomics-launches-mercurius-total-drug-seq-a-next-generation-full-length-transcriptome-profiling-platform-for-high-throughput-compound-screening-and-target-validation/) - Alithea Genomics, a pioneering biotech company based in Switzerland and the USA specializing in scalable RNA sequencing solutions, today announced the launch of MERCURIUS™ Total DRUG-seq, a new extraction-free, full-length transcriptome profiling library preparation kit designed to push the boundaries of high-throughput drug screens, toxicology screens and target validation by enabling the creation of large-scale
- [scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration](https://www.rna-seqblog.com/scextract-leveraging-large-language-models-for-fully-automated-single-cell-rna-seq-data-annotation-and-prior-informed-multi-dataset-integration/) - Single-cell RNA sequencing (scRNA-seq) is a powerful tool for understanding the diversity of cells in the body. However, analyzing the vast amount of data generated from these experiments can be difficult, especially when dealing with datasets that lack clear labeling. Researchers at Peking University have developed scExtract, an innovative tool that uses artificial intelligence to
- [RNA sequencing reveals heterogeneity of bone metastases across different and same cancer types](https://www.rna-seqblog.com/rna-sequencing-reveals-heterogeneity-of-bone-metastases-across-different-and-same-cancer-types/) - RNA sequencing of bone metastases from eight cancers reveals distinct immune cell patterns, highlighting the complexity of tumor...
- [scEVE - a single-cell RNA-seq ensemble clustering algorithm](https://www.rna-seqblog.com/sceve-a-single-cell-rna-seq-ensemble-clustering-algorithm/) - RNA sequencing data from individual cells can be hard to cluster consistently, but a new algorithm called scEVE helps address this by highlighting differences between clustering methods rather than ignoring them...
- [Decoding the interactions and functions of non-coding RNA with artificial intelligence](https://www.rna-seqblog.com/decoding-the-interactions-and-functions-of-non-coding-rna-with-artificial-intelligence/) - Messenger RNAs (mRNAs) are best known for carrying instructions from DNA to make proteins. But researchers are learning that mRNAs do much more than that. In addition to encoding proteins, mRNAs have regulatory regions that play important roles in how the cell works. These include parts of the RNA that do not code for proteins,
- [RNA sequencing reveals how short tandem repeats can shape RNA structure and influence gene expression](https://www.rna-seqblog.com/rna-sequencing-reveals-how-short-tandem-repeats-can-shape-rna-structure-and-influence-gene-expression/) - Short tandem repeats (STRs) are small, repeated sequences of DNA scattered throughout the human genome. While some of these repeats are known to cause severe genetic disorders, scientists are now beginning to understand how more subtle changes in these sequences might influence how genes are turned on or off. Researchers from Sweet Briar College explored
- [Two transparent worms shed light on evolution](https://www.rna-seqblog.com/two-transparent-worms-shed-light-on-evolution/) - Study finds pace of evolution in organisms varies by cell types. Two species of worms have retained remarkably similar patterns in the way they switch their genes on and off despite having split from a common ancestor 20 million years ago, a new study finds. “It was just remarkable, with this evolutionary distance, that we
- [TempO-seq and RNA-seq Gene Expression Levels are Highly Correlated for Most Genes: A Comparison Using 39 Human Cell Lines](https://www.rna-seqblog.com/tempo-seq-and-rna-seq-gene-expression-levels-are-highly-correlated-for-most-genes-a-comparison-using-39-human-cell-lines/) -  Recent advances in transcriptomics technologies allow for whole transcriptome gene expression profiling using targeted sequencing techniques, which is becoming increasingly popular due to logistical ease of data acquisition and analysis. As data from these targeted sequencing… Word L, Willis C, Judson R, Everett LJ, Davidson-Fritz S, Chambers B, et al. (2025) TempO-seq and RNA-seq
- [High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes](https://www.rna-seqblog.com/high-resolution-profiling-reveals-coupled-transcriptional-and-translational-regulation-of-transgenes/) - Researchers from the Massachusetts Institute of Technology have taken a detailed look at how genes are turned into proteins in cells engineered with synthetic DNA sequences. When scientists design synthetic genes, they often focus on getting the right amount of messenger RNA (mRNA) made, assuming that more RNA will naturally lead to more protein. But
- [The GTEx Consortium atlas of genetic regulatory effects across human tissues](https://www.rna-seqblog.com/the-gtex-consortium-atlas-of-genetic-regulatory-effects-across-human-tissues/) - What if you could look inside every major organ of the human body and see how genes behave, how they turn on, how much they’re used, and how that activity changes depending on your DNA? That’s exactly what the Genotype-Tissue Expression (GTEx) Consortium set out to do. Led by researchers from institutions including the Broad
- [Genes may help to predict which children will respond well to arthritis treatment](https://www.rna-seqblog.com/genes-may-help-to-predict-which-children-will-respond-well-to-arthritis-treatment/) - A set of genes that could be used to help doctors predict which children will respond well to treatment for juvenile idiopathic arthritis (JIA) have been identified by researchers at UCL and Great Ormond Street Hospital for Children (GOSH), who are part of the CLUSTER Consortium. JIA is a childhood immune disease where the immune
- [Low-input RNA-seq suggests gut bacteria shape-shift to survive](https://www.rna-seqblog.com/low-input-rna-seq-suggests-gut-bacteria-shape-shift-to-survive/) - The human gut is home to trillions of microbes, and even bacteria of the same species can look and behave very differently. A team led by researchers at the University of Würzburg has uncovered how one common gut bacterium, Bacteroides thetaiotaomicron, changes its shape depending on where it lives and what it’s doing. Researchers noticed
- [Groundbreaking TACIT algorithm offers new promise in diagnosing, treating cancer](https://www.rna-seqblog.com/groundbreaking-tacit-algorithm-offers-new-promise-in-diagnosing-treating-cancer/) - Scientists at VCU have created a new tool called TACIT that could help doctors better understand what is happening inside the body by using advanced computer models to identify different kinds of cells in tissues faster and more accurately than ever before, helping to guide better treatment decisions. Researchers at VCU Massey Comprehensive Cancer Center
- [How can RNA sequencing strengthen cancer diagnostics in precision medicine](https://www.rna-seqblog.com/how-can-rna-sequencing-strengthen-cancer-diagnostics-in-precision-medicine/) - When it comes to treating cancer, understanding a patient’s unique genetic profile is essential. Traditionally, DNA testing has been used to detect mutations that might predict how well a patient will respond to a particular therapy. However, DNA testing alone doesn’t always give the full picture. Most cancer drugs actually target proteins, and DNA mutations
- [Integrative exome sequencing and machine learning identify new genes contributing to systemic sclerosis risk](https://www.rna-seqblog.com/integrative-exome-sequencing-and-machine-learning-identify-new-genes-contributing-to-systemic-sclerosis-risk/) - Researchers conducted a genome-wide analysis study to find novel genes and rare variants contributing to SSc risk. Systemic sclerosis (SSc) is a severe autoimmune disease with complex genetic causes. Some genetic contributors have been identified, but others remain unknown, which has impeded development of targeted treatments. In a new study published in Annals of the Rheumatic
- [moPepGen - identification of non-canonical peptides from RNA-Seq data](https://www.rna-seqblog.com/mopepgen-identification-of-non-canonical-peptides-from-rna-seq-data/) - Understanding the full complexity of proteins in cancer is a major challenge for scientists. Many proteins are made in unusual ways that don’t follow the standard rules we learn in biology class. These “non-canonical” peptides can be important in disease, but they are often missed in typical genetic and protein studies. A team of researchers
- [City of Hope researchers use RNA sequencing to reveal how ecDNA shapes the tumor microenvironment in gliomas](https://www.rna-seqblog.com/city-of-hope-researchers-use-rna-sequencing-to-reveal-how-ecdna-shapes-the-tumor-microenvironment-in-gliomas/) - Scientists developed a new framework to improve the ability of doctors to use precision medicine to identify therapeutic targets and potentially spotlight ways to prevent disease recurrence City of Hope®, one of the largest and most advanced cancer research and treatment organizations in the U.S. with its National Medical Center named top 5 in the
- [RNA sequencing uncovers pheromone gene activity in the fingers of neotropical poison frogs](https://www.rna-seqblog.com/rna-sequencing-uncovers-pheromone-gene-activity-in-the-fingers-of-neotropical-poison-frogs/) - How Frankfurt biologist Diana Abondano Almeida discovered unknown communication pathways in neotropical frogs. Most people have probably seen them: wriggling tadpoles darting about in a pond or even a puddle. Rarely, however, does one encounter an adult frog. The situation is different with neotropical poison frogs (Dendrobatidae). These small amphibians, only around 2 to 3
- [Perturb-Multimodal - a platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue](https://www.rna-seqblog.com/perturb-multimodal-a-platform-for-pooled-genetic-screens-with-imaging-and-sequencing-in-intact-mammalian-tissue/) - Scientists at the Howard Hughes Medical Institute have created a powerful new tool called Perturb-Multimodal, or Perturb-Multi for short. This innovative method helps researchers explore how genes control the behavior and function of individual cells within complex tissues, like the liver.Every living organism, from tiny animals to humans, depends on thousands of genes working together
- [Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data](https://www.rna-seqblog.com/robustness-and-resilience-of-computational-deconvolution-methods-for-bulk-rna-sequencing-data/) - Understanding what types of cells are present in a tissue sample is key to unlocking how that tissue functions in health and disease. One way scientists estimate this information is through computational deconvolution, a method that uses RNA sequencing data to predict the proportions of different cell types within a mixed tissue sample. Researchers at
- [Workshop - RNA Sequencing](https://www.rna-seqblog.com/workshop-rna-sequencing/) - On 24 and 25 June, NeSI and Genomics Aotearoa will be delivering an online workshop on RNA Sequencing. The workshop will be taught over two mornings from 9:00am – 1:00pm NZT on both days. The focus of this workshop is to analyse RNA-seq data with the aim to identify differentially expressed genes. By the end of this workshop you
- [SugiExDB - data repository for Cryptomeria japonica RNA-sequencing read counts](https://www.rna-seqblog.com/sugiexdb-data-repository-for-cryptomeria-japonica-rna-sequencing-read-counts/) - Understanding how genes are turned on or off in different parts of a plant is a key step toward unlocking how that plant grows, functions, and adapts. Researchers from the Forest Research and Management Organization, Japan, have made a significant contribution to this field by studying gene expression in Cryptomeria japonica, also known as Japanese
- [How to Better Computationally Analyze Your Single-Cell RNA Sequencing Data](https://www.rna-seqblog.com/how-to-better-computationally-analyze-your-single-cell-rna-sequencing-data/) - Wednesday June 25th 2025 13.50 – 15.20 Room 050 Are you working with single-cell RNA sequencing data or planning to soon? This hands-on workshop is designed specifically for researchers, biologists, experimentalists and data analysts who are either new to scRNA-seq analysis or looking to strengthen their computational pipelines for data analysis skills. Whether you’re just getting started
- [Researchers identify how physical activity protects the brain - cell by cell - in Alzheimer's disease](https://www.rna-seqblog.com/researchers-identify-how-physical-activity-protects-the-brain-cell-by-cell-in-alzheimers-disease/) - Mass General Brigham study reveals how exercise rewires the brain at the cellular level, offering fresh insights into potential treatment strategies for Alzheimer’s Using advanced single-nuclei RNA sequencing (snRNA-seq) and a widely used preclinical model for Alzheimer’s disease, researchers from Mass General Brigham and collaborators at SUNY Upstate Medical University have identified specific brain cell
- [Imaging-based STAMP technique democratizes single-cell RNA research](https://www.rna-seqblog.com/imaging-based-stamp-technique-democratizes-single-cell-rna-research/) - Scientists at St. Jude Children’s Research Hospital, the National Center for Genomic Analysis and the University of Adelaide created a single-cell RNA analysis method that is 47 times cheaper and more scalable than other techniques. Single-cell RNA sequencing provides scientists with important information about gene expression in health and disease. However, the technique is expensive and often
- [Eclipsebio launches eVERSE™, a first‑of‑its‑kind comprehensive portfolio of RNA‑focused datasets for AI model success](https://www.rna-seqblog.com/eclipsebio-launches-everse-a-first‑of‑its‑kind-comprehensive-portfolio-of-rna‑focused-datasets-for-ai-model-success/) - Eclipsebio’s eVERSE™ provides access to AI-ready data from their comprehensive portfolio of next-generation sequencing technologies, including measurements of RNA secondary structure, protein translation, and regulatory regions. Eclipsebio’s partners can improve AI-powered drug discovery with reproducible and high-quality data capturing key determinants of siRNA, ASO, and mRNA-based therapy efficacy. Eclipse Bioinnovations, the leading partner for RNA-based
- [RNA sequencing reveals m6A modification patterns guiding early human embryo development](https://www.rna-seqblog.com/rna-sequencing-reveals-m6a-modification-patterns-guiding-early-human-embryo-development/) - A Powerful Tool: picoMeRIP-seq RNA modifications are tiny chemical marks added to RNA molecules to control how they work. One of the most common is m6A modification, which acts like a “sticky note” on RNA—telling the cell when to use it, store it, or discard it. These marks help fine-tune RNA activity during important processes
- [TORC - Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq](https://www.rna-seqblog.com/torc-target-oriented-reference-construction-for-supervised-cell-type-identification-in-scrna-seq/) - Single-cell RNA sequencing, or scRNA-seq, is a cutting-edge technique that lets scientists study gene activity in individual cells. This technology helps researchers uncover how different cell types function and interact in health and disease. One crucial step in analyzing scRNA-seq data is identifying which cell types are present in the sample. This process is called
- [AlidaBio Launches First Service Provider Partnership with Baylor College of Medicine's GARP Core to Offer Multiplexed RNA Modification Sequencing](https://www.rna-seqblog.com/alidabio-launches-first-service-provider-partnership-with-baylor-college-of-medicines-garp-core-to-offer-multiplexed-rna-modification-sequencing/) - Alida Biosciences, a leader in next-generation RNA modification analysis, is proud to announce its first official service provider: the Genomic and RNA Profiling (GARP) Core at Baylor College of Medicine. This new service offering is powered by AlidaBio’s EpiPlex™ Platform, the first and only solution that concurrently detects and quantifies multiple RNA modifications alongside gene expression
- [RNA ‘tail length’ could help doctors tell bacterial and viral infections apart in critically ill children](https://www.rna-seqblog.com/rna-tail-length-could-help-doctors-tell-bacterial-and-viral-infections-apart-in-critically-ill-children/) - Researchers from the Doherty Institute and The University of Melbourne have made a promising discovery that could help doctors quickly tell whether a very sick child has a bacterial or viral infection. This breakthrough could lead to faster treatment and help reduce the unnecessary use of antibiotics. In a world-first study published in BMC Infectious Diseases,
- [Nanocoding - lipid nanoparticle barcoding for multiplexed single-cell RNA sequencing](https://www.rna-seqblog.com/nanocoding-lipid-nanoparticle-barcoding-for-multiplexed-single-cell-rna-sequencing/) - Researchers from the University of Illinois-Champaign have introduced a groundbreaking technique called Nanocoding that advances single-cell RNA sequencing technology. Single-cell RNA sequencing is a powerful tool used to study the activity of genes within individual cells, providing scientists with detailed insights into how cells work, how they differ from one another, and how they respond
- [SpotSweeper - spatially aware quality control for spatial transcriptomics](https://www.rna-seqblog.com/spotsweeper-spatially-aware-quality-control-for-spatial-transcriptomics/) - As scientists explore how genes are expressed in different parts of tissues, they increasingly rely on spatially resolved transcriptomics (SRT), a type of RNA sequencing that provides both gene activity and spatial location information. However, ensuring the quality of data from SRT experiments is challenging. Traditional quality control methods borrowed from single-cell sequencing often miss
- [RNA sequencing reveals how viruses hijack our genes](https://www.rna-seqblog.com/rna-sequencing-reveals-how-viruses-hijack-our-genes/) - Viruses are masters of disguise and manipulation. They cannot replicate on their own, so they invade host cells and hijack the host’s biological machinery to make more copies of themselves. In the process, they often cause damage, disrupt normal cell functions, and trigger disease. Our immune system tries to fight back, but many viruses have
- [ScInfeR - an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics](https://www.rna-seqblog.com/scinfer-an-efficient-method-for-annotating-cell-types-and-sub-types-in-single-cell-rna-seq-atac-seq-and-spatial-omics/) - Accurately identifying different types of cells within tissues is essential for understanding how organs function, how diseases progress, and how treatments might work. With the rise of single-cell and spatial omics technologies, researchers can now study individual cells in great detail. However, a major challenge remains: how do we correctly label or annotate these cells
- [DeepDeconUQ - estimate malignant cell fraction prediction intervals in bulk RNA-seq tissue](https://www.rna-seqblog.com/deepdeconuq-estimate-malignant-cell-fraction-prediction-intervals-in-bulk-rna-seq-tissue/) - Researchers at the University of Southern California have developed a powerful new tool called DeepDeconUQ that improves how scientists estimate the percentage of cancer cells in tissue samples using RNA sequencing data. This advancement is important for doctors and researchers who rely on accurate cancer cell measurements to make informed decisions about diagnosis, treatment, and
- [Research Specialist D (Department of Translational Neuroscience)](https://www.rna-seqblog.com/research-specialist-d-department-of-translational-neuroscience/) - University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that provide opportunities for undergraduate, graduate and continuing
- [Neutrophil–tumor interactions revealed by RNA sequencing in aggressive breast cancer](https://www.rna-seqblog.com/neutrophil-tumor-interactions-revealed-by-rna-sequencing-in-aggressive-breast-cancer/) - Researchers at Tel Aviv University’s Gray Faculty of Medical & Health Sciences conducted a series of experiments using advanced technologies, focusing on the tumor microenvironment in advanced stages of breast cancer. They found that immune system cells called neutrophils are recruited by the tumor environment and support tumor progression in the later stages of the
- [RNA-based diagnostic studies in genetics - review and guidance](https://www.rna-seqblog.com/rna-based-diagnostic-studies-in-genetics-review-and-guidance/) - As genetic testing becomes more common in medical care, doctors are increasingly faced with interpreting results that are not always clear. Some genetic changes, called variants of uncertain significance, do not have obvious effects, making it difficult to know whether they cause disease or not. One key way to better understand these variants is by
- [GSNCASCR - an R package to identify differentially co-expressed curated gene sets with single-cell RNA-seq data](https://www.rna-seqblog.com/gsncascr-an-r-package-to-identify-differentially-co-expressed-curated-gene-sets-with-single-cell-rna-seq-data/) - Co-expression means two or more genes are active at the same time, often indicating they may be working together. When diseases like COVID-19 strike, the normal coordination between these genes can break down. GSNCASCR, developed at the National Heart, Lung, and Blood Institute, helps scientists spot these breakdowns more accurately than older tools, using a
- [CADRES - precise detection of differential RNA editing sites across varied biological conditions](https://www.rna-seqblog.com/cadres-precise-detection-of-differential-rna-editing-sites-across-varied-biological-conditions/) - RNA editing is a crucial process that allows cells to make changes to RNA molecules after they’re created, helping fine-tune gene expression and increase protein diversity. One type of RNA editing, where cytosine (C) is changed to uracil (U), has been particularly hard to detect because of technical challenges like sequencing errors and interference from
- [Rethinking gene regulation: beyond the blueprint](https://www.rna-seqblog.com/rethinking-gene-regulation-beyond-the-blueprint/) - In biology classrooms, we often learn that genes are transcribed into mRNA, which is then translated into proteins—a tidy, linear process. But gene expression in living cells is far more intricate, governed by a complex network of molecular players. Among these, transcription factors (TFs) have long been considered the master regulators—the proteins that “read” the
- [I2SysBio scientists explore a new gene sequencing technique that helps decipher diseases like cancer](https://www.rna-seqblog.com/i2sysbio-scientists-explore-a-new-gene-sequencing-technique-that-helps-decipher-diseases-like-cancer/) - Researchers at the Institute of Integrative Systems Biology (I2SysBio) have published a review of long-read transcriptomic sequencing technology, which allows RNA molecules present in all cells and containing genetic information essential for life to be analysed more precisely than traditional methods. This technique is essential for a better understanding of ageing, neurodegenerative diseases or cancer.
- [SLAM-RT&Tag - spatiotemporal profiling of RNA within nuclear compartments in situ](https://www.rna-seqblog.com/slam-rttag-spatiotemporal-profiling-of-rna-within-nuclear-compartments-in-situ/) - The nucleus of a cell contains several specialized regions known as nuclear compartments. These compartments are not surrounded by membranes, but they are highly organized and play essential roles in gene regulation. A new study led by researchers at the Fred Hutchinson Cancer Center shines a light on how different types of RNA behave within
- [PHOTON – subcellular level spatial transcriptomics](https://www.rna-seqblog.com/photon-subcellular-level-spatial-transcriptomics/) - RNA localization—its specific position within subcellular structures like the nucleus, mitochondria, or stress granules—is closely tied to its function, whether that’s being translated into protein, modified, stored, or degraded. Traditional RNA sequencing methods tell us what RNAs are present, but not where they are. A team led by researchers at the University of Texas Southwestern Medical
- [Worm Perturb-Seq - massively parallel whole-animal RNAi and RNA-seq](https://www.rna-seqblog.com/worm-perturb-seq-massively-parallel-whole-animal-rnai-and-rna-seq-2/) - Understanding how genes work and affect an organism’s traits is a big goal in biology. One powerful way to do this is by looking at transcriptomes, which are the complete sets of RNA molecules made in cells. RNA tells us which genes are active and how they change when genes are turned on or off.
- [scMCGF - multi-view clustering for single-cell RNA-seq data based on graph fusion](https://www.rna-seqblog.com/scmcgf-multi-view-clustering-for-single-cell-rna-seq-data-based-on-graph-fusion/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized how scientists understand the complexity of tissues by examining gene activity in individual cells. However, the data generated from scRNA-seq experiments is often noisy and high-dimensional, making it hard to group similar cells accurately, a process known as clustering. Researchers at Anhui University have developed a new computational method
- [OmiCLIP - a visual–omics foundation model to bridge histopathology with spatial transcriptomics](https://www.rna-seqblog.com/omiclip-a-visual-omics-foundation-model-to-bridge-histopathology-with-spatial-transcriptomics/) - Researchers are constantly looking for better ways to understand how genes function in the context of actual tissue structure. A new AI-powered tool developed by researchers at the Houston Methodist Research Institute aims to do just that. The tool, called OmiCLIP, connects gene expression data from RNA sequencing with histology images of tissues stained using
- [VarRNA - variant calling from RNA-Seq data](https://www.rna-seqblog.com/varrna-variant-calling-from-rna-seq-data/) - Understanding how genetic changes drive cancer is one of the biggest challenges in biomedical research. Traditionally, scientists look at DNA to find these changes, but now researchers are turning to RNA for even more answers. A team led by researchers from Nationwide Children’s Hospital has developed a new tool called VarRNA that analyzes RNA sequencing
- [SC2Spa - a deep learning based approach to map transcriptome to spatial origins at cellular resolution](https://www.rna-seqblog.com/sc2spa-a-deep-learning-based-approach-to-map-transcriptome-to-spatial-origins-at-cellular-resolution/) - Understanding how cells are organized within tissues is crucial to learning how organs function and how diseases like cancer or neurological disorders develop. Every tissue is made up of many different types of cells, and their physical arrangement influences how they communicate and work together. However, one of the biggest challenges in biology has been
- [MiniQuant - improving the accuracy of isoform quantification](https://www.rna-seqblog.com/miniquant-improving-the-accuracy-of-isoform-quantification/) - RNA sequencing has revolutionized the way scientists study gene expression, helping researchers identify not just which genes are active but also which isoforms, alternative versions of RNA produced from the same gene, are being expressed. This is especially important because different isoforms can have very different roles in health and disease. However, accurately quantifying these
- [Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus CNS infection](https://www.rna-seqblog.com/temporally-resolved-single-cell-rna-sequencing-reveals-protective-and-pathological-responses-during-herpes-simplex-virus-cns-infection/) - Herpes Simplex Virus 1, or HSV-1, is a common virus that many people carry, often causing cold sores. However, in some cases, HSV-1 can infect the brain, leading to serious conditions like encephalitis, which can cause brain inflammation and long-term neurological problems. Researchers at Aarhus University have used advanced RNA sequencing technologies to better understand
- [Gene expression after asbestos exposure explains development of malignant mesothelioma](https://www.rna-seqblog.com/gene-expression-after-asbestos-exposure-explains-development-of-malignant-mesothelioma/) - Gene expression leading to alterations in the DNA caused by asbestos exposure may explain the development of Malignant Pleural Mesothelioma (MPM), a rare and aggressive cancer. By analyzing public RNA-seq data through a comprehensive bioinformatics pipeline, scientists working with the Sbarro Health Research Organization (SHRO) have developed an in-depth view of the molecular mechanisms involved in asbestos-induced
- [RNA sequencing identifies PRCAT71 as a key driver and therapeutic target in prostate cancer](https://www.rna-seqblog.com/rna-sequencing-identifies-prcat71-as-a-key-driver-and-therapeutic-target-in-prostate-cancer/) - Northwestern Medicine investigators have discovered that a novel long noncoding RNA (lncRNA), which are usually 200 nucleotides longer than typical RNAs and are widely expressed in cells, could serve as a prognostic biomarker and therapeutic target for prostate cancer, according to a recent study published in Science Advances. Qi Cao, PhD, the Anthony J. Schaeffer, MD, Professor of Urology, and Rendong
- [RNA sequencing enhances warfighter readiness through field-deployable technologies](https://www.rna-seqblog.com/rna-sequencing-enhances-warfighter-readiness-through-field-deployable-technologies/) -  CB Defense Today is an interview program where experts discuss innovations, technologies, and partnerships pertinent to the U.S. Army Combat Capabilities Development Command Chemical Biological Center (DEVCOM CBC) and the chemical and biological defense community. In this episode, public affairs specialist Jack Bunja interviews Dr. Cory Bernhards, a research biologist at DEVCOM CBC, about
- [Cracking rare disorders - a new minimally invasive RNA-seq protocol](https://www.rna-seqblog.com/cracking-rare-disorders-a-new-minimally-invasive-rna-seq-protocol/) - A research team at Ghent University has developed a new way to improve genetic diagnoses using RNA sequencing. Their method focuses on a small blood sample and a simple lab treatment that makes it easier to detect problems with how genes are spliced, especially in people with neurodevelopmental disorders like epilepsy and intellectual disability. While
- [Novogene Single-cell and Spatial Multi-omics Case Study: Hematological Oncology Research and Application](https://www.rna-seqblog.com/novogene-single-cell-and-spatial-multi-omics-case-study-hematological-oncology-research-and-application-2/) - The team of Xiaofan Zhu and Tao Cheng from the Blood Disease Hospital of the Chinese Academy of Medical Sciences (Institute of Hematology, Chinese Academy of Medical Sciences) cooperated with the team of Jin Gu from Tsinghua University and conducted research on minimal residual disease of pediatric B-cell acute lymphoblastic leukemia. On February 10th, 2022,
- [Pythia Biosciences and Miraomics to Build a High-Quality Single-Cell Database for Drug Research and AI/ML Acceleration](https://www.rna-seqblog.com/pythia-biosciences-and-miraomics-to-build-a-high-quality-single-cell-database-for-drug-research-and-ai-ml-acceleration/) - Pythia Biosciences and Miraomics have announced a strategic collaboration to develop Pythiomics—a rich, high-quality and harmonized single-cell omics database designed to accelerate discoveries and AI/ML development in drug research. Pythiomics combines expert manual curation, rigorous quality control, metadata harmonization, and cutting-edge AI techniques for cell type annotation. The result is a standardized, reliable, and accessible
- [From chaos to clarity: New tool finds connections in complex cell data](https://www.rna-seqblog.com/from-chaos-to-clarity-new-tool-finds-connections-in-complex-cell-data/) - Gladstone scientists unveiled a powerful computation tool that integrates different forms of biological data to reveal how cell types are related across tissues, experiments, and species—information that’s crucial for understanding disease. Imagine looking at thousands of scattered puzzle pieces and trying to guess what picture they create. Without any reference point, it’s nearly impossible. In
- [Single-cell RNA sequencing of bone metastases from multiple cancer types reveals three distinct immune archetypes](https://www.rna-seqblog.com/single-cell-rna-sequencing-of-bone-metastases-from-multiple-cancer-types-reveals-three-distinct-immune-archetypes/) - Researchers use use RNA sequencing to characterize bone metastases from eight cancer types Bone is a common site for metastasis of solid cancers, but histological and molecular features of bone metastases are not well understood. In a new study published in Cell Genomics, researchers at Baylor College of Medicine and the University of Texas MD Anderson
- [RNA sequencing data shows clinical benefit and safety of Plus Therapeutics’ REYOBIQ™](https://www.rna-seqblog.com/rna-sequencing-data-shows-clinical-benefit-and-safety-of-plus-therapeutics-reyobiq/) - RNA sequencing reveals early apoptosis and immune activation in LM patients treated with REYOBIQ, highlighting its therapeutic potential and long-term survival benefits in central nervous system cancers...
- [The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution](https://www.rna-seqblog.com/the-curated-cancer-cell-atlas-provides-a-comprehensive-characterization-of-tumors-at-single-cell-resolution/) - Cancer is not just a single disease, it’s an ever-changing landscape of cells with different roles, mutations, and behaviors. Understanding this complexity at the level of individual cells is critical for developing more targeted and effective treatments. In recent years, scientists have turned to single-cell RNA sequencing to get a detailed look at how individual
- [Summit Health expands precision medicine with RNA sequencing and liquid biopsy services](https://www.rna-seqblog.com/summit-health-expands-precision-medicine-with-rna-sequencing-and-liquid-biopsy-services/) - Summit Health, part of Village MD and Genomic Testing Cooperative (GTC), the global leader in RNA innovation, are excited to announce today the launch of a newly established next generation sequencing service at the Summit Health laboratory in Woodland Park, NJ to offer comprehensive DNA and RNA profiling of solid tumors and hematologic neoplasms. The internalized
- [RNA sequencing reveals early mitochondrial dysfunction shared across ALS mutations](https://www.rna-seqblog.com/rna-sequencing-reveals-early-mitochondrial-dysfunction-shared-across-als-mutations/) - Using the gene scissors CRISPR and stem cells, researchers at Stockholm University and the UK Dementia Research Institute (UK DRI) at King’s College London have managed to identify a common denominator for different gene mutations that all cause the neurological disease ALS. Early signs in the mitochondria The research, recently published in the scientific journal
- [New method helps identify hormone-disrupting chemicals – without animal testing](https://www.rna-seqblog.com/new-method-helps-identify-hormone-disrupting-chemicals-without-animal-testing/) - A new study from the Institute of Environmental Medicine at Karolinska Institutet presents a promising method for identifying endocrine-disrupting chemicals – without the need for traditional animal testing. By combining RNA-sequencing of zebrafish embryos with a structured toxicological framework, researchers can now better predict harmful effects on human health. Chemicals that interfere with the hormone
- [Lexogen Launches miRVEL Discovery - Cutting-edge Small RNA-Seq Library Prep Kit for sRNA Discovery and Biomarker studies](https://www.rna-seqblog.com/lexogen-launches-mirvel-discovery-cutting-edge-small-rna-seq-library-prep-kit-for-srna-discovery-and-biomarker-studies/) - Lexogen, a leader in RNA sequencing technologies, is excited to announce the launch of the miRVEL Discovery Small RNA-Seq Library Prep Kit, an advanced solution for sRNA discoveries, with an optimized protocol for low-input biofluid samples such as blood and plasma. Unlocking Biofluid sRNA Transcriptomics Circulating small RNAs in biofluids can serve as diagnostic and prognostic
- [Biostate AI closes $12M to bring the Netflix model to molecular diagnostics](https://www.rna-seqblog.com/biostate-ai-closes-12m-to-bring-the-netflix-model-to-molecular-diagnostics/) - The company is reimagining the fragmented reality of molecular research by building the world’s largest RNA sequencing dataset. This dataset will train a general-purpose AI to understand—and eventually guide therapies for—all human diseases. Biostate AI, a leading innovator in artificial intelligence and RNA sequencing, announced the successful completion of a $12M Series A funding round,
- [Immunopipe - a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline](https://www.rna-seqblog.com/immunopipe-a-comprehensive-and-flexible-scrna-seq-and-sctcr-seq-data-analysis-pipeline/) - Understanding the human immune system at a cellular level has become increasingly important in fields like cancer research, infectious disease, and autoimmune disorders. Thanks to advancements in single-cell technologies, scientists can now analyze individual immune cells to see which genes are turned on and what receptors are present on their surfaces. Two powerful methods for
- [DUG unlocks faster RNA sequencing with VAST Data platform & Solidigm™ storage](https://www.rna-seqblog.com/dug-unlocks-faster-rna-sequencing-with-vast-data-platform-solidigm-storage/) - From seismic exploration to RNA sequencing, DUG harnesses VAST Data Platform & Solidigm QLC SSDs to redefine HPCaaS As a leader in high performance computing (HPC) solutions, DUG Technology Ltd (DUG) is driving innovation, with applications ranging from seismic analysis for the resources sector to decoding genomes for healthcare. With its high-powered HPC-as-a-service (HPCaaS) offerings,
- [Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage](https://www.rna-seqblog.com/integration-of-mass-cytometry-and-single-cell-rna-sequencing-of-cells-in-bronchoalveolar-lavage/) - Scientists often rely on cutting-edge tools to understand how cells behave, especially when studying complex environments like the human lungs. Researchers at the University of British Columbia describe how combining two technologies, single-cell RNA sequencing (sc-RNA-seq) and cytometry by time-of-flight (CyTOF), can offer a more complete understanding of immune cells found in lung fluid, known
- [Introducing Whole Transcriptome Subcellular Spatial Imaging: Reimagine Spatial Biology](https://www.rna-seqblog.com/introducing-whole-transcriptome-subcellular-spatial-imaging-reimagine-spatial-biology/) - Understanding the interactions between cells within their natural tissue environment is crucial for uncovering both normal physiological processes and disease mechanisms. Historically, capturing the full gene expression profile of a cell while preserving the spatial location of transcripts within tissues was a significant challenge. Traditional single-cell RNA sequencing (scRNA-seq) techniques, while powerful, lose spatial context,
- [scRDEN - single-cell dynamic gene rank differential expression network and robust trajectory inference](https://www.rna-seqblog.com/scrden-single-cell-dynamic-gene-rank-differential-expression-network-and-robust-trajectory-inference/) - Understanding how a single cell matures and takes on a specific role in the body is a major goal in biology and medicine. Thanks to the rise of single-cell RNA sequencing (scRNA-seq), scientists can now examine gene activity in individual cells to see how they change during development. But analyzing this data is tricky, cells
- [Scientists use RNA-seq to track down mutation that makes orange cats orange](https://www.rna-seqblog.com/scientists-use-rna-seq-to-track-down-mutation-that-makes-orange-cats-orange/) - It took researchers a century to find the genetic glitch that causes orange coloration in cats. Many an orange cat-affiliated human will vouch for their cat’s, let’s say, specialness. But now scientists have confirmed that there is, in fact, something unique about ginger-hued domestic felines. In a new study, Stanford Medicine researchers have discovered the
- [Uncovering sepsis biomarkers with Nanopore RNA sequencing](https://www.rna-seqblog.com/uncovering-sepsis-biomarkers-with-nanopore-rna-sequencing/) - Researchers are taking RNA sequencing to the next level to better understand sepsis, a serious condition caused by the body’s extreme response to infection. A team led by researchers a from the University of Melbourne used the Oxford Nanopore Technologies platform to directly sequence RNA from the blood of 12 patients with bacterial and viral
- [Predicting gene expression from DNA sequence using deep learning models](https://www.rna-seqblog.com/predicting-gene-expression-from-dna-sequence-using-deep-learning-models/) - Predicting how genes are turned on or off—also known as gene expression—has been one of the toughest challenges in genetics. That’s because gene expression is controlled by many DNA elements (like promoters and enhancers) and a host of transcription factors, all interacting in complex ways. But thanks to cutting-edge deep learning technologies, scientists are finally
- [How different diets impact your cells: Insights from a multitissue RNA sequencing study](https://www.rna-seqblog.com/how-different-diets-impact-your-cells-insights-from-a-multitissue-rna-sequencing-study/) - Metabolic syndrome (MetS)—a cluster of conditions like obesity, high blood sugar, and high cholesterol—affects millions worldwide and is strongly influenced by diet. But how exactly do different diets affect our organs and cells? A new study led by researchers from UCLA dives deep into this question using a powerful technique called single-cell RNA sequencing. In
- [Research Associate II](https://www.rna-seqblog.com/research-associate-ii/) - Job Description We are seeking a motivated and detail-oriented Research Associate II with strong computational skills and a keen interest in medicine and translational research for breast cancer. The successful candidate will work on cutting-edge projects involving RNA sequencing (bulk and single-cell), spatial transcriptomics, and other omics data types. This position is ideal for individuals
- [Oncogene aberrations drive medulloblastoma progression, not initiation](https://www.rna-seqblog.com/oncogene-aberrations-drive-medulloblastoma-progression-not-initiation/) - Medulloblastoma, a cancer that primarily affects children, is the most common malignant brain tumor in this age group. Particularly for the group 3/4 subtypes of medulloblastoma, treatment remains a major challenge. These tumors are notorious for their complexity and the difficulty in predicting how they will behave, making it difficult to provide tailored treatments for
- [Textbooks need to be rewritten: RNA, not DNA, is the main cause of acute sunburn](https://www.rna-seqblog.com/textbooks-need-to-be-rewritten-rna-not-dna-is-the-main-cause-of-acute-sunburn/) - Sunburn has traditionally been attributed to UV-induced DNA damage. However, a new study by the University of Copenhagen and Nanyang Technological University, Singapore, reveals that RNA, another vital cellular molecule, plays a major role in triggering acute sunburn reactions. We have all been told to avoid direct sunlight between 12 noon and 3 p.m., seek
- [RNA sequencing reveals glioblastoma heterogeneity and treatment resistance mechanisms](https://www.rna-seqblog.com/rna-sequencing-reveals-glioblastoma-heterogeneity-and-treatment-resistance-mechanisms/) - Glioblastoma is one of the most enigmatic and difficult-to-treat tumor types. Patients with the most common form of this brain cancer, IDH-wildtype glioblastoma, have a median survival of only 14.6 months, a number that has barely budged for decades. Two new studies seek to understand the disease more fully at the molecular level, with the ultimate
- [Bacteria: recording gene activity more efficiently](https://www.rna-seqblog.com/bacteria-recording-gene-activity-more-efficiently/) - Analysing the gene activity of every single bacterial cell in a colony? A new technique of single-cell transcriptomics developed in Würzburg can do this much more efficiently than other methods: It reliably detects 300 to 600 genes per bacterial cell with a high success rate of 95%, thereby surpassing the efficiency of established procedures. Not
- [TRANSECT - TRanscriptome ANalysis of StratifiEd CohorTs](https://www.rna-seqblog.com/transect-transcriptome-analysis-of-stratified-cohorts/) - Currently, there exists an unprecedented amount of publicly available RNA-seq data from cohorts of related and unrelated individuals available through repositories such as the Genotype-Tissue Expression database (GTEx) and the Cancer Genome Atlas (TCGA), amongst others. Concomitantly, there exists an ever-growing number of effective analysis and visualization tools for the interrogation of gene expression data
- [Improving the personalization of immunotherapy treatments](https://www.rna-seqblog.com/improving-the-personalization-of-immunotherapy-treatments/) - Researchers from the Ruth and Bruce Rappaport Faculty of Medicine have identified a genetic “fingerprint” that helps predict the effectiveness of these treatments Considered to be one of the greatest revolutions in cancer treatment, immunotherapy enhances the immune system’s ability to target and destroy cancer cells efficiently. One of the key challenges in immunotherapy is
- [9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025)](https://www.rna-seqblog.com/9th-berlin-summer-school-in-ngs-data-analysis-2025-june-30-july-4-2025/) - Gain hands-on experience in RNA sequencing data analysis and bioinformatics during the 9th Berlin Summer School in NGS Data Analysis 2025, designed especially for beginners in the field...
- [CORESH - a gene signature-based search engine for public gene expression datasets](https://www.rna-seqblog.com/coresh-a-gene-signature-based-search-engine-for-public-gene-expression-datasets/) - Public databases like the Gene Expression Omnibus (GEO) hold enormous amounts of gene expression data from past experiments—hundreds of thousands, in fact. But until recently, finding relevant data in these repositories was like searching for a needle in a haystack. That’s because most searches rely on keywords, and those keywords may not match the exact
- [How RNA sequencing uncovers unexpected sugar modifications in tRNAs](https://www.rna-seqblog.com/how-rna-sequencing-uncovers-unexpected-sugar-modifications-in-trnas/) - For years, scientists believed that RNA molecules only carried genetic information and helped in protein synthesis. But recent discoveries are changing that view—especially with the surprising finding that RNA can be modified by sugars, creating something called glycoRNA. These sugar-modified RNAs may have previously unknown biological functions, and researchers are now working to understand how
- [snCED-seq - high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues](https://www.rna-seqblog.com/snced-seq-high-fidelity-cryogenic-enzymatic-dissociation-of-nuclei-for-single-nucleus-rna-seq-of-ffpe-tissues/) - Formalin-fixed, paraffin-embedded (FFPE) tissue samples are widely used in clinical and research settings to preserve biological specimens. However, one big challenge scientists face when working with FFPE tissues is extracting usable genetic material—specifically intact nuclei—for detailed gene expression analysis. The problem lies in the harsh preservation process, which often damages the RNA inside cells, making
- [The Festival of Genomics & Biodata - June 24-25, 2025](https://www.rna-seqblog.com/the-festival-of-genomics-biodata-june-24-25-2025/) - Registration for The Festival of Genomics & Biodata in Boston is now open! Join us on Tuesday June 24th – Wednesday June 25th in Boston for inspirational speakers, the latest research and clinical breakthroughs, cutting-edge technology and incredible networking opportunities. Free for 90% of attendees, the Festival is designed to help you return to work
- [Cellecta launches blood microsampling assay that profiles 19,000 human protein-coding genes from one drop of dried blood](https://www.rna-seqblog.com/cellecta-launches-blood-microsampling-assay-that-profiles-19000-human-protein-coding-genes-from-one-drop-of-dried-blood/) - The combination of convenient at-home, finger-prick blood collection and the ultra-sensitive DriverMapTM EXP Human Genome-Wide Profiling Kit greatly simplifies the discovery of clinically relevant transcriptome biomarkers. Cellecta, Inc. today announced the launch of the DriverMap™ EXP Human Genome-Wide 19K Dried Blood Microsample Profiling kit, a targeted RNA expression profiling assay which provides a molecular snapshot of all
- [Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes](https://www.rna-seqblog.com/replicability-of-bulk-rna-seq-differential-expression-and-enrichment-analysis-results-for-small-cohort-sizes/) - Researchers at the University of Bern explored a common issue in RNA sequencing (RNA-Seq) research—how well results hold up when studies have only a few samples. RNA-Seq is a powerful tool for studying gene expression, but because it can be expensive and logistically difficult to collect many biological samples, many experiments are performed with small
- [TransCNN: A novel architecture combining transformer and TextCNN for detecting N4-acetylcytidine sites in human mRNA](https://www.rna-seqblog.com/transcnn-a-novel-architecture-combining-transformer-and-textcnn-for-detecting-n4-acetylcytidine-sites-in-human-mrna/) - RNA modifications are like fine-tuning knobs for how our genes are expressed. One such modification, N4-acetylcytidine (ac4C), plays a crucial role in keeping RNA stable and functional—and it’s been linked to several human diseases. But finding where these ac4C modifications occur in RNA molecules isn’t easy. Researchers are turning to artificial intelligence to solve this
- [TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation](https://www.rna-seqblog.com/tire-seq-simplifies-transcriptomics-via-integrated-rna-capture-and-library-preparation/) - RNA sequencing (RNA-seq) has become a go-to method for exploring how genes are expressed across different biological conditions. It plays a vital role in cancer research, immunology, neuroscience, and developmental biology. However, traditional RNA-seq workflows typically require a time-consuming and delicate step—extracting RNA from cells or tissues before library preparation. This step can introduce sample
- [Study uncovers how prenatal stress leaves a molecular imprint on babies](https://www.rna-seqblog.com/study-uncovers-how-prenatal-stress-leaves-a-molecular-imprint-on-babies/) - A new study has uncovered how stress experienced by mothers during pregnancy leaves a molecular imprint on their babies—starting before birth. The research shows that prenatal stress alters the expression of tiny RNA molecules in newborn blood, particularly in girls, and affects key enzymes in the brain’s stress-regulation system. These changes may help explain why
- [DeepSAP - improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring](https://www.rna-seqblog.com/deepsap-improved-rna-seq-alignment-by-integrating-transcriptome-guidance-with-transformer-based-splice-junction-scoring/) - RNA sequencing (RNA-seq) has opened up new frontiers in our understanding of gene expression and the complexities of how genes are regulated. One of the most significant breakthroughs in this field is the ability to examine how RNA is processed and spliced in various ways, providing insights into diseases, gene function, and even new therapeutic
- [Single-cell transcriptomics reveal how root tissues adapt to soil stress](https://www.rna-seqblog.com/single-cell-transcriptomics-reveal-how-root-tissues-adapt-to-soil-stress/) - Roots are the unsung heroes of plant survival. Buried underground, they must navigate a complex and often hostile environment—coping with challenges like low nutrients, soil compaction, and microbial threats. Despite these stressors, roots continue to grow, absorb water, and support the entire plant. But how do they do it? And what’s happening at the level
- [Insights into the spatial organization and tumor microenvironment of primary testicular diffuse large B-cell lymphomas](https://www.rna-seqblog.com/insights-into-the-spatial-organization-and-tumor-microenvironment-of-primary-testicular-diffuse-large-b-cell-lymphomas/) - New study reveals E2F and CREB as a novel therapeutic option for testicular DLBCL patients Primary testicular diffuse large B-cell lymphomas (PT-DLBCL), the most prevalent subtype of testicular lymphoma, occurs in an immune-privileged site within the testis. Although advances in genomic technologies have resulted in remarkable progress in understanding the pathogenesis of DLBCLs, the characterization
- [Jointly funded research explores cutting-edge RNA sequencing in rare ovarian cancer](https://www.rna-seqblog.com/jointly-funded-research-explores-cutting-edge-rna-sequencing-in-rare-ovarian-cancer/) - Two patient-driven ovarian cancer nonprofits – STAAR Low-Grade Serous Ovarian Cancer Foundation and Not These Ovaries – have awarded a $115,580 research grant to Dr. Kwong-Kwok Wong at The University of Texas MD Anderson Cancer Center to investigate new biomarkers that could improve treatment options for patients with low-grade serous ovarian cancer (LGSOC). The research study will utilize long-read
- [New discovery about circular RNA and wound healing](https://www.rna-seqblog.com/new-discovery-about-circular-rna-and-wound-healing/) - Researchers at Karolinska Institutet have identified a new mechanism where circular RNA plays a crucial role in wound healing, which could lead to new therapies to improve wound healing and reduce scarring. The study was published in Advanced Science. A new study shows how circular RNA (circRNA) affects wound healing in human skin. Researchers have
- [HPC-T-Assembly - a pipeline for de novo transcriptome assembly of large multi-specie datasets](https://www.rna-seqblog.com/hpc-t-assembly-a-pipeline-for-de-novo-transcriptome-assembly-of-large-multi-specie-datasets/) - In the past decade, RNA sequencing (RNA-seq) has revolutionized how researchers study gene expression, helping us understand how genes are turned on or off in different tissues, conditions, or species. But for many plants, animals, and microorganisms that haven’t been extensively studied—called non-model organisms—RNA-seq analysis presents a unique challenge. That challenge stems from the fact
- [Scipher Medicine and InnoSIGN announce partnership to advance precision medicine in immunology](https://www.rna-seqblog.com/scipher-medicine-and-innosign-announce-partnership-to-advance-precision-medicine-in-immunology/) - RNA sequencing data from Scipher Medicine and InnoSIGN’s pathway analysis platform team up to uncover disease-driving mechanisms and identify biomarkers in immune-mediated and metabolic conditions...
- [Single-cell RNA sequencing provides comprehensive map of acute myeloid leukemia cell states](https://www.rna-seqblog.com/single-cell-rna-sequencing-provides-comprehensive-map-of-acute-myeloid-leukemia-cell-states/) - A new gene expression atlas developed using single-cell RNA sequencing data shows how normal hematopoietic cells differentiate and was used to catalog the multiple ways that aberrant differentiation can lead to acute myeloid leukemia (AML), according to results presented at the American Association for Cancer Research (AACR) Annual Meeting 2025, held April 25-30. This study and an accompanying
- [Single-nucleus RNA sequencing reveals a preclinical model for the most common subtype of glioblastoma](https://www.rna-seqblog.com/single-nucleus-rna-sequencing-reveals-a-preclinical-model-for-the-most-common-subtype-of-glioblastoma/) - Glioblastoma (GBM) is one of the most aggressive and difficult-to-treat brain cancers. Scientists have learned that not all GBMs are the same—they can vary significantly based on their tumor microenvironment (TME), which includes the surrounding cells, molecules, and blood vessels that support tumor growth. Understanding these differences is essential for developing treatments that target specific
- [PlugNSeq - an easy, rapid, and streamlined mRNA-seq data analysis pipeline empowering insightful exploration with well-annotated organisms](https://www.rna-seqblog.com/plugnseq-an-easy-rapid-and-streamlined-mrna-seq-data-analysis-pipeline-empowering-insightful-exploration-with-well-annotated-organisms/) - Understanding gene activity using RNA sequencing (RNA-seq) has become a key part of modern biological research, but it usually requires specialized computational skills. To help bridge the gap between biology and computer science, Researchers at the Heinrich-Heine Universität Düsseldorf have developed a user-friendly pipeline called PlugNSeq. PlugNSeq is designed for researchers who may not have
- [Element Biosciences Accelerates Rollout of Direct in Sample Sequencing for the AVITI24™ Intelligent Multiomics System](https://www.rna-seqblog.com/element-biosciences-accelerates-rollout-of-direct-in-sample-sequencing-for-the-aviti24-intelligent-multiomics-system-to-meet-growing-demand/) - Company to present four abstracts at the American Association for Cancer Research 2025 annual meeting highlighting research from AVITI24, the Trinity™ workflow solution, and new direct in sample sequencing applications Element Biosciences, a company democratizing access to advanced life science solutions, today announced the accelerated rollout and availability of direct in sample sequencing on AVITI24,
- [Mapping the human virome with RNA sequencing to advance health research](https://www.rna-seqblog.com/mapping-the-human-virome-with-rna-sequencing-to-advance-health-research/) - A major new effort at Weill Cornell Medicine seeks to catalog the normal human virome, the immense ecosystem of viruses that lives in and on us. The work, part of a multi-institution collaboration called Viromes Across Space and Time (VAST), supported by the National Institute on Aging, part of the National Institutes of Health, will
- [Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq](https://www.rna-seqblog.com/single-nucleus-total-rna-sequencing-of-formalin-fixed-paraffin-embedded-samples-using-snrandom-seq/) - Formalin-fixed paraffin-embedded (FFPE) tissue samples are a cornerstone of clinical research and pathology. These preserved samples hold a treasure trove of information, often linked to detailed patient histories, disease progressions, and treatment outcomes. However, unlocking their molecular information, especially at the single-cell or single-nucleus level, has been extremely difficult because the preservation process can damage
- [PhD project: ‘Uncovering Genetic Drivers of Gene Expression in Elite Wheat Varieties’](https://www.rna-seqblog.com/phd-project-uncovering-genetic-drivers-of-gene-expression-in-elite-wheat-varieties/) - Are you a motivated undergraduate with a passion for genetics, genomics and plant science? Would you like to be at the cutting edge of agricultural research, working to secure the future of wheat breeding in the face of climate change and food insecurity? We’re offering an exciting PhD opportunity open to international students, with Prof
- [Novogene Single-cell and Spatial Multi-omics Case Study: Hematological Oncology Research and Application](https://www.rna-seqblog.com/novogene-single-cell-and-spatial-multi-omics-case-study-hematological-oncology-research-and-application/) - The team of Xiaofan Zhu and Tao Cheng from the Blood Disease Hospital of the Chinese Academy of Medical Sciences (Institute of Hematology, Chinese Academy of Medical Sciences) cooperated with the team of Jin Gu from Tsinghua University and conducted research on minimal residual disease of pediatric B-cell acute lymphoblastic leukemia. On February 10th, 2022,
- [The Festival of Genomics & Biodata](https://www.rna-seqblog.com/the-festival-of-genomics-biodata/) - The Festival of Genomics and Biodata is returning to Boston! Join us on Tuesday June 24th - Wednesday 25th June 2025 at the Boston Convention & Exhibition Center for inspirational speakers, the latest research and clinical breakthroughs, cutting-edge technology and incredible networking opportunities. Free for 90% of attendees, the Festival is designed to help you
- [Estimating complex immune cell structures by AI tools for survival prediction in advanced melanoma](https://www.rna-seqblog.com/estimating-complex-immune-cell-structures-by-ai-tools-for-survival-prediction-in-advanced-melanoma/) - Unique immune cell structures in tumors can boost immunotherapy effects and enhance survival, but testing is labor-intensive and not yet common. New AI-driven methods aim to hasten the standardization and adoption of testing for future melanoma patients. Researchers from the ECOG-ACRIN Cancer Research Group (ECOG-ACRIN) have applied AI-driven processes for detecting tertiary lymphoid structures (TLS) in
- [Immunai and the Parker Institute collaborate to build one of the largest single-cell datasets in cancer](https://www.rna-seqblog.com/immunai-and-the-parker-institute-collaborate-to-build-one-of-the-largest-single-cell-datasets-in-cancer/) - The collaboration integrates PICI’s RADIOHEAD real-world immunotherapy cohort into AMICA to optimize drug discovery and reduce clinical trial risk Immunai, a leading AI biotech company specializing in mapping the human immune system, and the Parker Institute for Cancer Immunotherapy (PICI), a collaborative consortium of the world’s leading immuno-oncology experts, announced today that they will build the
- [Singapore scientists unveil one of world’s largest long-read RNA sequencing datasets to advance disease research](https://www.rna-seqblog.com/singapore-scientists-unveil-one-of-worlds-largest-long-read-rna-sequencing-datasets-to-advance-disease-research/) - SG-NEx provides an open-access resource for the global research community, accelerating biomarker discovery and precision medicine through: Unprecedented Scale and Benchmarking: One of the world’s largest datasets comparing long-read sequencing techniques with conventional short-read methods. Enhanced RNA Insights: Demonstrates long-read sequencing’s ability to reveal complex RNA features like cancer-related fusion transcripts that short-read methods often miss. Global
- [Biostate AI and Weill Cornell Medicine collaborate to develop AI models for personalized leukemia care](https://www.rna-seqblog.com/biostate-ai-and-weill-cornell-medicine-collaborate-to-develop-ai-models-for-personalized-leukemia-care/) - Biostate AI, a leading innovator in artificial intelligence for RNA sequencing, and Weill Cornell Medicine have entered into a strategic collaboration to develop AI for personalized assessments of patient disease prognosis and evolution. Initially, the collaboration will focus on leukemia, leveraging the Weill Cornell Leukemia Program’s vast biorepository of bone marrow and blood samples. Under
- [WarpDemuX - demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing](https://www.rna-seqblog.com/warpdemux-demultiplexing-and-barcode-specific-adaptive-sampling-for-nanopore-direct-rna-sequencing/) - A team led by researchers at the Robert Koch Institute has developed a powerful new tool to make RNA sequencing using nanopore technology faster, more accurate, and more affordable. The tool, called WarpDemuX, solves a common problem in direct RNA sequencing (dRNA-seq): how to efficiently sort different RNA samples that have been combined in a
- [IgSeqR - identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data](https://www.rna-seqblog.com/igseqr-identification-assembly-and-characterization-of-tumor-immunoglobulin-transcripts-from-rna-sequencing-data/) - Researchers at the University of Southampton have developed a cutting-edge tool that can rapidly identify and characterize tumor-related immunoglobulin genes directly from RNA sequencing (RNA-seq) data. This groundbreaking technique has the potential to significantly enhance our understanding of B cell-related cancers like chronic lymphocytic leukemia (CLL) and lymphomas, ultimately improving diagnosis, prognosis, and treatment options.
- [RNA sequencing and somatic variant detection breakthrough unveiled by Dovetail Genomics](https://www.rna-seqblog.com/rna-sequencing-and-somatic-variant-detection-breakthrough-unveiled-by-dovetail-genomics/) - Dovetail Genomics, a leading innovator in genomic solutions, today announced an expanded comprehensive analysis solution for somatic variation detection, addressing the challenge of identifying structural variants (SVs) using NGS platforms. The solution offers ultra-sensitive discovery of SVs at base-pair resolution down to 1% variant allele frequency (VAF), and biologically meaningful interpretation of SVs through AI-driven
- [Uncovering the blueprint of gene editing: a new way to sequence CRISPR sgRNAs](https://www.rna-seqblog.com/uncovering-the-blueprint-of-gene-editing-a-new-way-to-sequence-crispr-sgrnas/) - CRISPR/Cas9 has revolutionized gene editing, making it easier than ever to modify DNA with precision. At the heart of this tool is a small but powerful molecule called single guide RNA (sgRNA), which guides the Cas9 enzyme to the exact spot in the genome that needs editing. Ensuring that sgRNA is accurately made and fully
- [miRglmm - a generalized linear mixed model of isomiR-level counts](https://www.rna-seqblog.com/mirglmm-a-generalized-linear-mixed-model-of-isomir-level-counts/) - MicroRNAs (miRNAs) are small but powerful molecules that play a crucial role in regulating gene activity. These tiny strands of RNA are known to control how genes are turned on or off, and they’re involved in many important processes, from development to disease. Researchers often use RNA sequencing to understand how miRNAs behave in different
- [MammOnc-DB - an integrative breast cancer data analysis platform for target discovery](https://www.rna-seqblog.com/mammonc-db-an-integrative-breast-cancer-data-analysis-platform-for-target-discovery/) - Breast cancer is not just one disease—it’s a collection of different types with varying molecular features and treatment responses. While many early-stage cases can be treated effectively, some forms, like triple-negative and metastatic breast cancer, remain particularly stubborn and difficult to manage. Developed by researchers at the University of Alabama at Birmingham (UAB), this powerful
- [Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes](https://www.rna-seqblog.com/detection-of-viral-sequences-at-single-cell-resolution-identifies-novel-viruses-associated-with-host-gene-expression-changes/) - With the explosion of RNA sequencing in research and medicine, scientists are getting an increasingly detailed look at how genes behave in different cells. Now, researchers at Cal Tech have developed a powerful tool that goes even further by detecting viral sequences hidden within gene expression data, all the way down to the single-cell level.
- [TRADE - ranscriptome-wide analysis of differential expression](https://www.rna-seqblog.com/trade-ranscriptome-wide-analysis-of-differential-expression/) - CRISPR technology has made it possible to systematically explore the effects of turning genes on or off, and when paired with RNA sequencing, it allows researchers to see how those genetic changes affect the entire transcriptome—essentially, a full snapshot of gene activity in a cell. One popular approach, called Perturb-seq, enables scientists to perform thousands
- [RNA sequencing reveals cancer-associated gene activity in cervical tissue after schistosomiasis infection and treatment](https://www.rna-seqblog.com/rna-sequencing-reveals-cancer-associated-gene-activity-in-cervical-tissue-after-schistosomiasis-infection-and-treatment/) - New research at the University Hospital Zurich has revealed that Schistosoma haematobium (S. haematobium), a parasitic infection affecting millions globally, can trigger cancer-related gene activity in the cervical lining, with changes becoming even more pronounced after treatment. Presented today at ESCMID Global 2025, this pivotal study sheds new light on how this often-overlooked parasitic disease
- [RNA sequencing reveals how CD40L boosts TIL therapy by activating B cells](https://www.rna-seqblog.com/rna-sequencing-reveals-how-cd40l-boosts-til-therapy-by-activating-b-cells/) - Researchers at Moffitt Cancer Center have found that tapping into the body’s own immune system and activating a type of immune cell known as B cells, could be the key to boosting the effectiveness of tumor-infiltrating lymphocyte, or TIL therapy. Results of their study were published in the Journal for Immunotherapy of Cancer. TIL therapy starts with doctor’s removing
- [RARE-seq - an ultrasensitive method for detection of cell-free RNA](https://www.rna-seqblog.com/rare-seq-an-ultrasensitive-method-for-detection-of-cell-free-rna/) - Researchers from Stanford University have developed a powerful new method called RARE-seq to detect extremely small amounts of cell-free RNA (cfRNA) in the blood. cfRNA are tiny fragments of RNA released by cells into the bloodstream, including cancer cells, and can provide valuable clues about a person’s health without the need for invasive procedures. Traditional
- [New RNA-Seq collaboration to uncover how the hidden language of genes shapes our immune system](https://www.rna-seqblog.com/new-rna-seq-collaboration-to-uncover-how-the-hidden-language-of-genes-shapes-our-immune-system/) - Scientists at the Wellcome Sanger Institute, in collaboration with Pacific Biosciences (PacBio), will use advanced long-read sequencing technology to profile gene expression at single-cell resolution. By applying this technology to nearly 1,500 blood and gut tissue samples from three major ongoing studies, researchers will be able to capture not only the extent to which genes
- [Circular RNA discovery with emerging sequencing and deep learning technologies](https://www.rna-seqblog.com/circular-rna-discovery-with-emerging-sequencing-and-deep-learning-technologies/) - Circular RNAs (circRNAs) are a unique type of RNA molecule that form a closed loop, unlike the more familiar linear RNAs. These loops may look simple, but they play surprisingly important roles in regulating genes and contributing to diseases like cancer and neurological disorders. Despite their potential, circRNAs are hard to detect because they’re often
- [RNA sequencing reveals ADAR1 as a key driver of lenalidomide resistance in multiple myeloma](https://www.rna-seqblog.com/rna-sequencing-reveals-adar1-as-a-key-driver-of-lenalidomide-resistance-in-multiple-myeloma/) - Investigators have identified a key component inhibiting responses to lenalidomide in patients with multiple myeloma, according to the results of a study recently published in Blood. They identified adenosine deaminase acting on RNA1 (ADAR1) as a novel driver of acquired resistance to lenalidomide in multiple myeloma cells but believe its effects could potentially be overcome. “As new
- [Cyber-biosecurity risks threaten RNA sequencing and genomic data integrity](https://www.rna-seqblog.com/cyber-biosecurity-risks-threaten-rna-sequencing-and-genomic-data-integrity/) - First comprehensive review of cyber-biosecurity risks released Publicly accessible DNA/RNA research is a prime target for hackers Risks threaten individual privacy, scientific integrity, and national security Government and other agencies need to prioritise investment in cyber-biosecurity research Next-generation DNA/RNA sequencing (NGS) – the same technology which is powering the development of tailor-made medicines, cancer diagnostics, infectious
- [A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues](https://www.rna-seqblog.com/a-simplified-preparation-method-for-single-nucleus-rna-sequencing-using-long-term-frozen-brain-tumor-tissues/) - Researchers at the German Cancer Research Center (DKFZ) have developed a new, streamlined method to isolate nuclei from long-term frozen pediatric glioma tissues—an innovation that could be a game-changer for studying rare brain tumors. Studying tumors at the single-cell level has been a major breakthrough in understanding how cancer develops and evolves. By analyzing the genetic
- [Genome Research publishes a special issue on long-read DNA and RNA sequencing applications in biology and medicine](https://www.rna-seqblog.com/genome-research-publishes-a-special-issue-on-long-read-dna-and-rna-sequencing-applications-in-biology-and-medicine-2/) - Genome Research publishes a second special issue highlighting advances in long-read sequencing applications in biology and medicine. In this second Special Issue, guest-edited by Dr. Ana Conesa, Dr. Alexander Hoischen, and Dr. Fritz Sedlazeck, Genome Research publishes a diverse collection of research, methods, and review articles highlighting novel applications and developments in long-read sequencing (LRS). Papers in this issue focus
- [Deep dive into plant signalling data reveals a noisy “elephant in the room”](https://www.rna-seqblog.com/deep-dive-into-plant-signalling-data-reveals-a-noisy-elephant-in-the-room/) - A far-reaching study has cast doubt on statistical methods used to identify long distance signalling networks in plants. The surprising findings by a John Innes Centre-led collaboration mean we may need to reevaluate a vital area of the life sciences. The movement of messenger RNAs (mobile mRNAs) between cells and tissues has been reported to
- [adverSCarial - assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks](https://www.rna-seqblog.com/adverscarial-assessing-the-vulnerability-of-single-cell-rna-sequencing-classifiers-to-adversarial-attacks/) - Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for analyzing gene expression at the individual cell level. With the help of machine learning (ML) algorithms, scientists can now detect and categorize different cell types based on their gene expression profiles. However, as machine learning models become more integrated into biomedical research, it is essential
- [Viome redefines health tracking with RNA sequencing in its Full Body Intelligence test](https://www.rna-seqblog.com/viome-redefines-health-tracking-with-rna-sequencing-in-its-full-body-intelligence-test/) - Viome’s Full Body Intelligence Test™ is the only science backed at-home test that decodes your body’s biological signals to give you precision health insights. It reveals not just what’s happening but why, and turns those insights into personalized daily nutrition advice to help you live healthier and longer. Built on unique RNA science and cutting-edge AI, Viome’s at-home
- [Identification of high-resolution gene expression atlas of woody tissue](https://www.rna-seqblog.com/identification-of-high-resolution-gene-expression-atlas-of-woody-tissue/) - Single cell techniques have revolutionized molecular life sciences. Ari Pekka Mähönen’s research group at the University of Helsinki used single cell RNA sequencing to generate high resolution gene expression map of Arabidopsis thaliana woody tissue. Left: Visualization of single-cell RNA sequencing data from the mature root of Arabidopsis using Uniform Manifold Approximation and Projection (UMAP).
- [RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling](https://www.rna-seqblog.com/riboss-detects-novel-translational-events-by-combining-long-and-short-read-transcriptome-and-translatome-profiling/) - In the world of molecular biology, a lot happens between DNA and proteins. A key part of that process is translation—when ribosomes read RNA messages and build proteins. But what if there are hidden messages in those RNA sequences that we’re missing? A new study led by researchers at the University of Otago introduces an
- [Biostate AI advances personalized medicine in multiple sclerosis with RNA sequencing and AI partnership](https://www.rna-seqblog.com/biostate-ai-advances-personalized-medicine-in-multiple-sclerosis-with-rna-sequencing-and-ai-partnership/) - Biostate AI, a leading innovator in artificial intelligence for RNA sequencing, today announced a strategic partnership with the Accelerated Cure Project (ACP), a nonprofit organization dedicated to accelerating research and improving outcomes for people with multiple sclerosis (MS). The partnership aims to develop next-generation AI models capable of predicting disease progression and treatment response in
- [Report release webinar - Charting a Future for Sequencing RNA and Its Modifications:](https://www.rna-seqblog.com/report-release-webinar-charting-a-future-for-sequencing-rna-and-its-modifications/) -  RNA modifications are pivotal players in diverse biological processes and have implications in various human diseases and disorders. However, our understanding of these crucial molecular features remains incomplete, hindered by current technological limitations. Existing methods cannot currently discover all RNA modifications, let alone comprehensively sequence them on every RNA molecule. This shortfall poses a
- [RNA sequencing enables development of biosensors for disease detection and environmental monitoring](https://www.rna-seqblog.com/rna-sequencing-enables-development-of-biosensors-for-disease-detection-and-environmental-monitoring/) - An effort involving Rutgers researchers could have applications for disease detection and environmental monitoring Scientists have transformed RNA, a biological molecule present in all living cells, into a biosensor that can detect tiny chemicals relevant to human health. Research by Rutgers University-New Brunswick scientists centers on RNA, a nucleic acid that plays a crucial role
- [Early detection of Parkinson’s with novel RNA-based blood test](https://www.rna-seqblog.com/early-detection-of-parkinsons-with-novel-rna-based-blood-test/) - Researchers have developed a simple and cost-effective blood test capable of detecting Parkinson’s disease long before symptoms emerge, comparing the current state of diagnosing neurodegenerative diseases to the fight against cancer 50 years ago—when most cases were identified too late for effective treatment. The test quantifies specific RNA fragments in the blood, focusing on a
- [The RMaP challenge - predicting RNA modifications by nanopore sequencing](https://www.rna-seqblog.com/the-rmap-challenge-predicting-rna-modifications-by-nanopore-sequencing/) - RNA isn’t just a messenger—it’s a dynamic molecule carrying layers of information that go far beyond the genetic code. In recent years, scientists have discovered that RNA is chemically modified in ways that affect everything from how genes are expressed to how cells respond to stress. These changes—known as epitranscriptomic modifications—include well-known players like m6A
- [Transcriptomic profiling of individual bacteria by MATQ-seq](https://www.rna-seqblog.com/transcriptomic-profiling-of-individual-bacteria-by-matq-seq/) - Understanding how individual bacterial cells behave—even when they’re part of the same population—has always been a challenge. But thanks to advances in single-cell RNA sequencing (scRNA-seq), researchers can now listen in on the gene activity of single bacteria like never before. In a new study led by researchers at the University of Würzburg, researchers introduced
- [scTrans - sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data](https://www.rna-seqblog.com/sctrans-sparse-attention-powers-fast-and-accurate-cell-type-annotation-in-single-cell-rna-seq-data/) - Understanding the complex mix of cell types in tissues is a major challenge in biology, especially when working with single-cell RNA sequencing (scRNA-seq) data. This type of data gives scientists detailed insight into gene expression at the single-cell level, but analyzing it is no easy task. One of the toughest parts is figuring out what
- [A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines](https://www.rna-seqblog.com/a-systematic-benchmark-of-nanopore-long-read-rna-sequencing-for-transcript-level-analysis-in-human-cell-lines-2/) - Understanding the full range of RNA molecules produced by our genes is crucial for insights into health and disease. While traditional short-read RNA sequencing has been instrumental, it often falls short in distinguishing between similar RNA variants, known as isoforms. A recent study led by researchers at the Genome Institute of Singapore addresses this challenge
- [Droplet vs picowell - considerations for single-cell transcriptomic profiling of human colon biopsies](https://www.rna-seqblog.com/droplet-vs-picowell-considerations-for-single-cell-transcriptomic-profiling-of-human-colon-biopsies/) - Advances in RNA sequencing have opened new frontiers in understanding how individual cells behave in healthy and diseased tissues. This is especially important for studying the human gastrointestinal (GI) tract, where diseases like colorectal cancer and inflammatory bowel disease often originate in epithelial cells—the cells lining the gut. These cells are critical for maintaining the
- [scCRAFT - separates cell-type-related signals from batch effects for reliable multi-batch integration](https://www.rna-seqblog.com/sccraft-separates-cell-type-related-signals-from-batch-effects-for-reliable-multi-batch-integration/) - Researchers at the Yale School of Public Health have introduced a new method called scCRAFT that makes single-cell RNA sequencing (scRNA-seq) data more accurate and consistent across different batches of experiments. When scientists use scRNA-seq, they often collect data in separate batches, which can lead to technical differences—also called batch effects—that make it hard to
- [RNA sequencing reveals guinea pig embryos as a valuable model for human development](https://www.rna-seqblog.com/rna-sequencing-reveals-guinea-pig-embryos-as-a-valuable-model-for-human-development/) - Researchers at Karolinska Institutet have identified the guinea pig as a promising model for studying the early development of human embryos. A new study shows that guinea pig embryos share many important characteristics with human embryos, which could open up new research opportunities in fertility and stem cell biology. Studying the early development of human
- [CHOIR improves significance-based detection of cell types and states from single-cell data](https://www.rna-seqblog.com/choir-improves-significance-based-detection-of-cell-types-and-states-from-single-cell-data/) - Single-cell technologies, like single-cell RNA sequencing (scRNA-seq), have become essential for exploring the complexity of tissues and organs, helping scientists understand how individual cells behave in health and disease. A key step in analyzing this data is clustering—grouping cells based on their gene expression profiles to identify distinct cell types or states. However, many commonly
- [RNA sequencing reveals how cells ensure accurate mRNA splicing](https://www.rna-seqblog.com/rna-sequencing-reveals-how-cells-ensure-accurate-mrna-splicing/) - Two molecular control factors play a decisive role in what is known as splicing, the cutting and assembly of mature messenger RNA – a prerequisite for protein synthesis in the cell. The poorly characterized factors are crucial to ensuring that the molecular machine responsible for splicing is working correctly. A research team led by Prof.
- [Identification of lncRNAs differentially expressed in Alzheimer’s disease brains using RNA sequencing](https://www.rna-seqblog.com/identification-of-lncrnas-differentially-expressed-in-alzheimers-disease-brains-using-rna-sequencing/) - In the search for a deeper understanding of Alzheimer’s disease (AD), scientists are turning their attention to long non-coding RNAs (lncRNAs)—a type of RNA that doesn’t produce proteins but plays a crucial role in regulating gene activity. A recent study led by researchers from the University of Lübeck has taken a major step forward by
- [A practical guide for single-cell transcriptome data analysis in neuroscience](https://www.rna-seqblog.com/a-practical-guide-for-single-cell-transcriptome-data-analysis-in-neuroscience/) - Single-cell RNA sequencing (scRNA-seq) is changing the way scientists study the brain. Instead of averaging gene expression across thousands or millions of cells, this technology allows researchers to see what’s happening in each individual cell—offering a much clearer picture of brain complexity. Researchers from the University of Tsukuba provide a step-by-step tutorial for researchers who
- [SpaGRN - Investigating spatially informed regulatory paths for spatially resolved transcriptomics data](https://www.rna-seqblog.com/spagrn-investigating-spatially-informed-regulatory-paths-for-spatially-resolved-transcriptomics-data/) - Researchers are constantly working to better understand how cells organize themselves within tissues. One important aspect of this organization is how cells “talk” to each other and respond to their neighbors. A new computational method called SpaGRN, developed by researchers from the BGI Research Institute, offers a powerful way to explore these spatial relationships using
- [CoupleVAE - coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data](https://www.rna-seqblog.com/couplevae-coupled-variational-autoencoders-for-predicting-perturbational-single-cell-rna-sequencing-data/) - As single-cell RNA sequencing becomes more advanced, scientists are now able to analyze the genetic activity of individual cells in extraordinary detail. This is especially useful for studying how cells respond to things like drugs, infections, or other environmental changes—called perturbations. But actually performing these experiments for every possible condition can be expensive and time-consuming.
- [Principle, Workflow, Application and Development of Overview of WGBS](https://www.rna-seqblog.com/principle-workflow-application-and-development-of-overview-of-wgbs/) - Epigenetic modifications, particularly DNA methylation, play an indispensable role in modulating gene expression, cell differentiation, embryogenesis, and disease pathogenesis. WGBS technology has transformed the field of epigenetics by enabling genome-wide, high-resolution mapping of DNA methylation patterns, thereby facilitating in-depth investigations into the molecular mechanisms underlying these biological phenomena. The Principle of WGBS The foundation of WGBS lies
- [Tutorial - Analyzing Bulk RNA-Seq Data Using CHIRP Pipeline](https://www.rna-seqblog.com/tutorial-analyzing-bulk-rna-seq-data-using-chirp-pipeline/) -  This tutorial provides a step-by-step guide on how to analyze bulk RNA-Seq data. We will discuss the key steps involved in RNA-Seq analysis and demonstrate how to use the CHIRP pipeline, a state-of-the-art software workflow used at the Minnesota Supercomputing Institute. CHIRP has been featured in over 30 high-impact publications and continues to be
- [A realistic FastQ-based framework - FastQDesign for scRNA-seq study design issues](https://www.rna-seqblog.com/a-realistic-fastq-based-framework-fastqdesign-for-scrna-seq-study-design-issues/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized the way scientists study gene expression at the individual cell level. However, designing an scRNA-seq experiment requires careful planning, particularly when balancing the number of cells analyzed and sequencing depth while staying within budget. A new study from the Medical College of Wisconsin introduces FastQDesign, a novel framework that
- [PANDORA-seq - optimized identification and characterization of small RNAs](https://www.rna-seqblog.com/pandora-seq-optimized-identification-and-characterization-of-small-rnas/) - Small noncoding RNAs (sncRNAs) are a diverse class of RNA molecules that play critical roles in gene regulation, cellular communication, and disease mechanisms. Unlike messenger RNAs (mRNAs), which are translated into proteins, sncRNAs function primarily by interacting with other RNAs or proteins to influence gene expression. However, many of these regulatory molecules remain undetected using
- [Scale Bio Joins Chan Zuckerberg Initiative's Billion Cells Project, Accelerating Single Cell Research at Unprecedented Scale](https://www.rna-seqblog.com/scale-bio-joins-chan-zuckerberg-initiatives-billion-cells-project-accelerating-single-cell-research-at-unprecedented-scale/) - Scale Biosciences, a leader in highly scalable single cell technologies, today announced its participation in the Chan Zuckerberg Initiative’s (CZI) Billion Cells Project at the Chan Zuckerberg Biohub New York Affiliate Symposium. Scale Bio joins technology partners 10x Genomics and Ultima Genomics in this landmark effort to generate an unprecedented one billion cell dataset to
- [Analytical validation of an RNA next-generation sequencing assay for the assessment of lung cancer risk in pulmonary nodules](https://www.rna-seqblog.com/analytical-validation-of-an-rna-next-generation-sequencing-assay-for-the-assessment-of-lung-cancer-risk-in-pulmonary-nodules/) - Lung cancer is often difficult to diagnose early, especially when small lung nodules appear on imaging scans. Researchers from Veracyte, Inc have developed the Percepta Nasal Swab (PNS) test, a noninvasive method that uses RNA sequencing (RNA-Seq) to assess lung cancer risk in individuals with a history of smoking. Cigarette smoke affects gene expression throughout
- [ICRAFT - identifying dual-action cancer immunotherapy targets using CRISPR and RNA sequencing](https://www.rna-seqblog.com/icraft-identifying-dual-action-cancer-immunotherapy-targets-using-crispr-and-rna-sequencing/) - Researchers from the Center for Quantitative Biology at the Peking University Academy for Advanced Interdisciplinary Studies, in collaboration with the Peking University-Tsinghua University Joint Center for Life Sciences, have developed ICRAFT, an innovative computational platform for identifying cancer immunotherapy targets. Their study has been published in Immunity, an immunology research journal. Why It Matters There
- [GeneCOCOA - detecting context-specific functions of individual genes using co-expression data](https://www.rna-seqblog.com/genecocoa-detecting-context-specific-functions-of-individual-genes-using-co-expression-data/) - Understanding how genes function is a major challenge in biology, especially when a gene lacks prior research. Traditional methods of gene expression analysis focus on entire gene sets, identifying which biological pathways are enriched. However, this approach isn’t ideal when researchers want to study a single gene in detail. To solve this problem, researchers from
- [Fatty acids promote immune suppression and therapy resistance in triple negative breast cancer](https://www.rna-seqblog.com/fatty-acids-promote-immune-suppression-and-therapy-resistance-in-triple-negative-breast-cancer/) - A new study published in the journal Immunity reveals a mechanism that allows triple negative breast cancer (TNBC) to develop resistance to therapy. Researchers at Baylor College of Medicine showed that lipid accumulation in tumor cells and nearby immune cells promotes immune suppression, but disrupting lipid formulation reverses treatment resistance and the immunosuppressive microenvironment. Standard-of-care treatment for
- [Ultima genomics offers 3 trillion free sequencing reads to support the scientific community](https://www.rna-seqblog.com/ultima-genomics-offers-3-trillion-free-sequencing-reads-to-support-the-scientific-community/) - Ultima Genomics, developer of an ultra-high-throughput sequencing architecture, today announced the launch of its "Count on Us" initiative. During the month of April, Ultima Genomics will provide 3 trillion DNA sequencing reads free of charge to researchers across the U.S. and Canada. As part of the "Count on Us" initiative, researchers affiliated with academic, public,
- [Key players in brain aging - RNA-seq identifies age-related damage on a cellular level](https://www.rna-seqblog.com/key-players-in-brain-aging-rna-seq-identifies-age-related-damage-on-a-cellular-level/) - Largest study on brain aging points to possible connections between diet, inflammation, and brain health Scientists at the Allen Institute have identified specific cell types in the brain of mice that undergo major changes as they age, along with a specific hot spot where many of those changes occur. The discoveries, published in the journal Nature, could pave
- [Study identifies novel pathway with potential to slow the progression of pulmonary fibrosis](https://www.rna-seqblog.com/study-identifies-novel-pathway-with-potential-to-slow-the-progression-of-pulmonary-fibrosis/) - A study published in The American Journal of Pathology demonstrates that Piezo2 is a critical mechanoreceptor involved in stiffness-mediated profibrotic fibroblast phenotypes Researchers have found a potential new way to slow the progression of lung fibrosis and other fibrotic diseases by inhibiting the expression or function of Piezo2, a receptor that senses mechanical forces in
- [Mapping the hidden proteins of <i>Campylobacter jejuni</i> with Ribo-Seq](https://www.rna-seqblog.com/mapping-the-hidden-proteins-of-campylobacter-jejuni-with-ribo-seq/) - Researchers from the University of Würzburg have created a high-resolution map of the proteins produced by Campylobacter jejuni, a major foodborne pathogen. Unlike larger, well-studied proteins, small proteins (typically under 100 amino acids) are difficult to detect, yet they play critical roles in bacterial survival and virulence. To overcome this challenge, the research team used
- [New machine learning tool enhances cancer detection in single-cell RNA sequencing](https://www.rna-seqblog.com/new-machine-learning-tool-enhances-cancer-detection-in-single-cell-rna-sequencing/) - Cancer is a complex disease, and even within a single tumor, not all cells are the same. Some are aggressive malignant cells, while others are normal or supportive cells. Identifying these malignant cells at the single-cell level is essential for understanding tumor progression and improving treatments. A team led by researchers at the Shanghai Institute
- [Transcriptomics in the era of long-read sequencing](https://www.rna-seqblog.com/transcriptomics-in-the-era-of-long-read-sequencing/) - RNA sequencing (RNA-seq) has transformed how scientists study gene expression, revealing new insights into how genes are turned on and off in different conditions. Traditionally, short-read sequencing has been the gold standard, helping researchers detect and quantify genes with great precision. However, short reads struggle to capture the full picture, particularly when it comes to
- [RNA sequencing reveals key regulator for activating adult stem cells in bone marrow regeneration](https://www.rna-seqblog.com/rna-sequencing-reveals-key-regulator-for-activating-adult-stem-cells-in-bone-marrow-regeneration/) - An international research team, led by scientists from Tel Aviv University and Sheba Medical Center, has unveiled an innovative method for activating adult stem cells from human bone marrow, enabling their expansion outside the body for use in bone marrow regeneration and the construction of a new blood and immune system. The findings, published in
- [Uncalled4 - a toolkit for nanopore signal alignment, analysis and visualization](https://www.rna-seqblog.com/uncalled4-a-toolkit-for-nanopore-signal-alignment-analysis-and-visualization/) - Nanopore sequencing has revolutionized the way scientists analyze DNA and RNA, allowing them to detect genetic sequences and modifications without extra processing steps. However, accurately identifying certain nucleotide modifications—especially in RNA—remains a challenge. A research team from Johns Hopkins University has developed a new computational toolkit called Uncalled4, which enhances the accuracy of detecting DNA
- [Complete Genomics Announces Commercial Partnership with Human Cell Atlas to Offer its Members Stereo-seq Spatial Transcriptomics](https://www.rna-seqblog.com/complete-genomics-announces-commercial-partnership-with-human-cell-atlas-to-offer-its-members-stereo-seq-spatial-transcriptomics/) - Complete Genomics, a leading innovator in genomic sequencing, announced at the NextGen Omics & Spatial Biology Conference that it has entered a commercial partnership with Human Cell Atlas (HCA) to offer its STOmics spatial transcriptomics products to HCA members. Human Cell Atlas (HCA), an international collaborative research consortium, is mapping all cell types in the healthy body, across
- [RNA sequencing reveals hidden metabolic pathways in Alzheimer’s disease through personalized modeling](https://www.rna-seqblog.com/rna-sequencing-reveals-hidden-metabolic-pathways-in-alzheimers-disease-through-personalized-modeling/) - Understanding the complex metabolic changes that occur in Alzheimer’s disease (AD) is essential for developing better diagnostic and therapeutic strategies. Traditionally, researchers use genome-scale metabolic models (GEMs) to map gene expression data to metabolic pathways, helping identify disease-related disruptions. However, these models often overlook another crucial factor—genetic variants that alter enzyme functionality. Now, a research
- [LocusMasterTE - integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression](https://www.rna-seqblog.com/locusmasterte-integrating-long-read-rna-sequencing-improves-locus-specific-quantification-of-transposable-element-expression/) - Transposable elements (TEs), often called “jumping genes,” are mobile DNA sequences that can relocate within the genome. While they have played a key role in evolution by reshuffling genetic material, their activity can also cause genetic instability, disrupt important genes, and contribute to various diseases, including cancer and neurological disorders. However, studying TEs has been
- [Creative Biolabs exosomal small RNA/miRNA sequencing: progressing in biomarkers of disease detection](https://www.rna-seqblog.com/creative-biolabs-exosomal-small-rna-mirna-sequencing-progressing-in-biomarkers-of-disease-detection/) - Creative Biolabs provides comprehensive services in exosome small RNA sequencing including exosome isolation, miRNA extraction, sequencing, and data processing. As important mediators of intercellular communication, exosomes are crucial to the onset, progression, and treatment of diseases. MicroRNAs (miRNAs), which are one of the carriers, are in the spotlight of precision medicine owing to their unique
- [Transcriptomic profiling of blood platelets identifies a diagnostic signature for pancreatic cancer](https://www.rna-seqblog.com/transcriptomic-profiling-of-blood-platelets-identifies-a-diagnostic-signature-for-pancreatic-cancer/) - Pancreatic cancer is one of the deadliest forms of cancer, largely because it is often diagnosed too late for effective treatment. Researchers at Wenzhou Medical University have discovered a potential breakthrough: using blood platelets to detect pancreatic cancer early through RNA sequencing. Their study, published in British Journal of Cancer, suggests that specific RNA markers
- [Developing advanced tools to improve accuracy and accessibility for long-read RNA sequencing](https://www.rna-seqblog.com/developing-advanced-tools-to-improve-accuracy-and-accessibility-for-long-read-rna-sequencing/) - In the ever-evolving world of computational biology, one of the greatest challenges has always been deriving knowledge and insight from the massive amount of both DNA (double helix) and RNA (single helix) data through which scientists must sift. For example, for those that remember, it took almost 13 years (1990–2003) to sequence and assemble the first
- [UT Dallas researcher recognized for spatial transcriptomics research in peripheral neuropathy](https://www.rna-seqblog.com/ut-dallas-researcher-recognized-for-spatial-transcriptomics-research-in-peripheral-neuropathy/) - A neuroscience researcher from The University of Texas at Dallas’ Center for Advanced Pain Studies has been selected to receive a seed grant from the Merkin Center at Johns Hopkins University School of Medicine. Dr. Diana Tavares Ferreira, assistant professor of neuroscience in the School of Behavioral and Brain Sciences, is one of nine researchers in the 2025 cohort of
- [spline-DV - single-cell gene expression variability](https://www.rna-seqblog.com/spline-dv-single-cell-gene-expression-variability/) - Researchers at Texas A&M University have developed a new method called spline-DV to analyze variability in gene expression using single-cell RNA sequencing (scRNA-seq) data. Traditional RNA sequencing studies focus on the average expression levels of genes across different conditions, but this approach ignores cell-to-cell variability, which plays a crucial role in biological processes like disease
- [Paired-Damage-seq - single-cell parallel analysis of DNA damage and transcriptome](https://www.rna-seqblog.com/paired-damage-seq-single-cell-parallel-analysis-of-dna-damage-and-transcriptome/) - Researchers at the New York Genome Center have developed a new method called Paired-Damage-seq to study how DNA damage affects gene regulation at the single-cell level. DNA damage is a constant challenge for cells, arising from both environmental factors (like UV radiation) and internal processes (such as oxidative stress). Understanding where and how DNA damage
- [RNA sequencing from long-stored biobank blood samples](https://www.rna-seqblog.com/rna-sequencing-from-long-stored-biobank-blood-samples/) - Biobanks store vast amounts of frozen blood samples, offering an invaluable resource for medical research. However, one major hurdle has been extracting high-quality RNA from these samples—especially when stored for long periods without RNA-preserving chemicals. Researchers at Umeå University have developed a method to overcome this challenge, allowing successful RNA sequencing from buffy coat samples stored
- [Combining deep learning techniques with statistical boosting to understanding single-cell RNA sequencing data](https://www.rna-seqblog.com/combining-deep-learning-techniques-with-statistical-boosting-to-understanding-single-cell-rna-sequencing-data/) - Researchers at the University of Freiburg have developed a novel method to improve how scientists analyze single-cell RNA sequencing (scRNA-seq) data. Their approach, called the boosting autoencoder (BAE), combines deep learning techniques with statistical boosting to make it easier to interpret complex cellular data. Single-cell RNA sequencing allows scientists to study gene expression at an
- [MulNet - mapping gene networks to understand cancer](https://www.rna-seqblog.com/mulnet-mapping-gene-networks-to-understand-cancer/) - Understanding how genes interact is crucial for studying diseases like cancer, but most existing models only capture a small portion of these complex relationships. Researchers at the Beijing Institute of Lifeomics have developed MulNet, a new computational framework that integrates multiple molecular interactions into a detailed network of gene regulation. This approach allows scientists to
- [Vevo Therapeutics Open Sources Tahoe-100M, the World's Largest Single-Cell Dataset, as the Inaugural Contribution to Arc Institute's New Virtual Cell Atlas](https://www.rna-seqblog.com/vevo-therapeutics-open-sources-tahoe-100m-the-worlds-largest-single-cell-dataset-as-the-inaugural-contribution-to-arc-institutes-new-virtual-cell-atlas/) - 300 million single cell atlas now accessible to the scientific community comprised of Vevo’s Tahoe-100M, mapping 60,000 drug-cell interactions, and Arc’s AI-curated scBaseCamp 200 million cell dataset Generated using Vevo’s Mosaic platform, Tahoe-100M leveraged Parse Biosciences’ GigaLab for single cell sample preparation and Ultima Genomics for sequencing. In a landmark move to advance AI-driven biological
- [Crafted experiments to evaluate feature selection methods for single-cell RNA-seq data](https://www.rna-seqblog.com/crafted-experiments-to-evaluate-feature-selection-methods-for-single-cell-rna-seq-data/) - Researchers at the University of North Carolina at Chapel Hill have developed a novel strategy called crafted experiments to improve the evaluation of single-cell RNA sequencing (scRNA-seq) analysis methods. While many computational tools exist for processing scRNA-seq data, comparing their accuracy and effectiveness has been difficult due to the lack of real-world reference datasets. Crafted
- [A new tool to improve single-cell RNA sequencing accuracy](https://www.rna-seqblog.com/a-new-tool-to-improve-single-cell-rna-sequencing-accuracy/) - Researchers at the University of Michigan have developed a computational tool called Originator to improve the accuracy of single-cell RNA sequencing (scRNA-seq). One common challenge in scRNA-seq is contamination from blood-derived immune cells during tissue sample preparation, which can distort results and make it difficult to study tissue-resident cells properly. The Originator tool helps researchers distinguish
- [The Application of RNA Sequencing in Systemic Lupus Erythematosus](https://www.rna-seqblog.com/the-application-of-rna-sequencing-in-systemic-lupus-erythematosus/) - Summary RNA sequencing (RNA-seq) has emerged as a powerful tool for gene expression analysis, allowing for the comprehensive study of the transcriptome. It has become an essential technique in various research fields, including disease research. Here, we will explore how RNA-seq was applied to investigate the mechanism of synaptic stripping by microglia in a mouse
- [How does UV/Vis spectroscopy enable RNA quantification?](https://www.rna-seqblog.com/how-does-uv-vis-spectroscopy-enable-rna-quantification/) - Accurate RNA quantification is one of the most important steps in molecular biology as it influences the success of downstream applications. Optical spectroscopy is used in most laboratories to quantify and assess RNA concentration and purity quickly and non-destructively. Most molecular biologists will know the expected ratio values to look for that indicate sample purity,
- [Tracking gene transfer in microbial communities with RNA barcoding](https://www.rna-seqblog.com/tracking-gene-transfer-in-microbial-communities-with-rna-barcoding/) - Researchers at Rice University have developed an innovative RNA-based method to track how genes move between microbes in complex environments like wastewater. This new approach, called universal RNA barcoding, enables scientists to study microbial gene transfer with far greater sensitivity than traditional genetic reporters or sequencing methods. To achieve this, the team engineered a synthetic
- [RNA sequencing reveals spatial immune patterns to predict hepatocellular carcinoma recurrence](https://www.rna-seqblog.com/rna-sequencing-reveals-spatial-immune-patterns-to-predict-hepatocellular-carcinoma-recurrence/) - Hepatocellular carcinoma (HCC), the most common type of liver cancer, has a high recurrence rate even after surgical removal. Detecting which patients are at higher risk of recurrence early on could help improve outcomes and allow doctors to personalize treatment strategies. A recent study led by researchers from the University of Science and Technology of
- [Decoding the interplay between genes and mechanics in tissues at single-cell resolution](https://www.rna-seqblog.com/decoding-the-interplay-between-genes-and-mechanics-in-tissues-at-single-cell-resolution/) - Researchers at the Kennedy Institute have developed a new computational framework that allows simultaneous analysis of gene expression and mechanical forces within cells and tissues, uncovering insights into how the interplay between transcriptional and mechanical signals guides processes such as cell fate decisions or the formation of spatially distinct tissue compartments. Representation of the spatial
- [Research Assistant I - Genetics](https://www.rna-seqblog.com/research-assistant-i-genetics/) - At the Guarnerio lab, we’re dedicated to unraveling the complex molecular mechanisms used by tumor cells to create a pro-tumorigenic tumor microenvironment (TME). We utilize cutting-edge technologies like single-cell RNA sequencing and spatial transcriptomics to study both mouse and human tissues. Our research is deeply rooted in translational science, with the goal of developing innovative
- [Ninetails - direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs](https://www.rna-seqblog.com/ninetails-direct-profiling-of-non-adenosines-in-polya-tails-of-endogenous-and-therapeutic-mrnas/) - Researchers at the International Institute of Molecular and Cell Biology in Warsaw have developed a powerful new computational tool called Ninetails to analyze mRNA poly(A) tails with unprecedented accuracy. This innovation, based on neural networks, helps scientists detect non-adenosine modifications in mRNA tails—an area previously difficult to study using existing methods. Poly(A) tails are crucial
- [scRNA-seq on a PDAC cohort identified distinct cell populations associated with tumor initiation and progression](https://www.rna-seqblog.com/single-cell-rna-sequencing-scrna-seq-on-a-pdac-cohort-identified-distinct-cell-populations-associated-with-tumor-initiation-and-progression/) - Pancreatic cancer is one of the leading causes of cancer-related mortality, with pancreatic ductal adenocarcinoma (PDAC) accounting for 90% of all cases. As most PDAC cases are diagnosed at advanced stages, surgical interventions are ineffective, and consequently, lymph node metastasis manifests in 70% of PDAC patients. Moreover, since the number of genetic mutations giving rise to
- [Scientists gain insight into RNA-editing protein that could lead to improved treatment for cancer, autoimmune diseases](https://www.rna-seqblog.com/scientists-gain-insight-into-rna-editing-protein-that-could-lead-to-improved-treatment-for-cancer-autoimmune-diseases/) - A team led by researchers at Rice University has uncovered new insights into the molecular mechanisms of ADAR1, a protein that regulates ribonucleic acid (RNA) induced immune responses. Their findings, published in Molecular Cell March 17, could open new pathways for treating autoimmune diseases and enhancing cancer immunotherapy. ADAR1 converts adenosine to inosine in double-stranded RNA, a process
- [RNA sequencing study reveals mesothelioma cell differentiators](https://www.rna-seqblog.com/rna-sequencing-study-reveals-mesothelioma-cell-differentiators/) - Researchers have long known that mesothelioma tumor cells have diverse characteristics. These differences, known as cell heterogeneity, have a direct impact on how the disease progresses and what treatments will work best, and understanding them is essential to the successful development of targeted therapies. The differences have also made accurate diagnosis much more challenging. A group of
- [RNA sequencing reveals novel gene regulatory mechanisms in Dravet syndrome](https://www.rna-seqblog.com/rna-sequencing-reveals-novel-gene-regulatory-mechanisms-in-dravet-syndrome/) - Investigators in the laboratory of Gemma Carvill, PhD, assistant professor in the Ken and Ruth Davee Department of Neurology Division of Epilepsy/Clinical Neurophysiology, have discovered novel mechanisms underlying Dravet syndrome, a rare genetic form of epilepsy in children, that may serve as promising therapeutic targets, according to findings published in JCI Insight. Dravet syndrome is a rare, genetic form of epilepsy that
- [SL-Smart-seq3xpress RNA sequencing reveals mechanisms of antigenic variation in trypanosomes](https://www.rna-seqblog.com/sl-smart-seq3xpress-rna-sequencing-reveals-mechanisms-of-antigenic-variation-in-trypanosomes/) - The immune system responds to an infection by producing antibodies that recognize and bind to the cell surface of the pathogen, thus marking it as an intruder and triggering an immune response. For this to work, the antibodies produced must exactly fit the membrane molecules of the pathogen, like a key fitting a lock. Many
- [scNET - integrating protein interaction networks with RNA sequencing](https://www.rna-seqblog.com/scnet-integrating-protein-interaction-networks-with-rna-sequencing/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to explore the diversity of cells in tissues. However, the data it provides often doesn’t capture the full picture, particularly when it comes to cellular pathways and protein complexes, which are more easily understood at the protein level. This limitation becomes
- [Innovative bead design will enhance single-cell transcriptomics accuracy](https://www.rna-seqblog.com/innovative-bead-design-will-enhance-single-cell-transcriptomics-accuracy/) - Researchers at NDORMS have made an important advancement in the field of single-cell transcriptomics by developing a novel bead design that reduces errors in DNA synthesis and improves the reliability of gene expression measurements. Single-cell transcriptomics has revolutionised the study of cellular diversity and function by enabling gene expression analysis at single-cell resolution. The technique
- [GeneDx to present findings from an RNA sequencing program at the ACMG annual meeting](https://www.rna-seqblog.com/genedx-to-present-findings-from-an-rna-sequencing-program-at-the-acmg-annual-meeting/) - GeneDx, a leader in delivering improved health outcomes through genomic insights, announced today its scientific contributions will be presented at the 2025 American College of Medical Genetics and Genomics (ACMG) Annual Clinical Genetics Meeting. Featured as a Top 20 Poster, GeneDx will also present findings from an RNA sequencing program used to aid in variant
- [Researchers use RNA sequencing to compare pig and human retinal organoids for vision restoration](https://www.rna-seqblog.com/researchers-use-rna-sequencing-to-compare-pig-and-human-retinal-organoids-for-vision-restoration/) - Inside the human eye, the retina is made up of several types of cells, including the light-sensing photoreceptors that initiate the cascade of events that lead to vision. Damage to the photoreceptors, either through degenerative disease or injury, leads to permanent vision impairment or blindness. A retinal organoid examined at an early stage of differentiation
- [Landscape transcriptomics offers new approach to identifying stressors affecting bumble bees](https://www.rna-seqblog.com/landscape-transcriptomics-offers-new-approach-to-identifying-stressors-affecting-bumble-bees/) - A new method of examining gene expression patterns called landscape transcriptomics may help pinpoint what causes bumble bees stress and could eventually give insight into why bee populations are declining overall, according to a study led by researchers at Penn State. The team published their findings in the journal Molecular Ecology. The new method may eventually
- [A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines](https://www.rna-seqblog.com/a-systematic-benchmark-of-nanopore-long-read-rna-sequencing-for-transcript-level-analysis-in-human-cell-lines/) - Understanding the complexity of RNA transcripts is a major challenge in genomics. The human genome contains instructions for producing over 200,000 RNA molecules, but many of these originate from the same gene, generating highly similar alternative isoforms. Accurately quantifying these isoforms is crucial for understanding gene regulation, disease mechanisms, and potential therapeutic targets. To tackle
- [Sequencing study spotlights tight web of genes tied to autism](https://www.rna-seqblog.com/sequencing-study-spotlights-tight-web-of-genes-tied-to-autism/) - From The Transmitter by Katie Moisse The findings, shared in a preprint, help to illuminate how a large and heterogeneous group of genes could be involved in autism. Who’s the boss: Some 78 “central regulators” (large circles) control the expression of other genes (small circles), some of which have a link to autism (red and yellow),
- [AnomalGRN - deciphering single-cell gene regulation network with graph anomaly detection](https://www.rna-seqblog.com/anomalgrn-deciphering-single-cell-gene-regulation-network-with-graph-anomaly-detection/) - Understanding how genes interact and regulate each other at the cellular level is essential for uncovering the mechanisms behind development, disease, and treatment responses. Researchers from the Wenzhou University of Technology have developed AnomalGRN, a novel artificial intelligence (AI)-based tool designed to improve the accuracy of single-cell gene regulatory network (GRN) analysis. Single-cell RNA sequencing
- [Post-doc position available - RNA-seq Analyst](https://www.rna-seqblog.com/post-doc-position-available-rna-seq-analyst-2/) - Job Summary Applications are invited for appointment as a Post-doctoral Fellow in Single Cell and Spatial Omics for two years, with the possibility of renewal subject to funding availability and satisfactory performance. The appointee will work on interdisciplinary projects related to the use of single-cell RNA-seq, single-cell imaging, spatial transcriptomics, and bioinformatics methods to study bone
- [Spotiphy integrative analysis tool turns spatial imager into RNA sequencer](https://www.rna-seqblog.com/spotiphy-integrative-analysis-tool-turns-spatial-imager-into-rna-sequencer/) - Scientists at St. Jude Children’s Research Hospital and the University of Wisconsin-Madison today share a generative algorithm for achieving both high genome and image resolution in spatial transcriptomics. Co-first author Jiyuan Yang, PhD, St. Jude Department of Computational Biology and co-senior and corresponding author Jiyang Yu, PhD, St. Jude Department of Computational Biology interim chair look at spatial transcriptomics data. Spatial
- [AcImpute - a constraint-enhancing smooth-based approach for imputing single-cell RNA sequencing data](https://www.rna-seqblog.com/acimpute-a-constraint-enhancing-smooth-based-approach-for-imputing-single-cell-rna-sequencing-data/) - Single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression at the individual cell level, offering valuable insights into cellular diversity. However, one major challenge in scRNA-seq is dropout events, where some genes appear inactive simply because their expression wasn’t detected—not because they aren’t being used. This can lead to misleading results in studies of
- [sciRED - interpretable single-cell factor decomposition using](https://www.rna-seqblog.com/scired-interpretable-single-cell-factor-decomposition-using/) - Single-cell RNA sequencing (scRNA-seq) allows scientists to analyze gene expression at the level of individual cells, offering insights into how tissues function and respond to disease. However, analyzing this data is complex due to noise, technical artifacts, and high dimensionality. Researchers from the University of Toronto, have developed a new tool called sciRED (Single-Cell Interpretable
- [SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data](https://www.rna-seqblog.com/scement-scalable-and-memory-efficient-integration-of-large-scale-single-cell-rna-sequencing-data/) - Understanding how different cell types function in the body requires analyzing large amounts of data from single-cell RNA sequencing (scRNA-seq). However, combining data from multiple experiments is challenging due to differences in processing methods, computational limits, and memory constraints. A new method developed by researchers at the Georgia Institute of Technology offers a solution to
- [Combining single-cell ATAC and RNA sequencing for supervised cell annotation](https://www.rna-seqblog.com/combining-single-cell-atac-and-rna-sequencing-for-supervised-cell-annotation/) - Researchers at Imperial College London and AstraZeneca have explored how combining two powerful techniques—single-cell RNA sequencing and ATAC sequencing—can enhance our ability to identify and classify different cell types. This step, called cell type annotation, is essential for understanding the roles individual cells play in health and disease. While RNA sequencing provides valuable information about
- [Scale Biosciences launches five single-cell profiling products, unlocking single-cell RNA studies at any scale.](https://www.rna-seqblog.com/scale-biosciences-launches-five-single-cell-profiling-products-unlocking-single-cell-rna-studies-at-any-scale/) - Scale Biosciences, a leader in innovative and scalable single cell analysis solutions, has announced the availability of its QuantumScale Single Cell RNA kits, a set of next-generation single cell products which can capture and process from 84,000 to 4 million cells without any specialized partitioning instrumentation. The revolutionary platform, based on the company’s Quantum Barcoding technology,
- [paraCell - interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data](https://www.rna-seqblog.com/paracell-interactive-analysis-and-visualization-of-standard-and-dual-host-parasite-single-cell-rna-seq-data/) - Researchers from the University of Glasgow have developed paraCell, a new software tool designed to make single-cell RNA sequencing (scRNA-seq) data more accessible to parasitologists. While single-cell transcriptomic datasets have expanded dramatically, analyzing them often requires advanced computational skills, limiting their use among researchers without bioinformatics expertise. Unlocking Single-Cell Insights in Parasitology Single-cell RNA sequencing
- [A brief overview of single-cell RNA sequencing technologies and applications](https://www.rna-seqblog.com/a-brief-overview-of-single-cell-rna-sequencing-technologies-and-applications/) - Researchers from the Lars Bolund Institute of Regenerative Medicine have provided a concise yet insightful overview of single-cell RNA sequencing (scRNA-seq) in a recent review published in Clinical and Translational Medicine. This cutting-edge technology allows scientists to study the genetic activity of individual cells, offering a deeper understanding of cellular diversity within tissues, organs, and
- [Decoding bone health: single-cell insights into type 2 diabetes](https://www.rna-seqblog.com/decoding-bone-health-single-cell-insights-into-type-2-diabetes/) - A pioneering study offers unprecedented insights into the bone immune microenvironment of type 2 diabetic mice, uncovering a unique genetic profile that includes decreased osteoclast differentiation. This research is pivotal as it sheds light on the cellular and molecular mechanisms that could be targeted to address bone health complications associated with type 2 diabetes, potentially
- [The INTERVAL RNA-seq Portal](https://www.rna-seqblog.com/the-interval-rna-seq-portal/) - New RNA-Seq resource helps bridge the gap between identifying genetic changes linked to health conditions and understanding how these changes impact biological processes. Large-scale research has mapped how thousands of inherited genetic variants play a role in developing chronic conditions, including hypertension and dermatitis, uncovering new connections between genes and health. In this new study, published
- [Upcoming webinar - Nanopore Sequencing for RNA Vaccines and Therapeutics: Advancing Drug Development and Quality Control](https://www.rna-seqblog.com/upcoming-webinar-nanopore-sequencing-for-rna-vaccines-and-therapeutics-advancing-drug-development-and-quality-control/) - In this free webinar, learn how nanopore sequencing is transforming biopharmaceutical development with real-time genetic analysis. Attendees will gain insight into its expanding applications beyond traditional uses, including RNA analysis and good manufacturing practice (GMP) environments. The featured speakers will discuss integrating nanopore technology to complement existing analytical methods. The speakers will also share how
- [Baylor researchers develop and validate clinical diagnostic RNA sequencing test](https://www.rna-seqblog.com/baylor-researchers-develop-and-validate-clinical-diagnostic-rna-sequencing-test/) - RNA sequencing has emerged as a powerful supplement to DNA sequencing for Mendelian disease diagnosis, but clinical translation of diagnostic RNA-seq has not been widely achieved. Researchers at Baylor College of Medicine’s Medical Genetics and Multiomics Laboratory published the clinical validation of the first RNA sequencing test for diagnostic whole-transcriptome analysis for genetic disorders. The findings, published
- [RNA extraction and RNA-sequencing method for transcriptomic analysis of Mycobacterium tuberculosis](https://www.rna-seqblog.com/rna-extraction-and-rna-sequencing-method-for-transcriptomic-analysis-of-mycobacterium-tuberculosis/) - Understanding how Mycobacterium tuberculosis (M. tuberculosis) responds to drug treatments at the molecular level is crucial for improving tuberculosis (TB) therapies. Researchers at the National Microbiology Laboratory in Canada present a refined RNA sequencing (RNA-seq) method designed to analyze gene expression in M. tuberculosis with high precision. The researchers tested their protocol on 11 different
- [LETSmix - a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics](https://www.rna-seqblog.com/letsmix-a-spatially-informed-and-learning-based-domain-adaptation-method-for-cell-type-deconvolution-in-spatial-transcriptomics/) - Understanding where genes are active within tissues is crucial for advancing biology and medicine. Spatial transcriptomics (ST) is a powerful tool that allows scientists to see gene expression patterns in their spatial context. However, a major challenge with many ST technologies is resolution—each measurement often includes a mix of multiple cell types, making it difficult
- [How long-read RNA sequencing is shedding light on neurodegenerative disease](https://www.rna-seqblog.com/how-long-read-rna-sequencing-is-shedding-light-on-neurodegenerative-disease/) - Microglia, the immune cells of the brain and spinal cord, play a critical role in neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Scientists have long suspected that genetic variants associated with these diseases affect microglia-specific regulatory elements, but until now, identifying how these genetic variations impact gene splicing has been challenging due to the limitations
- [New tool to map the origins and journeys of cells in development and disease](https://www.rna-seqblog.com/new-tool-to-map-the-origins-and-journeys-of-cells-in-development-and-disease/) - Cell2fate, a new computational tool, allows researchers to map cellular trajectories in development and disease. A new computational tool allows researchers to understand how the diverse cell types of the human body are made during development, and how diseases progress over time at the cellular level. Researchers from the Wellcome Sanger Institute and the German Cancer
- [Qlucore launches the first CE-marked RNA sequencing diagnostic test for pediatric leukemia in Europe](https://www.rna-seqblog.com/qlucore-launches-the-first-ce-marked-rna-sequencing-diagnostic-test-for-pediatric-leukemia-in-europe/) - Qlucore introduces the first CE-marked diagnostic test for pediatric leukemia according to the mandatory regulatory framework in Europe (IVDR). Now available for delivery and clinical use, Qlucore Diagnostics provides enhanced accuracy and marks a significant step forward in the ability to diagnose this common childhood cancer. With improved diagnosis, more personalized treatment and better outcomes
- [Advancing rare disease research innovations in RNA and long read sequencing](https://www.rna-seqblog.com/advancing-rare-disease-research-innovations-in-rna-and-long-read-sequencing/) - The Rare Disease RNA Phenotyping and Long Read Sequencing projects are advancing rare disease research by improving genetic diagnosis and data analysis. With key milestones in sequencing and collaborations with leading institutions, these technologies are enhancing our understanding of disease mechanisms and patient care. Two cutting-edge technologies currently used in the NIHR BioResource are RNA
- [Emerging clinical applications of single-cell RNA sequencing in oncology](https://www.rna-seqblog.com/emerging-clinical-applications-of-single-cell-rna-sequencing-in-oncology/) - Researchers from the Weizmann Institute of Science explore how single-cell RNA sequencing (scRNA-seq) is reshaping our understanding of cancer biology and its potential clinical applications. They discuss how this technology helps uncover the diverse genetic and functional states of cancer cells and their surrounding environment. The Power of scRNA-seq in Cancer Research For years, scientists
- [Total Acre partners with Crop Diagnostix to bring RNA sequencing technology to predictive agronomy](https://www.rna-seqblog.com/total-acre-partners-with-crop-diagnostix-to-bring-rna-sequencing-technology-to-predictive-agronomy/) - TOTAL ACRE, renowned for its record-setting yields and commitment to agronomic excellence, is proud to announce a preferred partnership with Crop Diagnostix-an innovative ag-tech company using RNA gene expression and AI to predict asymptomatic plant stress, empowering smarter decisions to maximize ROI. TOTAL ACRE takes a systematic approach to farming by equipping growers with the
- [RNA sequencing reveals potential link between herpesvirus and Alzheimer’s disease](https://www.rna-seqblog.com/rna-sequencing-reveals-potential-link-between-herpesvirus-and-alzheimers-disease/) - Research combining genomics, database analysis and RNA sequencing suggests possible role for antiviral drug therapy Researchers have outlined a pathway by which human herpesvirus may contribute to Alzheimer’s disease (AD) in the aging brain. In a report published in Alzheimer’s & Dementia, a Cleveland Clinic-led investigative team also identified two commercially available antiviral drugs that reverse this pathway
- [New data tool could bring RNA sequencing into standard clinical practice, improving diagnosis and treatment](https://www.rna-seqblog.com/new-data-tool-could-bring-rna-sequencing-into-standard-clinical-practice-improving-diagnosis-and-treatment/) - Researchers have developed a new tool that could help clinicians diagnose the most common type of breast cancer more accurately and make better treatment decisions. The tool, called EMBeddER (EMBER), integrates two types of datasets – previously not seen as compatible – to provide more comprehensive information about a person’s cancer. In this study, led
- [RNA sequencing reveals GATA6 as a potential therapeutic target for colon cancer](https://www.rna-seqblog.com/rna-sequencing-reveals-gata6-as-a-potential-therapeutic-target-for-colon-cancer/) - Northwestern Medicine scientists have discovered that inhibiting the GATA6 protein in mouse models of colon cancer reduced tumor growth and improved survival, underscoring the potential of a new therapeutic target for colon cancer, according to a recent study published in Science Advances. “This is the first time we show that GATA6 is a global regulator and controls many
- [AI accelerates discovery of neurodevelopmental disorder-associated genes](https://www.rna-seqblog.com/ai-accelerates-discovery-of-neurodevelopmental-disorder-associated-genes/) - Researchers have developed an artificial intelligence (AI) approach that accelerates the identification of genes that contribute to neurodevelopmental conditions such as autism spectrum disorder, epilepsy and developmental delay. This new powerful computational tool can help fully characterize the genetic landscape of neurodevelopmental disorders, which is key to making accurate molecular diagnosis, elucidating disease mechanism and
- [A new way to measure long noncoding RNA levels in cells](https://www.rna-seqblog.com/a-new-way-to-measure-long-noncoding-rna-levels-in-cells/) - Long noncoding RNAs (lncRNAs) play important roles in normal biology and disease, but studying them can be tricky. One key challenge is determining how many molecules of a particular lncRNA exist inside a cell. Traditional methods, such as single-molecule RNA fluorescence in situ hybridization (smFISH) and calibrated reverse-transcription quantitative PCR (RT-qPCR), have been used to
- [Bruker announces advancements in transcriptomics and spatial biology at AGBT 2025](https://www.rna-seqblog.com/bruker-announces-advancements-in-transcriptomics-and-spatial-biology-at-agbt-2025/) - Bruker Corporation (Nasdaq: BRKR) announced today that it will unveil significant advancements in spatial biology at the 2025 Advances in Genome Biology and Technology (AGBT) General Meeting. Bruker Spatial Biology will announce the following four innovations that underscore Bruker’s leading commitment to advancing spatial biology with pioneering, best-in-class platforms: the first and only Whole Transcriptome Panel (WTX) on
- [RNA sequencing reveals immune programs that impact glioma treatment effectiveness](https://www.rna-seqblog.com/rna-sequencing-reveals-immune-programs-that-impact-glioma-treatment-effectiveness/) - Researchers find four coordinated gene expression programs in immune cells from glioma tumors, including two that could lead to immunotherapy resistance. Immunotherapy has revolutionized the treatment of many cancers, but brain tumors such as gliomas remain particularly difficult to treat, in part because they potently suppress immune responses. New findings from researchers at the Broad
- [Worm Perturb-Seq - massively parallel whole-animal RNAi and RNA-seq](https://www.rna-seqblog.com/worm-perturb-seq-massively-parallel-whole-animal-rnai-and-rna-seq/) - Understanding how genes control biological processes is a fundamental goal of genetics. One powerful way to study this is by systematically turning genes on or off and measuring how other genes respond. However, doing this in whole living organisms has been a major challenge. Researchers from the University of Massachusetts Chan Medical School have developed a
- [UC San Diego physicist recognized by NAI for innovations in RNA sequencing and computing](https://www.rna-seqblog.com/uc-san-diego-physicist-recognized-by-nai-for-innovations-in-rna-sequencing-and-computing/) - A researchers from the University of California San Diego have been elected senior members of the National Academy of Inventors (NAI) in recognition of their innovative work. Professor of Physics Massimiliano di Ventra is part of NAI’s 2025 class of senior members. This year’s cohort of 162 inventors comes from 64 NAI member institutions around
- [RNA sequencing reveals distinct white matter astrocyte subtypes with potential for brain repair](https://www.rna-seqblog.com/rna-sequencing-reveals-distinct-white-matter-astrocyte-subtypes-with-potential-for-brain-repair/) - Astrocytes, known for their crucial role in supporting neurons and maintaining brain health, have been predominantly studied in gray matter (GM), which is involved in information processing. However, white matter astrocytes, which support long-range neural connections, remain poorly understood. This study fills a major knowledge gap by showing that WM astrocytes are not a uniform
- [Arc Virtual Cell Atlas launches, combining data from over 300 million cells](https://www.rna-seqblog.com/arc-virtual-cell-atlas-launches-combining-data-from-over-300-million-cells/) - Arc Institute today launched the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements, starting with data from over 300 million cells. The initial release of the Atlas is Arc’s first step toward assembling, curating, and generating large-scale cellular data to fuel new insights from AI-driven biological discovery. The Atlas debuts with two foundational
- [University of Maryland researchers use RNA sequencing to study genetic drivers of opioid relapse](https://www.rna-seqblog.com/university-of-maryland-researchers-use-rna-sequencing-to-study-genetic-drivers-of-opioid-relapse/) - University of Maryland experts in genomics and psychology have teamed up to explore new approaches to help those struggling to leave opioid use disorder behind. Najib El-Sayed, a professor of cell biology and molecular genetics, is working with Xuan “Anna” Li, an assistant professor of psychology, to uncover genetic and epigenetic changes—how genes are turned
- [Dovetail Genomics announces early access service for FFPE sample analysis, enhancing cancer research capabilities](https://www.rna-seqblog.com/dovetail-genomics-announces-early-access-service-for-ffpe-sample-analysis-enhancing-cancer-research-capabilities/) - Dovetail Genomics, a leading innovator in genomic solutions, today announces the availability of its early access services for FFPE (Formalin-Fixed Paraffin-Embedded) sample analysis, offering new capabilities for detecting structural variants and profiling RNA in oncology research. This service includes the detection of structural variants using Dovetail’s proprietary linked-read chemistry, along with RNA profiling to validate
- [Endogenous DNA damage at sites of terminated transcripts](https://www.rna-seqblog.com/endogenous-dna-damage-at-sites-of-terminated-transcripts/) - Researchers from Baylor College of Medicine have uncovered a previously unknown way that DNA damage occurs during transcription—when genes are being read to produce RNA. This discovery adds a fourth mechanism to the known ways that transcription can harm DNA, shedding light on potential contributors to cancer, aging, and neurodegenerative diseases. Understanding DNA Damage During Transcription
- [RNA sequencing helps identify a novel gene linked to a rare neurodevelopmental disorder](https://www.rna-seqblog.com/rna-sequencing-helps-identify-a-novel-gene-linked-to-a-rare-neurodevelopmental-disorder/) - A clinical research team from the LKS Faculty of Medicine, the University of Hong Kong (HKUMed), and international genetic researchers led a global research study using multi-omics analysis and identified a novel gene, DDX39B, for a rare disease. Genetic mutations in this gene impact brain function, leading to developmental delay and hypotonia (diminished muscle tone), which are
- [RNA sequencing reveals NEAT1 depletion disrupts autophagy in Rett syndrome](https://www.rna-seqblog.com/rna-sequencing-reveals-neat1-depletion-disrupts-autophagy-in-rett-syndrome/) - Researchers at the Josep Carreras Leukaemia Research Institute revealed a new aspect of Rett Syndrome’s pathogenesis that can lead to new therapeutical approaches in the future. According to the research by Dr. Edilene Siqueira and Dr. Sònia Guil, loss of function of MeCP2 – hallmark of the disease – affects the long non-coding RNA NEAT1,
- [Element is advancing RNA sequencing with AVITI24 to unlock high-dimensional biology](https://www.rna-seqblog.com/element-is-advancing-rna-sequencing-with-aviti24-to-unlock-high-dimensional-biology/) - Element Biosciences, Inc., a company democratizing access to advanced life science solutions, today announced the Innovation Roadmap for AVITI24,™ the world’s first natively paired spatial multiomic solution. The roadmap is being unveiled during an exclusive webinar, titled “High Dimensional Biology Unlocked,” and spearheads Element’s attendance at AGBT 2025 in Marco Island, Florida from February 23-26. The “High
- [Scientists find new biomarker that predicts cancer aggressiveness](https://www.rna-seqblog.com/scientists-find-new-biomarker-that-predicts-cancer-aggressiveness/) - Novel technology enables discovery, which could help predict tumor recurrence Using a new technology and computational method, researchers from Fred Hutch Cancer Center and The University of Texas MD Anderson Cancer Center have uncovered a biomarker capable of accurately predicting outcomes in meningioma brain tumors and breast cancers. In the study, published today in Science, the researchers discovered that the amount
- [Linking single-cell transcriptomes with secretion using SEC-seq](https://www.rna-seqblog.com/linking-single-cell-transcriptomes-with-secretion-using-sec-seq/) - Cells are constantly communicating with each other by releasing proteins and other biomolecules into their surroundings. This process, called secretion, is crucial for many biological functions—whether it’s sending signals to other cells, fighting off infections, or even delivering therapeutic drugs. However, scientists still don’t fully understand the gene activity that drives different secretion patterns in
- [Parse Biosciences launches 5 million cell Evercode WT Penta kit for single-cell sequencing](https://www.rna-seqblog.com/parse-biosciences-launches-5-million-cell-evercode-wt-penta-kit-for-single-cell-sequencing/) - The most scalable and high-resolution single cell solution available Parse Biosciences, the leader in high-throughput single cell sequencing, today announced the launch of Evercode™ WT Penta and Penta 384, the first single cell RNA sequencing kits to profile 5 million cells and 384 samples in a single run. Evercode Penta and Penta 384 will begin
- [RNA sequencing reveals novel antigens from alternative splicing for cancer immunotherapy](https://www.rna-seqblog.com/rna-sequencing-reveals-novel-antigens-from-alternative-splicing-for-cancer-immunotherapy/) - UCSF scientists find a trove of new targets for cancer immunotherapy in cancer’s unique version of RNA splicing. Immune therapy has transformed how cancer is treated, but many tumors continue to evade these treatments, thanks to their resemblance to healthy tissue. Now, researchers at UC San Francisco have found that some cancers, like brain cancer
- [PbImpute - precise zero discrimination and balanced imputation in single-cell RNA sequencing data](https://www.rna-seqblog.com/pbimpute-precise-zero-discrimination-and-balanced-imputation-in-single-cell-rna-sequencing-data/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular diversity by allowing scientists to examine gene expression at an individual cell level. However, a major challenge in scRNA-seq data analysis is the presence of “dropout zeros”—instances where genes appear to have no expression, not because they are truly inactive, but due to technical limitations
- [Uncovering the genetic basis of sugar beet yield and sugar content with RNA sequencing and genome-wide association studies](https://www.rna-seqblog.com/uncovering-the-genetic-basis-of-sugar-beet-yield-and-sugar-content-with-rna-sequencing-and-genome-wide-association-studies/) - Sugar beet (Beta vulgaris) is the world’s second-most important crop for sugar production, trailing only behind sugarcane. While significant advances in breeding have increased sugar content from 4% to 20% over the past century, further progress has been hindered by genetic and environmental limitations. The current bottleneck in sugar beet production underscores the urgent need
- [Single-cell atlas reveals parallels between horse, human pregnancies](https://www.rna-seqblog.com/single-cell-atlas-reveals-parallels-between-horse-human-pregnancies/) - New research has resulted in the first high-resolution molecular picture of the equine endometrium – the inner lining of the uterus – before and after embryo implantation. This picture, or cell atlas, highlights key similarities in immune cells between early human and horse pregnancy, a surprise given the vastly different placentas. Unlike most mammals, implantation
- [Halfpipe - a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives](https://www.rna-seqblog.com/halfpipe-a-tool-for-analyzing-metabolic-labeling-rna-seq-data-to-quantify-rna-half-lives/) - Understanding how long RNA molecules last inside cells is crucial for studying gene expression and cellular function. A new tool called Halfpipe, developed by researchers at the University of Cologne, helps scientists analyze RNA sequencing (RNA-seq) data from metabolic labeling experiments. This tool provides precise measurements of RNA stability, a key factor in gene regulation.
- [Understanding transcription elongation rates with RNA sequencing](https://www.rna-seqblog.com/understanding-transcription-elongation-rates-with-rna-sequencing/) - A research team from Cold Spring Harbor Laboratory has introduced new computational methods to predict transcription elongation rates using nascent RNA sequencing data. Transcription elongation is the process where RNA polymerase moves along DNA, synthesizing RNA. The speed of this process varies depending on different factors within the gene and surrounding regulatory elements. Understanding these variations
- [WCSGNet - a graph neural network approach using weighted cell-specific networks for cell-type annotation in scRNA-seq](https://www.rna-seqblog.com/wcsgnet-a-graph-neural-network-approach-using-weighted-cell-specific-networks-for-cell-type-annotation-in-scrna-seq/) - Single-cell RNA sequencing (scRNA-seq) has become an essential tool for understanding the complexity of cells within tissues. It provides scientists with the ability to examine gene expression at the single-cell level, giving unprecedented insight into cellular heterogeneity. However, one challenge researchers face is the accurate classification of cell types based on gene expression patterns. Traditional
- [Using Transcriptome Sequencing to identify DEGs in response to chemical challenges](https://www.rna-seqblog.com/using-transcriptome-sequencing-to-identify-degs-in-response-to-chemical-challenges-2/) - mRNA sequencing (RNA-seq) is a powerful tool that uses next-generation sequencing technologies to examine a cell’s transcriptome profile. This technology has a wide range of applications, from discovering novel transcripts and alternative splicing to analysing the transcriptome of samples in response to internal and external environmental changes. RNA-seq is also used to identify developmental mechanisms
- [Past, present, and future strategies for detecting and quantifying circular RNA variants](https://www.rna-seqblog.com/past-present-and-future-strategies-for-detecting-and-quantifying-circular-rna-variants/) - Circular RNAs (circRNAs) are a unique class of RNA molecules found in nearly all eukaryotic organisms. Unlike traditional linear RNAs, circRNAs form covalently closed loops through a process called backsplicing, where a segment of RNA is joined end-to-end to create a continuous circular structure. Because their sequence does not align in a straightforward manner with
- [RNA sequencing reveals human sense of touch consists of 16 unique types of nerve cells](https://www.rna-seqblog.com/rna-sequencing-reveals-human-sense-of-touch-consists-of-16-unique-types-of-nerve-cells/) - No less than 16 different types of nerve cells have been identified by scientists in a new study on the human sense of touch. Comparisons between humans, mice and macaques show both similarities and significant differences. The study is a collaboration between researchers at Linköping University, Karolinska Institutet and the University of Pennsylvania. “Our study
- [A refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples](https://www.rna-seqblog.com/a-refined-variant-calling-pipeline-on-rna-seq-data-of-breast-cancer-cell-lines-without-matched-normal-samples/) - RNA sequencing (RNA-seq) is a powerful tool for studying gene expression and identifying mutations in cancer cells. However, one challenge researchers face is detecting true cancer-related mutations when a normal, non-cancerous counterpart for comparison is unavailable. Without a matched-normal sample, distinguishing between common genetic variations and tumor-specific mutations becomes difficult. A recent study led by
- [RNA sequencing powers companion diagnostics in Foundation Medicine and Sumitomo Pharma collaboration for acute leukemia treatment](https://www.rna-seqblog.com/rna-sequencing-powers-companion-diagnostics-in-foundation-medicine-and-sumitomo-pharma-collaboration-for-acute-leukemia-treatment/) - Foundation Medicine, Inc. a genomics company committed to transforming cancer care, today announced a collaboration with Sumitomo Pharma America, Inc. (SMPA) to develop the FoundationOne®Heme platform as a companion diagnostic to identify patients with acute leukemia with a KMT2A rearrangement, also known as mixed lineage leukemia (MLL) rearrangement, or NPM1 mutations for potential treatment with SMPA’s enzomenib (DSP-5336),
- [Upcoming Webinar: Advancing Disease Research with Single-Cell Sequencing](https://www.rna-seqblog.com/advancing-disease-research-with-single-cell-sequencing/) - Join Biocompare and SEQanswers for an informative webinar that showcases how single-cell sequencing is improving the way we study diseases at the cellular level. This webinar features three experts who discuss how this powerful technology is being used to uncover new biological insights...
- [Interactive exploration of multimodal sequencing in major depressive disorder](https://www.rna-seqblog.com/interactive-exploration-of-multimodal-sequencing-in-major-depressive-disorder/) - What is this project? This project is a web application, developed by Anjali Chawla and Malosree Maitra from the labs of Dr. Turecki and Dr. Nagy, for the interactive visualization of ATAC and single-cell RNA sequencing data. This project was supported by the inaugural competition of the Douglas Open Science Awards, in 2022. This web application aims to facilitate the understanding of
- [Massively parallel in vivo Perturb-seq screening](https://www.rna-seqblog.com/massively-parallel-in-vivo-perturb-seq-screening/) - Scientists have identified thousands of genes linked to human health and disease, but understanding exactly how these genes influence biological processes remains a major challenge. Simply knowing a gene is associated with a disease doesn’t tell us how it functions, which cells it affects, or how we might target it for treatment. Perturb-seq, a powerful
- [Fusion transcript detection from short-read RNA-Seq](https://www.rna-seqblog.com/fusion-transcript-detection-from-short-read-rna-seq/) - Genetic mutations are at the root of many diseases, including cancer. One particularly important type of mutation is the formation of fusion proteins, which occur when parts of two different genes combine abnormally. These fusion proteins can drive cancer growth by disrupting normal cellular functions. Identifying these genetic alterations is crucial for understanding cancer progression
- [Exploring the suitability of FFPE samples for single-cell RNA sequencing in breast cancer research](https://www.rna-seqblog.com/exploring-the-suitability-of-ffpe-samples-for-single-cell-rna-sequencing-in-breast-cancer-research/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to study complex tissues, allowing researchers to explore gene expression at the level of individual cells. However, a major challenge in cancer research is obtaining high-quality samples that preserve the diverse cell populations within tumors. Formalin-fixed, paraffin-embedded (FFPE) tissue samples have long been used in pathology, but
- [‘Junk’ RNA segments play role in protein production, cell stress response](https://www.rna-seqblog.com/junk-rna-segments-play-role-in-protein-production-cell-stress-response/) - Scientists have discovered that some tiny segments of RNA thought to be junk instead have a functional role in suppressing production of certain messenger RNAs and appear to help cells respond to oxidative stress. The segments in question are introns, short sequences of a subset of transfer RNAs, the RNA molecules that help guide assembly of amino
- [ELLIPSIS - robust quantification of splicing in scRNA-seq](https://www.rna-seqblog.com/ellipsis-robust-quantification-of-splicing-in-scrna-seq/) - Our genes don’t just work like simple on/off switches—they can be finely tuned through a process called alternative splicing, which allows a single gene to produce multiple versions of a protein. This process is crucial for cell function and is especially important in diseases like cancer, where abnormal splicing can lead to aggressive cell behavior.
- [NYGC Summer Internship](https://www.rna-seqblog.com/nygc-summer-internship/) - Internship Program Description NYGC’s Summer Internship Program is designed to provide students hands-on mentorship from an assigned mentor. You will gain exposure to Laboratory Automation, working in a Next Generation Sequencing wet lab , and the research that we do, as well as have the opportunity to interact with top genomic researchers. In addition, NYGC
- [The importance of data transformation in RNA-Seq preprocessing](https://www.rna-seqblog.com/the-importance-of-data-transformation-in-rna-seq-preprocessing/) - RNA-Seq is crucial for understanding cancer at the genetic level. By analyzing gene expression, it allows researchers to categorize cancers into different molecular subtypes. These subtypes can provide important information about the disease’s behavior, prognosis (how the disease might progress), and potential treatment options. But, there’s a catch—how the RNA-Seq data is prepared (or “preprocessed”)
- [tagtango - an application to compare single-cell annotations](https://www.rna-seqblog.com/tagtango-an-application-to-compare-single-cell-annotations/) - Single-cell analysis has become an essential method for studying the individual cells that make up tissues and organs. Unlike traditional methods, which analyze groups of cells, single-cell technologies allow researchers to examine the unique characteristics of each cell. This detailed approach helps to uncover the complexity of biological systems, like how different types of cells
- [RNA sequencing identifies novel genetic fusion linked to drug resistance in non-small cell lung cancer patient](https://www.rna-seqblog.com/rna-sequencing-identifies-novel-genetic-fusion-linked-to-drug-resistance-in-non-small-cell-lung-cancer-patient/) - In this case report, Jenny L. Wu from Vanderbilt University School of Medicine and Wade T. Iams from Vanderbilt-Ingram Cancer Center describe a rare case of drug resistance in a patient with advanced non-small cell lung cancer (NSCLC). The patient, a 42-year-old man who had never smoked, initially responded well to lorlatinib, a targeted therapy designed to treat
- [What pythons can teach us about intestinal regeneration](https://www.rna-seqblog.com/what-pythons-can-teach-us-about-intestinal-regeneration/) - When we think about how the intestine repairs itself, most research focuses on small pockets of stem cells in structures called crypts. These crypts produce new cells that migrate to the tips of finger-like projections called villi, which help absorb nutrients. But what if there was another way for intestines to regenerate—one that didn’t rely
- [TaDRIM-seq - simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions](https://www.rna-seqblog.com/tadrim-seq-simultaneous-profiling-of-chromatin-associated-rna-at-targeted-dna-loci-and-rna-rna-interactions/) - The study of RNA molecules in our cells has revealed much about how genes are regulated and how different parts of the genome communicate with each other. Eukaryotic genomes (the DNA found in the nucleus of cells) are transcribed into many different types of RNA, which play crucial roles in controlling gene expression. Some of
- [Simpler, more affordable new single-cell solution for any lab](https://www.rna-seqblog.com/simpler-more-affordable-new-single-cell-solution-for-any-lab/) - To help make single-cell sequencing more accessible, Illumina is excited to introduce a new easy-to-use, affordable solution that readily scales to experiments of any size. More Cells, More Discoveries, Same Budget Fast, Accurate, and Cost-Effective Single-cell Sequencing with Illumina Once samples are prepared, libraries can be loaded onto flow cells and sequenced. While libraries are
- [Webinar Tutorial: How to Easily Perform Effective scRNA-Seq Cell-Type Predictions](https://www.rna-seqblog.com/webinar-tutorial-how-to-easily-perform-effective-scrna-seq-cell-type-predictions/) - Cell-type prediction is one of the most challenging steps in single-cell RNA sequencing (scRNA-Seq) analysis, often requiring already annotated references. Finding suitable references is time-consuming, and relying on a single source may compromise accuracy. Want to learn more? Register for our free, one-hour webinar on Thursday, February 13th at 9:30 and 18:30 CET. In this
- [Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)](https://www.rna-seqblog.com/single-cell-rna-seq-data-analysis-a-practical-introduction-march-17-19-2025-in-berlin-germany/) - Single-Cell RNA-Seq Data Analysis: A Practical Introduction Master the tools and techniques to confidently analyze single-cell RNA-seq data and gain new insights into complex biological systems When? March 17-19, 2025 Where? Berlin, Germany Link? Website In a nutshell Explore sequencing technologies for single-cell analysis Process QC and analyze single-cell RNA-seq data Learn how to identify and annotate cell clusters Discover how to
- [New method enhances understanding of tissue architecture using spatial transcriptomics](https://www.rna-seqblog.com/new-method-enhances-understanding-of-tissue-architecture-using-spatial-transcriptomics/) - Spatial transcriptomics (ST) is an innovative technique that allows researchers to study gene activity within the context of tissue architecture. This technology helps scientists understand how cells interact and form complex structures within tissues. However, a challenge has emerged with some of the current ST technologies—many operate at low resolution, which means that a single
- [RNA sequencing reveals immune cell interactions driving aggressive brain tumors](https://www.rna-seqblog.com/rna-sequencing-reveals-immune-cell-interactions-driving-aggressive-brain-tumors/) - A type of aggressive, treatment-resistant brain tumor has a distinct population of immune cells that support its growth, according to new research led by investigators at the Johns Hopkins Kimmel Cancer Center Bloomberg~Kimmel Institute for Cancer Immunotherapy and the Johns Hopkins University School of Medicine. Searching for subtypes of immune cells seen only in the most serious, grade 4
- [ScRecover - discriminating true and false zeros in single-cell RNA-seq data for imputation](https://www.rna-seqblog.com/screcover-discriminating-true-and-false-zeros-in-single-cell-rna-seq-data-for-imputation/) - Researchers analyze the expression of genes in individual cells to understand cellular functions and behaviors. However, one challenge researchers face with scRNA-seq data is the presence of many “zero” values—indicating either that a gene is not being expressed in a cell or that the data was not properly detected due to technical issues, like a
- [RNA sequencing reveals immune dysregulation and tumor diversity in Waldenstrom’s macroglobulinemia](https://www.rna-seqblog.com/rna-sequencing-reveals-immune-dysregulation-and-tumor-diversity-in-waldenstroms-macroglobulinemia/) - Waldenstrom’s Macroglobulinemia (WM) is a rare type of blood cancer that affects the bone marrow and causes the overproduction of IgM antibodies. It often starts as an asymptomatic condition called Asymptomatic Waldenstrom’s Macroglobulinemia (AWM) before progressing into full-blown cancer. Scientists at the Dana-Farber Cancer Institute recently conducted a study using single-cell RNA sequencing to better
- [Most engineered human cells created for studying disease](https://www.rna-seqblog.com/most-engineered-human-cells-created-for-studying-disease/) - The most complex engineering of human cell lines ever has been achieved by scientists, revealing that our genomes are more resilient to significant structural changes than was previously thought. Researchers from the Wellcome Sanger Institute, Imperial College London, Harvard University in the US and their collaborators used CRISPR prime editing to create multiple versions of
- [SIMO - spatial integration of multi-omics single-cell data](https://www.rna-seqblog.com/simo-spatial-integration-of-multi-omics-single-cell-data/) - Understanding how cells function within tissues requires more than just studying individual molecular layers like gene expression or DNA modifications. Scientists need a way to integrate multiple layers of biological data while preserving the spatial context of cells within their environment. However, current technologies in spatial and single-cell omics sequencing have technical limitations that make
- [AlidaBio Launches EpiPlex™ Platform to Advance Epitranscriptomic Research](https://www.rna-seqblog.com/alidabio-launches-epiplex-platform-to-advance-epitranscriptomic-research/) - Alida Biosciences (AlidaBio), an innovator in epigenomic research tools, today announced the full commercial launch of its EpiPlex™ platform, the first to concurrently detect and quantify multiple RNA modifications by short-read sequencing in addition to providing gene expression data. The platform, which pairs the EpiPlex™ RNA Reagent Kit and the EpiScout™ Analysis Suite, provides a
- [RNA sequencing reveals unique endothelial cell signatures in the pancreatic islets](https://www.rna-seqblog.com/rna-sequencing-reveals-unique-endothelial-cell-signatures-in-the-pancreatic-islets/) - Islet-specific endothelial cells (red) form specialized blood vessels that support and nourish pancreatic islets (green). Credit: Dr. Ge Li The distinct population of endothelial cells that line blood vessels in the insulin-producing “islets” of the human pancreas have been notoriously difficult to study, but Weill Cornell Medicine investigators have now succeeded in comprehensively detailing the
- [IMMCG scientist earns NSF grant to advance glycan sequencing technology](https://www.rna-seqblog.com/immcg-scientist-earns-nsf-grant-to-advance-glycan-sequencing-technology/) - “Think of it as upgrading from a manual map-making process to a GPS system — it’s faster, more precise and easier to use,” Chiang added. The new technology helps scientists better understand how these sugars affect the safety and effectiveness of medicines, which could lead to improved drug development and new treatments for diseases. “Dr.
- [PERFF-seq - transcript-specific enrichment enables profiling rare cell states via scRNA-seq](https://www.rna-seqblog.com/perff-seq-transcript-specific-enrichment-enables-profiling-rare-cell-states-via-scrna-seq/) - In biology, each cell tells its own unique story—a narrative shaped by its gene expression profile and molecular interactions. Yet, uncovering these individual narratives within a sea of cellular diversity has long been a daunting task. Enter single-cell genomics—a revolutionary technology that promises to unravel the complex web of cellular heterogeneity with unprecedented precision. However, traditional
- [St. Jude researchers create tool incorporating transcriptome size to improve RNA-seq analysis](https://www.rna-seqblog.com/st-jude-researchers-create-tool-incorporating-transcriptome-size-to-improve-rna-seq-analysis/) - Scientists at St. Jude Children’s Research Hospital created a computational tool that uses the number of RNA molecules per cell to improve gene expression analysis. Researchers studying gene expression have access to vast amounts of data from cells or tissues. This is thanks to advances in bulk and single-cell RNA-sequencing (RNA-seq) technologies which can capture every
- [KAIST discovers molecular switch that reverses cancerous transformation at the critical moment of transition](https://www.rna-seqblog.com/kaist-discovers-molecular-switch-that-reverses-cancerous-transformation-at-the-critical-moment-of-transition/) - Professor Kwang-Hyun Cho’s research team has recently been highlighted for their work on developing an original technology for cancer reversal treatment that does not kill cancer cells but only changes their characteristics to reverse them to a state similar to normal cells. This time, they have succeeded in revealing for the first time that a molecular
- [scSMD - a deep learning method for accurate clustering of single cells based on auto-encoder](https://www.rna-seqblog.com/scsmd-a-deep-learning-method-for-accurate-clustering-of-single-cells-based-on-auto-encoder/) - Single-cell RNA sequencing (scRNA-seq) has revolutionized the way scientists study cells. Unlike traditional sequencing methods that analyze a mix of many cells, scRNA-seq allows researchers to examine gene expression at an individual cell level. This breakthrough has helped scientists better understand cellular diversity, developmental biology, and disease mechanisms. However, analyzing scRNA-seq data is challenging because
- [RiboTIE - deep learning to decode sites of RNA translation in normal and cancerous tissues](https://www.rna-seqblog.com/ribotie-deep-learning-to-decode-sites-of-rna-translation-in-normal-and-cancerous-tissues/) - RNA translation is one of the most essential processes in biology—it’s how our cells take the genetic instructions in RNA and use them to build proteins. This process is crucial for life and plays a major role in human health, including diseases like cancer. However, studying RNA translation in detail has been challenging due to
- [SeqTagger - a rapid and accurate tool to demultiplex direct RNA nanopore sequencing datasets](https://www.rna-seqblog.com/seqtagger-a-rapid-and-accurate-tool-to-demultiplex-direct-rna-nanopore-sequencing-datasets/) - Nanopore direct RNA sequencing (DRS) is an advanced technology that allows scientists to study RNA molecules directly, without converting them into cDNA (complementary DNA) first. This direct approach provides detailed insights into RNA, including native modifications, which are important for understanding gene expression and regulation. However, one challenge with this technique is the lack of
- [New sequencing approach resolves the genetic complexity of a rare Mendelian condition](https://www.rna-seqblog.com/new-sequencing-approach-resolves-the-genetic-complexity-of-a-rare-mendelian-condition/) - PacBio, a leader in high-quality, long-read sequencing, is proud to announce its critical role in a study to be published in Nature Genetics. The study, titled Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition, showcases how researchers leveraged PacBio’s advanced sequencing solutions, including the synchronized Fiber-seq and Kinnex (formerly MAS-seq) multiomic approach,
- [A single-cell RNA sequencing dataset of peripheral blood cells in long COVID patients on herbal therapy](https://www.rna-seqblog.com/a-single-cell-rna-sequencing-dataset-of-peripheral-blood-cells-in-long-covid-patients-on-herbal-therapy/) - Since the COVID-19 pandemic, many people have continued to experience lingering symptoms, a condition known as long COVID. Some of the most common issues include fatigue, brain fog, and breathing difficulties, making daily life challenging for many. As researchers work to understand and treat long COVID, interest in complementary and alternative medicine—such as herbal remedies—has
- [Genialis and Debiopharm expand collaboration to advance RNA biomarkers](https://www.rna-seqblog.com/genialis-and-debiopharm-expand-collaboration-to-advance-rna-biomarkers/) - Genialis, the RNA biomarker company, today announced an extension of its collaboration with Debiopharm, a Swiss-based global biopharmaceutical company, to develop a predictive biomarker for WEE1-targeted therapy. This extension builds on a 2024 agreement to define and discover biomarkers within the DNA damage response (DDR) biological space to predict the clinical benefit of one or more drugs
- [Single-cell RNA and mass cytometry reveal immune cell trajectories across the lifespan](https://www.rna-seqblog.com/single-cell-rna-and-mass-cytometry-reveal-immune-cell-trajectories-across-the-lifespan/) - As we age, our immune system changes. These changes are crucial for understanding how our body responds to infections, diseases, and even how we age itself. However, we didn’t fully understand how our immune system evolves over a lifetime—until now. Researchers at the Shanghai Cancer Institute set out to fill in this gap. The researchers looked
- [Correcting scale distortion in RNA sequencing data](https://www.rna-seqblog.com/correcting-scale-distortion-in-rna-sequencing-data/) - RNA sequencing (RNA-seq) is a powerful tool used to measure gene expression in biological samples, helping researchers understand how genes contribute to various diseases. It has become an essential method in studying the genetic basis of diseases, particularly in large-scale population studies like the Cancer Genome Atlas (TCGA), Stand Up 2 Cancer (SU2C), and the
- [RNA sequencing reveals T-cell potential for future liver cancer immunotherapy](https://www.rna-seqblog.com/rna-sequencing-reveals-t-cell-potential-for-future-liver-cancer-immunotherapy/) - T-cells from the liver and lymph nodes show promising potential for future treatments of liver cancer, according to a new study. Researchers at Karolinska Institutet have investigated how immune cells react to tumor-specific antigens in the complex environment surrounding liver cancer. Liver cancer, or hepatocellular carcinoma (HCC), is a disease characterized by a unique and
- [Transforming Pipeline Outputs into Biological Insights](https://www.rna-seqblog.com/transforming-pipeline-outputs-into-biological-insights/) - Best Practices for Curio Seeker Data Analysis DATE: January 30, 2025 TIME: 1:00 pm EDT / 10:00 am PDT Sequencing-based spatial transcriptomics technologies have introduced exciting new data and new challenges in data analysis. While these data share similarities with traditional single-cell RNAseq data, including feature-by-pixel expression matrices, they also present new complexities. Each pixel can
- [Beyond genomics: using RNA-seq from dried blood spots to unlock the clinical relevance of splicing variation in a diagnostic setting](https://www.rna-seqblog.com/beyond-genomics-using-rna-seq-from-dried-blood-spots-to-unlock-the-clinical-relevance-of-splicing-variation-in-a-diagnostic-setting/) - Researchers at CENTOGENE GmbH aimed to assess the clinical relevance of splicing variants by analyzing the gene expression of blood samples using RNA sequencing (RNA-seq). These variants, which are mutations that affect how genes are spliced during the process of protein production, are important because they can alter normal cellular functions and contribute to various
- [Multimodal learning for mapping genotype–phenotype dynamics](https://www.rna-seqblog.com/multimodal-learning-for-mapping-genotype-phenotype-dynamics/) - One of the biggest questions in biology is how our genes control complex traits or phenotypes—things like physical characteristics, disease resistance, or behavior. Genes don’t act alone in determining these traits; instead, they interact in complex ways, with each gene contributing to the overall picture. Scientists have been working hard to understand these interactions better,
- [Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview](https://www.rna-seqblog.com/single-cell-rna-sequencing-analysis-a-step-by-step-overview/) - Single-cell RNA sequencing (scRNA-seq) has opened doors to uncovering the complexities of cellular diversity and understanding how different cells function, interact, and respond to their environment—all at an unparalleled level of detail. What Makes Single-Cell RNA Sequencing Special? Traditional RNA sequencing examines the average gene expression across a group of cells. While useful, this method
- [RNA sequencing reveals soybean's genetic defense against nematode pathogens](https://www.rna-seqblog.com/rna-sequencing-reveals-soybeans-genetic-defense-against-nematode-pathogens/) - “Fight-or-flight” is not an option for plants, unfortunately, when it comes to pathogen attacks. Instead, plants opt for “do-or-die.” A deeper insight into the genetic mechanisms that enable plants to resist pathogen infections has equipped researchers with tools to tackle the most devastating pathogens in agriculture. Using advanced RNA sequencing, researchers have recently uncovered how varieties
- [Intermediate RNA-Seq Analysis Using R](https://www.rna-seqblog.com/intermediate-rna-seq-analysis-using-r/) - Dates – February 20, 2025 Time – 9:00am-12:00pm PST Location – Online RNA-seq is a powerful tool to interrogate cellular functions. In this intermediate workshop, you’ll learn the skills you need to get the most out of your RNA-seq data through analysis in R. By the end of the workshop, you’ll know how to: Go
- [RNA sequencing sheds light on immune cell dynamics in the gut](https://www.rna-seqblog.com/rna-sequencing-sheds-light-on-immune-cell-dynamics-in-the-gut/) - Scientists show how a special group of T cells travels through the small intestine to combat pathogens An image produced through Xenium analysis of mouse small intestines. Protruding “villi” stick up from the lining of the small intestine. Valley-like “crypts” fill in the gaps. Image from the Reina Lab, La Jolla Institute for Immunology Your
- [dscHi-C - a high-throughput single-cell Hi-C approach using droplet microfluidics](https://www.rna-seqblog.com/dschi-c-a-high-throughput-single-cell-hi-c-approach-using-droplet-microfluidics/) - Three-dimensional (3D) structure of DNA in our cells changes across different tissues. The study of these chromatin structures—how DNA is packaged within the cell—has revealed important insights into how cells function. However, previous methods have had limitations, especially when it comes to studying a large number of cells at once. Researchers at the Peking University
- [Integrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patients](https://www.rna-seqblog.com/integrated-cancer-cell-specific-single-cell-rna-seq-datasets-of-immune-checkpoint-blockade-treated-patients/) - Immune checkpoint blockade (ICB) therapies represent a groundbreaking approach in oncology, offering the potential to harness the immune system to effectively target and eliminate cancer cells. While the clinical success of ICB therapies is evident, their efficacy varies significantly across different patients and cancer types, prompting a need for a deeper understanding of the underlying
- [scGFT - single-cell RNA-seq data augmentation using generative Fourier transformer](https://www.rna-seqblog.com/scgft-single-cell-rna-seq-data-augmentation-using-generative-fourier-transformer/) - Single-cell RNA sequencing (scRNA-seq) offers an unprecedented opportunity to understand the cellular complexity and heterogeneity that defines both healthy and diseased states. By measuring the gene expression profiles of individual cells, researchers can uncover the complex workings of different cell types and their roles in broader biological systems. However, the full potential of scRNA-seq is
- [Automated laser-assisted single-cell sorting for cell functional and RNA sequencing](https://www.rna-seqblog.com/automated-laser-assisted-single-cell-sorting-for-cell-functional-and-rna-sequencing/) - The world of cellular research moves quickly, and scientists are always looking for new methods to gain more precise insights into cell function and behavior. One critical aspect of this research involves sorting single cells for downstream analysis, such as RNA sequencing, to explore cellular heterogeneity and uncover functional characteristics. Traditional techniques like manual micromanipulation
- [Moscot - multi-omics single-cell optimal transport](https://www.rna-seqblog.com/moscot-multi-omics-single-cell-optimal-transport/) - The world of genomics has rapidly advanced in recent years, with single-cell technologies enabling scientists to study millions of individual cells. These techniques allow us to understand how cells function and interact with one another in various tissues, which is crucial for understanding everything from development to disease. However, there are challenges in capturing the
- [Profiling rare C-to-U editing events via direct RNA sequencing](https://www.rna-seqblog.com/profiling-rare-c-to-u-editing-events-via-direct-rna-sequencing/) - RNA editing is a biological process where RNA molecules are chemically altered after being transcribed from DNA. In mammals, two key types of editing occur: adenosine (A) is changed to inosine (I), and cytosine (C) is changed to uracil (U). These modifications are facilitated by enzyme families called ADAR and APOBEC, respectively. Understanding RNA editing
- [Sequencing technologies to measure translation in single cells](https://www.rna-seqblog.com/sequencing-technologies-to-measure-translation-in-single-cells/) - Translation is a critical biological process where cells build proteins based on the genetic instructions found in messenger RNA (mRNA). This process, while essential, is also very energy-intensive and tightly regulated, ensuring that proteins are synthesized at the right time, in the right amounts, and at the right location. Over the years, researchers have developed
- [The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer](https://www.rna-seqblog.com/the-spatially-informed-mfishseq-assay-resolves-biomarker-discordance-and-predicts-treatment-response-in-breast-cancer/) - Breast cancer is notoriously complex, making it challenging to predict how patients will respond to treatments. Traditional tests often fall short in capturing this complexity, leading to inconsistent results and less effective treatment strategies. Researchers at the Comenius University Science Park have developed a new tool called mFISHseq that offers a more accurate and detailed
- [Chronocell - trajectory inference from single-cell genomics data with a process time model](https://www.rna-seqblog.com/chronocell-trajectory-inference-from-single-cell-genomics-data-with-a-process-time-model/) - Understanding how cells function and change over time is a cornerstone of biology. However, capturing dynamic processes in single cells can be challenging, especially when experiments provide only “snapshots” of gene expression across a diverse population of cells at one moment in time. Single-cell transcriptomics, which measures gene activity in individual cells, has been used
- [scRICA - An R package for multiple-sample single-cell RNA-seq data integrative comparative analysis](https://www.rna-seqblog.com/scrica-an-r-package-for-multiple-sample-single-cell-rna-seq-data-integrative-comparative-analysis/) - Single-cell RNA sequencing (scRNA-seq) is a powerful technology that allows scientists to study gene activity in individual cells. This level of detail can reveal new insights into biology, such as how different cell types function or how diseases develop at the cellular level. However, as scRNA-seq studies grow to include more cells and more diverse
- [UDA-seq - universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing](https://www.rna-seqblog.com/uda-seq-universal-droplet-microfluidics-based-combinatorial-indexing-for-massive-scale-multimodal-single-cell-sequencing/) - Single-cell sequencing is a powerful tool in biology, allowing scientists to study individual cells in great detail. This method has opened up new ways to understand how different cells in a tissue behave, interact, and contribute to diseases like cancer. One of the challenges with single-cell analysis, though, is that many methods are either costly
- [Insights from RNA sequencing reveal how HIV-1 hijacks host cell machinery](https://www.rna-seqblog.com/insights-from-rna-sequencing-reveal-how-hiv-1-hijacks-host-cell-machinery/) - A team of scientists at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg and the University of Regensburg has unveiled insights into how HIV-1, the virus responsible for AIDS, skillfully hijacks cellular machinery for its own survival. By dissecting the molecular interplay between the virus and its host, the researchers identified novel strategies
- [Smart-seq+5′ sheds light on transcriptional regulation during early mammalian development](https://www.rna-seqblog.com/smart-seq5′-sheds-light-on-transcriptional-regulation-during-early-mammalian-development/) - The transcriptional activation of the embryonic genome (EGA) is a key event in early development, marking the transition from maternal control to the embryo’s own genetic regulation. However, the details of how this process works and how it varies across different species are still not fully understood. To explore this, researchers at Helmholtz Munich developed
- [New partnership integrates transcriptome genomic data from Scipher's PrismRA Test into OMNY's EMR network](https://www.rna-seqblog.com/new-partnership-integrates-transcriptome-genomic-data-from-sciphers-prismra-test-into-omnys-emr-network/) - OMNY Health, the leading healthcare ecosystem for compliant real-world data insights at scale, and Scipher Medicine, which has the world’s largest immunology clinico-transcriptomics data set and is focused on advancing precision medicine with proprietary AI network biology solutions, today announced a partnership to advance precision medicine efforts for immunology. This collaboration marks a significant leap forward
- [BTEP Course - Introduction to Bulk RNA Sequencing Analysis](https://www.rna-seqblog.com/btep-course-introduction-to-bulk-rna-sequencing-analysis/) - When: February 13, 2025 – March 13, 2025 This course series provides hands-on experience in analyzing bulk RNA sequencing data. Participants will be guided through exercises using student accounts furnished by Biowulf, the NIH Unix-based high performance computing system, which has approximately 1,000 scientific softwares installed including those for RNA sequencing analysis. At the end
- [miTEA-HiRes - inferring single-cell and spatial microRNA activity from transcriptomics data](https://www.rna-seqblog.com/mitea-hires-inferring-single-cell-and-spatial-microrna-activity-from-transcriptomics-data/) - MicroRNAs (miRNAs) are small molecules that play a key role in regulating gene expression, affecting which proteins and long non-coding RNAs (lncRNAs) are produced in cells. Their activity can vary across different cell types and systems, influencing how cells function in both healthy and disease states. When miRNAs are active, they typically reduce the levels
- [AI-Powered MISO tool advances transcriptomics to detect cancer at the cellular level](https://www.rna-seqblog.com/ai-powered-miso-tool-advances-transcriptomics-to-detect-cancer-at-the-cellular-level/) - A new artificial intelligence-powered tool called MISO (Multi-modal Spatial Omics) can detect cell-level characteristics of cancer by looking at data from extremely small pieces of tissue—some as small as 400 square micrometers, equivalent to the width of five human hairs. Constructed by researchers at the Perelman School of Medicine at the University of Pennsylvania, the tool analyzes reams of
- [singleDeep - analysis of scRNA-Seq data training deep neural networks for predicting sample phenotypes](https://www.rna-seqblog.com/singledeep-analysis-of-scrna-seq-data-training-deep-neural-networks-for-predicting-sample-phenotypes/) - Recent advancements in single-cell RNA sequencing (scRNA-Seq) have transformed how scientists study individual cells, providing unprecedented insights into the molecular mechanisms underlying various diseases and conditions. By analyzing gene expression at the single-cell level, researchers can explore how different cell types function, how they respond to stimuli, and how diseases manifest. However, analyzing these vast
- [TRIAGE - an R package for regulatory gene analysis](https://www.rna-seqblog.com/triage-an-r-package-for-regulatory-gene-analysis/) - When it comes to understanding how cells develop, function, and respond to disease, regulatory genes are the unsung heroes. These genes control the activity of other genes, shaping a cell’s identity and guiding its role in the body. But identifying and studying these regulatory genes can be tricky, especially when using traditional RNA sequencing (RNA-seq)
- [RNA sequencing reveals key mechanism behind Huntington’s disease and potential therapeutic strategies](https://www.rna-seqblog.com/rna-sequencing-reveals-key-mechanism-behind-huntingtons-disease-and-potential-therapeutic-strategies/) - Researchers studying brain cells from Huntington’s patients show that the mutation, which changes over decades, becomes toxic only later in life. Scientists at the Broad Institute of MIT and Harvard, Harvard Medical School, and McLean Hospital have discovered a surprising mechanism by which the inherited genetic mutation known to cause Huntington’s disease leads to the
- [Fermentation Engineer/Bacterial RNA Specialist](https://www.rna-seqblog.com/fermentation-engineer-bacterial-rna-specialist/) - Job Description: We are a team of computational and experimental scientists and seeking a highly motivated and talented Bacterial RNA Specialist to join an international and collaborative team in an outstanding and competitive scientific environment. Responsibilities: The successful candidate will decipher regulatory mechanisms in bacteria by combining global genome-wide methods (RNAseq) with the molecular analysis.
- [gneSeqCOO - a novel method for classifying diffuse large B-cell lymphoma cell of origin based on bulk tumor RNA sequencing profiles](https://www.rna-seqblog.com/gneseqcoo-a-novel-method-for-classifying-diffuse-large-b-cell-lymphoma-cell-of-origin-based-on-bulk-tumor-rna-sequencing-profiles/) - Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, and while treatable, its outcomes can vary widely depending on the molecular characteristics of the tumor. To better predict outcomes and guide treatment, researchers classify DLBCL into subtypes based on its “cell of origin” (COO). These subtypes offer insights into the tumor’s
- [Researchers will use RNA sequencing to study gene regulation in Prader-Willi Syndrome](https://www.rna-seqblog.com/researchers-will-use-rna-sequencing-to-study-gene-regulation-in-prader-willi-syndrome/) - In most cases, Prader-Willi Syndrome is caused by a random genetic error — a section of the paternal copy of chromosome 15 is deleted. Several genes are in the missing section, and it’s not yet known how their loss contributes to PWS symptoms. Prader-Willi syndrome, a genetic condition that affects 350,000 people worldwide, causes chronic
- [chILD atlas - an open-source single-nucleus RNA-seq lung tissue atlas to create targeted treatments for interstitial lung disease](https://www.rna-seqblog.com/child-atlas-an-open-source-single-nucleus-rna-seq-lung-tissue-atlas-to-create-targeted-treatments-for-interstitial-lung-disease/) - John Kennedy, MD, MSc, remembers the relative simplicity of his first genetic mapping project. In a Harvard Medical School lab, he helped map a gene for the neurological disease mucolipidosis type IV in less than a year. “I was fresh out of college. I thought with the global momentum of the Human Genome Project, we were going to
- [SNIP - single-nuclei isolation and RNA sequencing of parasitic nematodes](https://www.rna-seqblog.com/snip-single-nuclei-isolation-and-rna-sequencing-of-parasitic-nematodes/) - Single-cell and single-nucleus transcriptomics have greatly advanced our understanding of how individual cells and tissues function in both healthy and diseased states. This technology allows scientists to study gene expression at the level of individual cells, giving them a more detailed picture of how diseases develop and how organisms function overall. While this approach has
- [New single-cell RNA sequencing study adds important insights into complex childhood cancer](https://www.rna-seqblog.com/new-single-cell-rna-sequencing-study-adds-important-insights-into-complex-childhood-cancer/) - Researchers in the group of Associate Professor Ninib Baryawno, Department of Women’s and Children’s Health, KI, have made significant strides in the fight against pediatric cancer by studying tumors of the nervous system, particularly neuroblastoma. The study is published in Cancer Research, the journal of the American Association for Cancer. Neuroblastoma, a heterogeneous and complex
- [Semblans - automated assembly and processing of RNA-Seq data](https://www.rna-seqblog.com/semblans-automated-assembly-and-processing-of-rna-seq-data/) - With the rapid growth of RNA sequencing (RNA-seq) technologies, researchers now have access to vast amounts of short-read sequence data, enabling them to study gene expression in greater detail. However, analyzing this data to construct an accurate transcriptome – the complete set of RNA molecules in a cell – can be a challenging and time-consuming
- [Benchmarking cross-species single-cell RNA-seq data integration methods](https://www.rna-seqblog.com/benchmarking-cross-species-single-cell-rna-seq-data-integration-methods/) - The study of how different cell types evolved across species is key to understanding life’s diversity and unlocking the secrets of biology. One powerful tool for this is single-cell RNA sequencing (scRNA-seq), which allows scientists to examine gene expression in individual cells. By applying this technology across species, researchers can compare and contrast cellular function
- [Canopy2 - tumor phylogeny inference by bulk DNA and single-cell RNA sequencing](https://www.rna-seqblog.com/canopy2-tumor-phylogeny-inference-by-bulk-dna-and-single-cell-rna-sequencing/) - Tumors are not made up of just one type of cell; instead, they consist of a mix of cells that vary genetically and functionally. This diversity in tumor cells, known as heterogeneity, is a key factor in why cancer treatments can sometimes fail, especially when cells evolve to resist drugs. Understanding this complexity can help
- [tomoseqr - spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography](https://www.rna-seqblog.com/tomoseqr-spatial-reconstruction-and-visualization-of-3d-gene-expression-patterns-based-on-rna-tomography/) - RNA tomography is an innovative technique used to map gene expression patterns in three dimensions (3D). Imagine trying to get a detailed picture of how genes are active within the cells of a tissue sample, not just from a flat 2D view, but from all angles—this is what RNA tomography aims to do. It provides
- [RNA sequencing identifies genetic drivers of cancer metastasis](https://www.rna-seqblog.com/rna-sequencing-identifies-genetic-drivers-of-cancer-metastasis/) - Cancer metastasis—the spread of cancer to other organs—is the leading cause of death among cancer patients. Researchers have now uncovered a “genetic signature” of 177 genes shared across multiple cancer types that drives this deadly process. “Through our research, we have uncovered critical pan-cancer drivers of metastasis that not only enhance our understanding of cancer
- [BioBam presents OmicsBox 3.4, including CellKB’s advanced cell-type annotation](https://www.rna-seqblog.com/biobam-presents-omicsbox-3-4-including-cellkbs-advanced-cell-type-annotation/) - BioBam, a leading bioinformatics solutions provider, proudly presents OmicsBox Version 3.4 at the San Diego Plant and Animal Genome Conference (PAG 32). This latest release introduces a range of enhancements designed to address the evolving needs of modern genomics and transcriptomics research. A key highlight of OmicsBox 3.4 is the integration of CellKB, a robust
- [St. Jude scientists create scalable solution for analyzing single-cell data](https://www.rna-seqblog.com/st-jude-scientists-create-scalable-solution-for-analyzing-single-cell-data/) - Scientists at St. Jude Children’s Research Hospital used machine learning and graphics processing power to improve analysis of large single-cell gene expression datasets. Researchers have amassed vast single-cell gene expression databases to understand how the smallest details impact human biology. However, current analysis methods struggle with the large volume of data and, as a result, produce
- [A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing](https://www.rna-seqblog.com/a-conserved-graft-formation-process-in-norway-spruce-and-arabidopsis-identifies-the-pat-gene-family-as-central-regulators-of-wound-healing/) - Abstract This study developed a micrografting method for conifers, enabling efficient grafting between closely and distantly related species. Graft junctions rapidly formed vascular connections and activated thousands of genes, including those involved in auxin signalling and cell wall modification. Comparison of conifer grafting with Arabidopsis grafting revealed shared gene activation patterns related to vascular differentiation.
- [cgSHAPE-seq - a new method to uncover the secrets of viral RNA structures](https://www.rna-seqblog.com/cgshape-seq-a-new-method-to-uncover-the-secrets-of-viral-rna-structures/) - One of the most effective ways to combat RNA viruses like SARS-CoV-2 is to target the unique structures in their RNA. These viruses rely on highly organized regions in their RNA, called untranslated regions (UTRs), to control essential processes like replication and protein production. Understanding these structures at a detailed level is crucial, and researchers
- [PERFF-seq - transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing](https://www.rna-seqblog.com/perff-seq-transcript-specific-enrichment-enables-profiling-of-rare-cell-states-via-single-cell-rna-sequencing/) - Recent advances in genomics have made it possible to understand the diverse states of individual cells, leading to breakthroughs in fields like immunology and cancer research. Single-cell RNA sequencing (scRNA-seq) has been at the forefront of these efforts, offering a way to study gene expression in single cells and identify rare populations of cells with
- [NASA's GeneLab for Colleges and Universities (GL4U) launches on-demand intro and RNAseq courses](https://www.rna-seqblog.com/nasas-genelab-for-colleges-and-universities-gl4u-launches-on-demand-intro-and-rnaseq-courses/) - NASA GeneLab’s GeneLab for Colleges and Universities (GL4U) initiative is revolutionizing how students and researchers access space biology education. Now, with the launch of its On-Demand Intro and RNAseq Courses, GL4U offers flexible, self-paced learning opportunities designed to empower the next generation of scientists. The Introductory Course provides an overview of NASA’s Science Mission Directorate, Space Biology, Open
- [Tempus announces a collaboration with Genialis to develop RNA-based biomarker algorithms](https://www.rna-seqblog.com/tempus-announces-a-collaboration-with-genialis-to-develop-rna-based-biomarker-algorithms/) - Tempus AI, a technology company leading the adoption of AI to advance precision medicine and patient care, today announced a collaboration with Genialis, the RNA-biomarker company. The multi-year agreement allows Genialis to leverage Tempus’ multimodal dataset to develop new RNA-based algorithms across cancer types. Clinical care for cancer patients is hindered by insufficient biomarkers that
- [Allen Institute scientists develop ‘suspended animation’ technique for blood draws that will aid research for underserved populations](https://www.rna-seqblog.com/allen-institute-scientists-develop-suspended-animation-technique-for-blood-draws-that-will-aid-research-for-underserved-populations/) - A new approach that keeps blood cells alive in deep freeze promises to expand reach of cutting-edge single-cell technologies to underserved populations. Your blood is a delicate mixture. Researchers and clinicians often use blood to learn what’s going on inside our bodies, in part because siphoning off a tube of blood is easier and less painful than taking biopsies of an internal
- [Borzoi - predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation](https://www.rna-seqblog.com/borzoi-predicting-rna-seq-coverage-from-dna-sequence-as-a-unifying-model-of-gene-regulation/) - In recent years, machine learning has become an essential tool in understanding the complexities of genetics, particularly in interpreting the impact of genetic variants. One exciting development in this field is the introduction of Borzoi, a new machine-learning model developed at Calico Life Sciences designed to predict RNA expression profiles from DNA sequences, a task
- [In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)](https://www.rna-seqblog.com/in-person-workshop-bulk-rna-seq-data-analysis-workshop-march-24-27-2025-in-halle-germany/) - RNA-Seq Data Analysis Workshop Quality Control, Read Mapping, Visualization and Downstream Analyses When? March 24 - 27, 2025 Where? Halle (Saale), Germany Link? Website Advance your research. Understand RNA-Seq analyses challenges and solve them yourself. In a nutshell Learn the essential computing skills for NGS bioinformatics Understand NGS analysis algorithms (e.g. read alignment) and data formats Use bioinformatics tools for handling
- [RNA sequencing unveils TTP's role in regulating allergic inflammation in basophils](https://www.rna-seqblog.com/rna-sequencing-unveils-ttps-role-in-regulating-allergic-inflammation-in-basophils/) - Inflammation is a crucial part of the body’s defense mechanism, playing a key role in fighting infections and repairing tissue damage. Basophils, a type of immune cell that makes up less than 1% of white blood cells, have recently emerged as critical players in triggering allergic responses by releasing pro-inflammatory cytokines like IL-4. Despite the
- [Optimized methods for scRNA-seq and snRNA-seq of skeletal muscle stored in nucleic acid stabilizing preservative](https://www.rna-seqblog.com/optimized-methods-for-scrna-seq-and-snrna-seq-of-skeletal-muscle-stored-in-nucleic-acid-stabilizing-preservative/) - Single-cell studies have revolutionized the way we understand diseases by showing how individual cells behave differently, even within the same tissue. However, these studies often rely on freshly collected samples, which can make global collaborations and research on archived tissues challenging. A recent study tackles this problem by creating a protocol that allows high-quality single-cell
- [ATLAS-seq - a microfluidic single-cell TCR screen for antigen-reactive TCRs](https://www.rna-seqblog.com/atlas-seq-a-microfluidic-single-cell-tcr-screen-for-antigen-reactive-tcrs/) - T cell immunotherapy, a cutting-edge approach in fighting cancer and infectious diseases, relies on finding the right T cell receptors (TCRs) to target harmful antigens. TCRs are like “keys” that fit into specific “locks” on harmful cells, activating T cells to attack and destroy them. Traditionally, scientists have used a method called MHC multimer staining
- [Predicting microbial transcriptome using genome sequence](https://www.rna-seqblog.com/predicting-microbial-transcriptome-using-genome-sequence/) - Understanding how genes are expressed in microbial genomes is crucial for unraveling the complexities of their biology and harnessing their potential for applications like biotechnology and medicine. However, studying gene expression in microbes has been challenging, particularly for species that haven’t yet been characterized at the transcriptional level. Researchers at the Beijing Institute of Technology
- [Optimizing antibody use for accurate m6A mapping in RNA research](https://www.rna-seqblog.com/optimizing-antibody-use-for-accurate-m6a-mapping-in-rna-research/) - In the ever-evolving field of RNA research, N6-methyladenosine (m6A) has emerged as a key player in regulating gene expression. m6A is a chemical modification on RNA that influences various processes, including RNA stability, translation, and cellular responses. To study m6A patterns, researchers use a method called m6A RNA immunoprecipitation sequencing (MeRIP-seq), which involves isolating and
- [Mercer University freshman awarded best conference presentation for work using single-cell RNA sequencing](https://www.rna-seqblog.com/mercer-university-freshman-awarded-best-conference-presentation-for-work-using-single-cell-rna-sequencing/) - Mercer University freshman Ridhi Koner was awarded the best conference presentation at the recent Georgia Undergraduate Research Conference (GURC) held at Oxford College of Emory. Twenty-six Mercer undergraduate students participated in the conference, presenting nine posters and giving seven oral presentations. Koner’s presentation was titled “Understanding Progression Between Neoplasia and Malignancy of Pancreatic Ductal Adenocarcinoma Through
- [Scientist I RNA R&D](https://www.rna-seqblog.com/scientist-i-rna-rd/) - Eclipsebio is an industry-leading RNA technology company at the forefront of innovation in RNA-based therapeutic development. By leveraging next-generation sequencing (NGS) technology, Eclipsebio develops precise tools for the characterization and optimization of RNA-based therapeutic, enabling a deeper understanding of RNA function and therapeutic potential. With a commitment to innovation and quality, Eclipsebio continues to shape
- [RNA-ModX - a multilabel prediction and interpretation framework for RNA modifications](https://www.rna-seqblog.com/rna-modx-a-multilabel-prediction-and-interpretation-framework-for-rna-modifications/) - RNA plays a critical role in how our cells function, acting as a messenger, regulator, and more. However, the full story of RNA is far from simple. Beyond the familiar A, C, G, and U nucleotides, RNA molecules often undergo chemical modifications that influence their behavior and functions. These modifications are vital for understanding RNA’s
- [scRNA-Seq identifies key players in brain aging](https://www.rna-seqblog.com/scrna-seq-identifies-key-players-in-brain-aging/) - Scientists at the Allen Institute have identified specific cell types in the brain of mice that undergo major changes as they age, along with a specific hot spot where many of those changes occur. The discoveries, published in the journal Nature, could pave the way for future therapies to slow or manage the aging process in
- [MBCdeg4 - a modified clustering-based method for identifying differentially expressed genes from RNA-seq data](https://www.rna-seqblog.com/mbcdeg4-a-modified-clustering-based-method-for-identifying-differentially-expressed-genes-from-rna-seq-data/) - RNA sequencing (RNA-seq) is a powerful tool for studying gene expression, enabling researchers to identify differentially expressed genes (DEGs)—genes that are turned “on” or “off” under specific conditions, such as healthy versus diseased cells. Identifying DEGs helps scientists understand biological processes and disease mechanisms. In this study, researchers at The University of Tokyo introduce MBCdeg4,
- [Isolating high-quality RNA for RNA-Seq from 10-year-old blood samples](https://www.rna-seqblog.com/isolating-high-quality-rna-for-rna-seq-from-10-year-old-blood-samples/) - RNA sequencing (RNA-Seq) has become an invaluable tool for research and diagnostics, helping scientists explore gene expression, identify disease markers, and develop new therapies. However, one of the challenges when working with RNA is its instability...
- [SDEvelo - multivariate stochastic modeling for transcriptional dynamics](https://www.rna-seqblog.com/sdevelo-multivariate-stochastic-modeling-for-transcriptional-dynamics-with-cell-specific-latent-time/) - Recent advances in RNA sequencing, particularly in single-cell RNA sequencing (scRNA-seq), have introduced a new approach to understanding how cells change and differentiate over time. One of these advances is the concept of RNA velocity, which helps predict the direction of cellular changes by measuring the dynamics of RNA molecules in individual cells. This process
- [smRandom-seq2 - a high-throughput and high-resolution single-microbe RNA sequencing method](https://www.rna-seqblog.com/smrandom-seq2-a-high-throughput-and-high-resolution-single-microbe-rna-sequencing-method/) - The human gut microbiome is complex and diverse, with significant implications for health and disease. Researchers at the Zhejiang University School of Medicine have developed smRandom-seq2, a droplet-based method that overcomes the limitations of existing techniques by capturing RNA from a wide variety of species. The method uses optimized random primers and a triple-module computational
- [RNA Sequencing advances in cancer research with MaCroDNA platform for single-cell data integration](https://www.rna-seqblog.com/rna-sequencing-advances-in-cancer-research-with-macrodna-platform-for-single-cell-data-integration/) - Rice-developed platform sets new standard for single-cell sequencing data integration Cancers begin with abnormal changes in individual cells, and the ability to track the accumulation of mutations at the single-cell level can shed new light on the early stages of the disease. Such knowledge could enable more effective early detection and treatment options for patients
- [RDDpred - a condition-specific RNA-editing prediction model from RNA-seq data](https://www.rna-seqblog.com/rddpred-a-condition-specific-rna-editing-prediction-model-from-rna-seq-data/) - RNA-editing is an important post-transcriptional RNA sequence modification performed by two catalytic enzymes, "ADAR"(A-to-I) and "APOBEC"(C-to-U). By utilizing high-throughput sequencing technologies, the biological function of RNA-editing has been actively investigated. Currently, RNA-editing is considered to be a key regulator that controls various cellular functions, such as protein activity, alternative splicing pattern of mRNA, and substitution
- [Transcriptomic modulation of Alzheimer’s disease by activated protein C using single-cell RNA-seq](https://www.rna-seqblog.com/transcriptomic-modulation-of-alzheimers-disease-by-activated-protein-c-using-single-cell-rna-seq/) - “We believe our study utilizing Single-Cell RNA sequencing will provide additional rationale towards the effects on APC treatment observed in previous studies on 5xFAD AD mice.” A new research paper was published in Aging (listed by MEDLINE/PubMed as “Aging (Albany NY)” and “Aging-US” by Web of Science) Volume 16, Issue 4, entitled, “Single-Cell RNA-seq reveals transcriptomic modulation of
- [TempO-LINC - gene expression without cDNA generation](https://www.rna-seqblog.com/tempo-linc-gene-expression-without-cdna-generation/) - Researchers at BioSpyder Technologies have developed a new technology called TempO-LINC, a cutting-edge platform that allows scientists to perform high-throughput transcriptomic analysis on single cells and even cell nuclei...
- [Delineating the effective use of self-supervised learning in single-cell genomics](https://www.rna-seqblog.com/delineating-the-effective-use-of-self-supervised-learning-in-single-cell-genomics/) - Single-cell genomics (SCG) helps scientists study individual cells—analyzing their genes and functions to uncover the complex dynamics of life. However, working with this type of data can be challenging due to its complexity and the sheer volume of information involved. That’s where self-supervised learning (SSL), a cutting-edge machine learning approach, comes into play. What Is
- [Spatiotemporal single-cell analysis reveals new insights into wound healing](https://www.rna-seqblog.com/spatiotemporal-single-cell-analysis-reveals-new-insights-into-wound-healing/) - A new study from Karolinska Institutet maps the cellular and molecular dynamics of human wound healing in exceptional detail. The study was published in Cell Stem Cell. Self-healing of wounds is vital, but little is known about how cells cooperate during this process. To better understand this, researchers studied skin and wounds from the same
- [RNA sequencing reveals structural cell protein also directly regulates gene transcription](https://www.rna-seqblog.com/rna-sequencing-reveals-structural-cell-protein-also-directly-regulates-gene-transcription/) - A cell protein previously believed only to provide a scaffolding for DNA has also been shown to directly influence DNA transcription into RNA – the first step of the process by which an organism’s genetic code expresses itself. The fundamental breakthrough was discovered in apple cells but is relevant to all living organisms made of
- [Single-cell RNA sequencing of chronic idiopathic erythroderma defines disease-specific markers](https://www.rna-seqblog.com/single-cell-rna-sequencing-of-chronic-idiopathic-erythroderma-defines-disease-specific-markers/) - Chronic idiopathic erythroderma (CIE) is a complex skin disorder characterized by widespread redness and inflammation, but its exact cause has remained largely unclear. To shed light on the underlying mechanisms of this disease, researchers at the Icahn School of Medicine at Mount Sinai employed advanced technologies, including single-cell RNA sequencing and T-cell receptor sequencing, to
- [Combining long- and short-read sequencing in single cells reveals new mRNAs in neurodegenerative diseases](https://www.rna-seqblog.com/combining-long-and-short-read-sequencing-in-single-cells-reveals-new-mrnas-in-neurodegenerative-diseases/) - 3D rendering of a strand of messenger RNA Scientists at Sanford Burnham Prebys used two sequencing methods in tandem to uncover gene product mRNA alterations and relationships from brains affected by three common diseases. Diseases marked by progressive deterioration of the brain — neurodegeneration — have proven challenging to understand and treat. These common conditions
- [VeloVGI - accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data](https://www.rna-seqblog.com/velovgi-accurate-rna-velocity-estimation-based-on-multibatch-network-reveals-complex-lineage-in-batch-scrna-seq-data/) - When scientists want to understand how cells grow, change, and develop, they often turn to single-cell RNA sequencing (scRNA-seq). This technology gives us a snapshot of the genes being used by individual cells at a particular moment in time. But what if we could take it a step further and predict where those cells are
- [MrHAMER2 - high-accuracy long-read RNA sequencing to decode isoform-specific variation in viral transcripts during latency](https://www.rna-seqblog.com/mrhamer2-high-accuracy-long-read-rna-sequencing-to-decode-isoform-specific-variation-in-viral-transcripts-during-latency/) - The ability of HIV to hide in a latent state, lying dormant within host cells, is one of the biggest challenges in combating the virus. Researchers have long sought to understand how the virus manipulates the host’s genetic machinery to maintain its grip, especially during latency. A recent study sheds light on this mystery by
- [Fish environmental RNA sequencing sensitively captures accumulative stress responses through short-term aquarium sampling](https://www.rna-seqblog.com/fish-environmental-rna-sequencing-sensitively-captures-accumulative-stress-responses-through-short-term-aquarium-sampling/) - Environmental RNA (eRNA) is a technique that allows scientists to track biological responses to environmental stresses by detecting genetic material released into the environment. This approach has gained attention because it offers a way to monitor the health of organisms, such as fish, without needing to capture or harm them. However, a limitation of eRNA
- [IBDverse - the largest single-cell RNA sequencing dataset of terminal ileal biopsies](https://www.rna-seqblog.com/ibdverse-the-largest-single-cell-rna-sequencing-dataset-of-terminal-ileal-biopsies/) - Crohn’s disease (CD) is a long-term condition that causes inflammation in the digestive system, often making life challenging for those affected. What makes CD particularly complex is its variability—symptoms and treatment responses can differ greatly between individuals. To better understand this condition, scientists have turned to cutting-edge technologies, including single-cell RNA sequencing (scRNA-seq), to unravel
- [Comparing the utility of snRNA-seq and scRNA-seq in profiling human bladder tissue](https://www.rna-seqblog.com/comparing-the-utility-of-snrna-seq-and-scrna-seq-in-profiling-human-bladder-tissue/) - In recent years, scientists have made remarkable progress in studying the diversity of cells within our bodies, thanks to groundbreaking sequencing technologies. Two key methods, single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq), have opened the door to exploring gene activity in individual cells. These tools are helping researchers understand how cells work in
- [O-MAPping the cell for a spatial understanding of basic biology](https://www.rna-seqblog.com/o-mapping-the-cell-for-a-spatial-understanding-of-basic-biology/) - From the Cancer Consortium Shechner lab, Department of Pharmacology, University of Washington Mapping is crucial in understanding and contextualizing our environments. Mapping serves many purposes – it helps us establish efficient paths between destinations, locate new restaurants or find our friends’ apartments, or even predict which areas to avoid. Similarly, in biology, different part of
- [Unlocking medical mysteries with RNA sequencing and multiomics diagnostics](https://www.rna-seqblog.com/unlocking-medical-mysteries-with-rna-sequencing-and-multiomics-diagnostics/) - Transcriptomics, proteomics and other technologies could provide additional diagnostic power to help solve medical mysteries. In a review published in the journal Pediatric Research, scientists at the University of Miami Miller School of Medicine explored how several technologies can help diagnose rare diseases. In addition to genomics, which can identify the faulty genes that underlie many
- [Researchers explore prognostic value of transcriptomic data in multiple myeloma](https://www.rna-seqblog.com/researchers-explore-prognostic-value-of-transcriptomic-data-in-multiple-myeloma/) - Prediction and bioinformatic data could prove valuable for therapeutic interventions targeting this malignancy A new analysis, spearheaded by a multi-institutional team of experts, highlights a computational methodology that supports the identification of multiple myeloma patients who are most suited to a particular treatment regimen, thereby contributing to improved patient care. The study also offers strategies
- [HIPSD&R-seq - scalable genomic copy number and transcriptome profiling](https://www.rna-seqblog.com/hipsdr-seq-scalable-genomic-copy-number-and-transcriptome-profiling/) - Understanding cancer at the cellular level is crucial for developing better treatments and therapies. One of the challenges in cancer research is identifying the genetic differences between cancer cells, especially when those differences are rare or subtle. Traditional methods of studying cancer cells often fall short, either by being too slow or not allowing researchers
- [RNA sequencing reveals how venetoclax enhances CAR T cell function in treatment-resistant lymphoma](https://www.rna-seqblog.com/rna-sequencing-reveals-how-venetoclax-enhances-car-t-cell-function-in-treatment-resistant-lymphoma/) - About a third of patients with diffuse large B cell lymphoma (DLBCL), a fast-growing form of lymphoma, will see their disease advance or recur following treatment. Seeking a new treatment strategy that might boost the effectiveness of existing DLBCL therapies, a team from Roswell Park Comprehensive Cancer Center has been working to understand the underlying
- [RNA sequencing unveils cell types and immune interactions in craniopharyngioma subtypes](https://www.rna-seqblog.com/rna-sequencing-unveils-cell-types-and-immune-interactions-in-craniopharyngioma-subtypes/) - Scientists analyzed individual cells isolated from two craniopharyngioma subtypes to identify the specific cell types, their features, and their crosstalk Craniopharyngiomas are brain tumors that negatively impact the hormonal function of the nearby pituitary. The tumor location often prevents necessary surgical intervention. Alternative pharmacological therapy requires an in-depth understanding of the tumor molecular characteristics. To
- [scPAS - single-cell phenotype-associated subpopulation identifier](https://www.rna-seqblog.com/scpas-single-cell-phenotype-associated-subpopulation-identifier/) - Recent advancements in single-cell sequencing have allowed scientists to explore the complexity of tissues by studying individual cells. This has helped us better understand how different cell types contribute to diseases like cancer or atherosclerosis. However, despite these technological advancements, it remains challenging to pinpoint how specific groups of cells are related to particular disease
- [RiboD-PETRI - an improved bacterial single-cell RNA-seq reveals biofilm heterogeneity](https://www.rna-seqblog.com/ribod-petri-an-improved-bacterial-single-cell-rna-seq-reveals-biofilm-heterogeneity/) - Bacterial cells, unlike mammalian cells, do not have mRNA polyadenylated tails, which presents a challenge when trying to isolate mRNA for study, especially in single-cell RNA sequencing (scRNA-seq). This issue is made more difficult because of the high abundance of ribosomal RNA (rRNA) that can overwhelm the detection of mRNA. To address this problem, researchers
- [Single-cell RNA sequencing reveals transcriptional changes in patients with severe asthma induced by biologics](https://www.rna-seqblog.com/single-cell-rna-sequencing-reveals-transcriptional-changes-in-patients-with-severe-asthma-induced-by-biologics/) - Severe eosinophilic asthma is a type of asthma that is driven by an overactive immune response, particularly involving certain immune cells called eosinophils. For patients with this condition, managing symptoms often requires systemic medications like corticosteroids and biologics that target specific immune pathways. While these treatments, especially those targeting type 2 cytokines (like IL-4, IL-5,
- [SurfR - identifying surface protein coding genes from expression data](https://www.rna-seqblog.com/surfr-identifying-surface-protein-coding-genes-from-expression-data/) - Cell-surface proteins play a crucial role in how cells communicate with each other and interact with their environment. These proteins are not only essential for cell function but also serve as key indicators of a cell’s state, offering important insights into health and disease. By studying the variations in the proteins present on the surface
- [Wobble Genomics’ Technology Demonstrates Potential in Accelerating Precision Medicine Innovations](https://www.rna-seqblog.com/wobble-genomics-technology-demonstrates-potential-in-accelerating-precision-medicine-innovations/) - Wobble Genomics, a healthcare and biotechnology company at the forefront of long-read RNA sequencing, will today present new data at the San Antonio Breast Cancer Symposium (SABCS) that demonstrates the ability of its technology platform to provide deep biological insights critical for drug discovery and development, building on previous data which established the technology’s strong
- [End-to-End Analysis of Long Reads in OmicsBox](https://www.rna-seqblog.com/end-to-end-analysis-of-long-reads-in-omicsbox/) - Long-read sequencing has gained widespread popularity in many areas of biological research due to the many advantages these technologies offer over short reads, as well as the decreasing error rates and costs. Nature Methods named it the method of the year 2022. The field of transcriptomics shows particular interest in long reads, as long-read RNA-sequencing can
- [MGI Tech's innovative sequencing technology drives mangrove conservation efforts in Thailand](https://www.rna-seqblog.com/mgi-techs-innovative-sequencing-technology-drives-mangrove-conservation-efforts-in-thailand/) - MGI Tech, a company dedicated to developing core tools and technologies that drive innovation in life sciences, has partnered with National Omics Center (NOC) under the National Science and Technology Development Agency (NSTDA) to leverage advanced sequencing technology for mangrove conservation research. The joint efforts aim to address the environmental challenges facing mangroves, which play a
- [RNA sequencing identifies compounds that stimulate neural regeneration in retinal disease](https://www.rna-seqblog.com/rna-sequencing-identifies-compounds-that-stimulate-neural-regeneration-in-retinal-disease/) - Retinal degeneration in mammals, which leads to permanent vision loss, is a challenging condition because, unlike some animals, mammals cannot naturally regenerate their retinal cells. However, research has shown that certain non-mammalian vertebrates, such as fish and amphibians, can regenerate retinal neurons through a specialized process involving Muller glia (MG), a type of supportive cell
- [Director, Translational Research Sequencing Technologies](https://www.rna-seqblog.com/director-translational-research-sequencing-technologies/) - The Role In this role, you will envision and lead the execution of the strategy to harness advanced sequencing technologies, to drive translational research across diverse therapeutic areas, including cancer vaccines, immuno-oncology, and immune therapeutics targeting autoimmune and inflammatory diseases. Leveraging your deep expertise in state-of-the-art DNA and RNA sequencing platforms, you will design, implement,
- [Bulk RNA-Seq Workshop](https://www.rna-seqblog.com/bulk-rna-seq-workshop/) - This workshop briefly introduces techniques, platforms, and methods used in bulk RNA-Seq experiments, followed by a software demonstration using the HSLS-licensed CLC Genomics Workbench. Participants will learn how to: access the CLCbio Genomics Server hosted on the HTC Cluster by Pitt CRC import RNA-Seq FASTQ reads from a GEO dataset assess the quality of RNA-Seq data align reads to a
- [Student Workshop - Single Cell RNA Sequencing](https://www.rna-seqblog.com/student-workshop-single-cell-rna-sequencing/) -  This session was presented at the 2024 World Congress on In Vitro Biology Meeting held in St. Louis, Missouri from June 8 – 12, 2024 and was recorded as part of the In-Person and On-Demand Limited Access Program. Single cell RNA sequencing (SC-RNA-seq) is the state-of-the-art technology for transcriptome analysis that allows the dissection
- [New AI tool pinpoints gene splicing with unmatched precision](https://www.rna-seqblog.com/new-ai-tool-pinpoints-gene-splicing-with-unmatched-precision/) - A recent innovation from Johns Hopkins researchers enables deeper insights into gene function and disease-linked mutations Johns Hopkins researchers have developed a powerful new AI tool called Splam that can identify where splicing occurs in genes—an advance that could help scientists analyze genetic data with greater accuracy, offering new insights into how genes function and mutations contribute
- [Genevia introduces the RNA-seq Bioinformatics Grant 2025](https://www.rna-seqblog.com/genevia-introduces-the-rna-seq-bioinformatics-grant-2025/) - Genevia RNA-seq Bioinformatics Grant 2025 is aimed at supporting an academic research group in getting their transcriptomics data analyzed at the highest standards of the field. Genevia Technologies has been providing bioinformatics services for scientists in over 100 universities since 2011. In accordance with their mission to support researchers in embracing new computational technologies, they are proud
- [RNA sequencing identified how venetoclax influences the phenotypic and qualitative changes in CAR T cells](https://www.rna-seqblog.com/rna-sequencing-identified-how-venetoclax-influences-the-phenotypic-and-qualitative-changes-in-car-t-cells/) - New work from Roswell Park adds evidence that FDA-approved leukemia drug improves T cell quality and function Standard therapies prove ineffective for a third of patients with DLBCL Roswell Park team studying whether Bcl-2-inhibiting drug may enhance CAR T Underlying mechanism hinges on calcium signaling, scientists reveal About a third of patients with diffuse large
- [FedPyDESeq2 - a federated framework for bulk RNA-seq differential expression analysis](https://www.rna-seqblog.com/fedpydeseq2-a-federated-framework-for-bulk-rna-seq-differential-expression-analysis/) - RNA sequencing (RNA-seq) has opened up new frontiers in understanding gene activity and its role in health and disease. However, when researchers work with sensitive patient data—especially data collected from multiple institutions—sharing and combining information becomes a tricky balancing act. On one hand, pooling data can lead to deeper insights and more robust statistical analyses.
- [CellTran - a statistical approach for systematic identification of transition cells from scRNA-seq data](https://www.rna-seqblog.com/celltran-a-statistical-approach-for-systematic-identification-of-transition-cells-from-scrna-seq-data/) - In multicellular organisms, cells go through complex transitions, changing from one type to another or adopting new functional states. Understanding these cellular shifts is essential because they underpin many critical biological processes, from tissue development to responses in disease. Single-cell RNA sequencing (scRNA-seq) has become a revolutionary tool for scientists, allowing them to peek into
- [Nanopore direct RNA sequencing reveals unique molecular fingerprints for early cancer detection](https://www.rna-seqblog.com/nanopore-direct-rna-sequencing-reveals-unique-molecular-fingerprints-for-early-cancer-detection/) - Different types of cancer have unique molecular ‘fingerprints’ which are detectable in early stages of the disease and can be picked up with near-perfect accuracy by small, portable scanners in just a few hours, according to a study published today in the journal Molecular Cell. The discovery by researchers at the Centre for Genomic Regulation (CRG)
- [UAlbany chemist receives federal support to advance tool for complete RNA sequencing](https://www.rna-seqblog.com/ualbany-chemist-receives-federal-support-to-advance-tool-for-complete-rna-sequencing-2/) - University at Albany’s Shenglong Zhang, associate professor in the Department of Chemistry and the RNA Institute, has received two Small Business Technology Transfer (STTR) grants from the National Institutes of Health totaling over $620,000. The grants were jointly awarded to the University and UAlbany spinoff company DirectSeq Biosciences, Inc., which Zhang has directed as founder and president since November 2022.
- [Vevo Therapeutics Partners with the Parse Biosciences GigaLab to Generate 100M Cell Atlas for AI Powered Drug Discovery](https://www.rna-seqblog.com/vevo-therapeutics-partners-with-the-parse-biosciences-gigalab-to-generate-100m-cell-atlas-for-ai-powered-drug-discovery/) - Parse Biosciences, a leading provider of accessible and scalable single cell sequencing solutions, today announced the generation of the world’s largest single cell dataset to date, totaling 100 million cells. This impressive milestone was achieved in just one month using Parse Biosciences’ GigaLab and done in partnership with Vevo Therapeutics to advance their AI-based drug discovery efforts. The first-of-its-kind
- [Unraveling RNA sequencing challenges: a new approach to understanding nascent and mature mRNA](https://www.rna-seqblog.com/unraveling-rna-sequencing-challenges-a-new-approach-to-understanding-nascent-and-mature-mrna/) - RNA sequencing (RNA-seq) has revolutionized our ability to study gene expression by providing detailed snapshots of RNA molecules within cells. In the context of single-cell and single-nucleus RNA sequencing, researchers face a unique challenge: dealing with the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA). This mix creates hurdles in accurately mapping sequencing
- [Unveiling the role of YgaV in iron uptake dynamics of E. coli: insights from RNA sequencing studies](https://www.rna-seqblog.com/unveiling-the-role-of-ygav-in-iron-uptake-dynamics-of-e-coli-insights-from-rna-sequencing-studies/) - Researchers establish the role of YgaV, a hydrogen sulfide dependent transcription factor in regulating iron uptake dynamics in Escherichia coli Hydrogen sulfide (H2S) plays an important role in various cellular activities such as oxidative stress response through activation of iron uptake in bacteria. However, the underlying mechanism by which intracellular H2S regulates iron uptake remains
- [Unveiling the epigenome - Oxford Nanopore and UK Biobank advance disease research with DNA/RNA Sequencing](https://www.rna-seqblog.com/unveiling-the-epigenome-oxford-nanopore-and-uk-biobank-advance-disease-research-with-dna-rna-sequencing/) - Pioneering research with potential to transform health outcomes through early detection, precise diagnoses, and personalised treatment for major diseases Initiative will map the epigenome using 50,000 samples with the goal of advancing early disease detection, diagnosis and treatment in cancer, neurological disease and other common complex diseases Oxford Nanopore’s direct sequencing technology to provide the
- [Aventa FusionPlus test that detects gene fusions, translocations, and rearrangements receives favorable pricing determination from CMS](https://www.rna-seqblog.com/aventa-fusionplus-test-that-detects-gene-fusions-translocations-and-rearrangements-receives-favorable-pricing-determination-from-cms/) - Aventa™ Genomics, LLC, a clinical laboratory deploying 3D genomics to improve patient outcomes, and a wholly-owned subsidiary of Arima Genomics, Inc., today announced that it has received a favorable final pricing determination for the 2025 Centers for Medicare and Medicaid Services (CMS) Clinical Laboratory Fee Schedule (CLFS). The pricing determination is for the Aventa FusionPlus test, a
- [Alithea Genomics Launches Full-Length DRUG-Seq to Unlock Full Power of Transcriptomics for Drug Discovery](https://www.rna-seqblog.com/alithea-genomics-launches-full-length-drug-seq-to-unlock-full-power-of-transcriptomics-for-drug-discovery/) - Multiplexed, extraction-free, full-length library preparation technology facilitates large-scale RNA sequencing, combining ever more content with high throughput Alithea Genomics, a leader in the field of large-scale RNA sequencing and transcriptomics, announced today the launch of MERCURIUS™ Full-Length DRUG-seq library preparation technology, which combines, for the first time, massive sample multiplexing, an extraction-free workflow and full
- [RNA sequencing unveils the heart's 'mini-brain': a breakthrough in understanding cardiac neural networks](https://www.rna-seqblog.com/rna-sequencing-unveils-the-hearts-mini-brain-a-breakthrough-in-understanding-cardiac-neural-networks/) - New research from Karolinska Institutet and Columbia University shows that the heart has a mini-brain – its own nervous system that controls the heartbeat. A better understanding of this system, which is much more diverse and complex than previously thought, could lead to new treatments for heart diseases. The heart has long been thought to
- [Breakthrough AI model can translate the language of plant life](https://www.rna-seqblog.com/breakthrough-ai-model-can-translate-the-language-of-plant-life/) - A pioneering Artificial Intelligence (AI) powered model able to understand the sequences and structure patterns that make up the genetic “language” of plants, has been launched by a research collaboration. Plant RNA-FM, believed to be the first AI model of its kind, has been developed by a collaboration between plant researchers at the John Innes
- [SoupLadle - label-free single-cell RNA multiplexing leveraging genetic variability](https://www.rna-seqblog.com/soupladle-label-free-single-cell-rna-multiplexing-leveraging-genetic-variability/) - Single-cell RNA sequencing (scRNA-seq) is revolutionizing our understanding of human biology, especially in how cells respond to and contribute to disease. By examining gene expression at the level of individual cells, scRNA-seq allows researchers to uncover the molecular signals that drive disease processes. However, despite its incredible potential, scRNA-seq is expensive and technically complex, which
- [Pantry - multimodal analysis of RNA sequencing data from populations for genomic interpretation](https://www.rna-seqblog.com/pantry-multimodal-analysis-of-rna-sequencing-data-from-populations-for-genomic-interpretation/) - RNA sequencing (RNA-seq) is an invaluable tool for studying how genes are regulated in the body. It allows researchers to measure gene expression—the amount of RNA produced by a gene—and gain insights into cellular functions and disease mechanisms. However, gene regulation is far more complex than simply measuring gene expression. It involves various processes such
- [Single-cell RNA sequencing - a precision medicine approach to diagnosing and treating Fuchs’ Endothelial Corneal Dystrophy](https://www.rna-seqblog.com/single-cell-rna-sequencing-a-precision-medicine-approach-to-diagnosing-and-treating-fuchs-endothelial-corneal-dystrophy/) - CERA researchers have explored the potential of genetic analysis to transform how Fuchs’ endothelial corneal dystrophy is diagnosed and treated, with the hope of improving future outcomes for patients. Imagine if treatment for your eye condition was tailored to your individual genetic makeup, not what works for most patients. This is the potential of precision
- [RNA sequencing unlocks non-destructive selection of high-quality brain organoids for cell replacement therapy](https://www.rna-seqblog.com/rna-sequencing-unlocks-non-destructive-selection-of-high-quality-brain-organoids-for-cell-replacement-therapy/) - By combining morphological and single-cell level gene expression analyses, a team of researchers led by Professor Jun Takahashi (Department of Clinical Application) has established a new non-destructive system to select high-quality brain organoids as a potential tissue source for cell replacement therapy to treat patients after stroke or traumatic brain injuries. Organoids, or self-organizing miniature organs, represent
- [QClus - a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples](https://www.rna-seqblog.com/qclus-a-droplet-filtering-algorithm-for-enhanced-snrna-seq-data-quality-in-challenging-samples/) - Single-nuclei RNA sequencing (snRNA-seq) is a powerful tool for studying gene expression in individual nuclei, providing crucial insights into complex biological systems. However, the technique often struggles with a significant issue: background noise. Contamination from empty droplets or debris can obscure the true gene activity specific to different cell types, complicating analysis and risking inaccurate
- [RNA Sequencing reveals cell-type-specific link between alternative splicing and autoimmune disease inheritance](https://www.rna-seqblog.com/rna-sequencing-reveals-cell-type-specific-link-between-alternative-splicing-and-autoimmune-disease-inheritance/) - Computational researchers from the National University of Singapore (NUS) have uncovered how RNA splicing – a crucial process for isoform expression and protein diversity – is regulated across different cell types in the peripheral blood. This important discovery helps explain how individuals’ genetic differences contributes to their predisposition to complex diseases such as systemic lupus
- [Integrating single-cell RNA sequencing into Bgee - expanding gene expression analysis across species and cell types](https://www.rna-seqblog.com/integrating-single-cell-rna-sequencing-into-bgee-expanding-gene-expression-analysis-across-species-and-cell-types/) - Bgee is a database designed to retrieve and compare gene expression patterns across multiple animal species. Expression data is integrated and made comparable between species through consistent data annotation and processing. In recent years, Bgee has incorporated single-cell RNA sequencing expression data by carefully curating public datasets from multiple species. Researchers at the Swiss Institute
- [Unlocking the Cellular Universe: The Importance of Single-Cell Sequencing in Animal and Plant Research](https://www.rna-seqblog.com/unlocking-the-cellular-universe-the-importance-of-single-cell-sequencing-in-animal-and-plant-research/) - The advent of single-cell RNA sequencing (scRNA-seq) in 2009 marked a turning point in biological research. With rapid advancements in sequencing technologies, single-cell sequencing has become increasingly accessible and affordable, enabling scientists to explore the complexities of life at an unprecedented level of detail. What is Single-Cell RNA Sequencing? Single-cell RNA sequencing is a method that allows researchers
- [Research Scientist/Engineer 2, Long-Read Sequencing](https://www.rna-seqblog.com/research-scientist-engineer-2-long-read-sequencing/) - This is an exciting opportunity for a Research Scientist/Engineer 2 (RSE2) to work with new long-read DNA and RNA sequencing technology. Projects will include using long-read sequencing technology to investigate the role of genomic structural variation in human disease...
- [Single-nucleus RNA sequencing revealed specialized regions within the placenta's multinucleated cell](https://www.rna-seqblog.com/single-nucleus-rna-sequencing-revealed-specialized-regions-within-the-placentas-multinucleated-cell/) - During gestation, the placenta takes on the roles of many of the fetus’ developing organs and serves as a barrier between parent and child. Critical to this is the outermost layer of the organ, the syncytiotrophoblast (STB), a single, multinucleated cell that forms from repeated fusion events between mononucleated cytotrophoblasts (CTB). In addition to producing
- [NanoConsensus - characterizing bacterial ribosomal RNA modifications](https://www.rna-seqblog.com/nanoconsensus-characterizing-bacterial-rrna-modifications/) - RNA modifications are crucial for many biological processes, and scientists have been studying these changes in messenger RNA (mRNA) for years. However, much less attention has been given to the modifications in ribosomal RNA (rRNA), which plays a key role in protein synthesis within cells. A recent study has shed light on how these rRNA
- [MoPEDE - combining RNA sequencing and brain measurements to advance epilepsy treatment](https://www.rna-seqblog.com/mopede-combining-rna-sequencing-and-brain-measurements-to-advance-epilepsy-treatment/) - Researchers from Professor Vijay Tiwari’s research group at the Department of Molecular Medicine, University of Southern Denmark, have developed a new method called MoPEDE, which has the potential to improve epilepsy treatment. The method combines brain measurements with genetic analyses, offering deeper insights into the origins and mechanisms of epileptic seizures. How MoPEDE works: Bridging
- [WLGG - identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty](https://www.rna-seqblog.com/wlgg-identifying-cell-types-by-lasso-constraint-regularized-gaussian-graphical-model-based-on-weighted-distance-penalty/) - Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for exploring the diversity of cell types within a biological sample. By analyzing gene expression in individual cells, scientists can uncover details about cellular functions, interactions, and unique roles in complex biological systems. But accurately identifying cell types from scRNA-seq data remains a challenge. Why Is
- [Advances in the molecular diagnostic methods for circular RNA](https://www.rna-seqblog.com/advances-in-the-molecular-diagnostic-methods-for-circular-rna/) - Circular RNA (circRNA) is a unique type of non-coding RNA produced by back splicing of mRNA to form the covalent junction without 3’-5’ polarity and poly(A) tail. CircRNA was first discovered about 30 years ago and was considered a byproduct of abnormal splicing without regulatory function. In 2013, it is the regulatory mechanism of circRNA as
- [PhOxi-seq - detecting enzyme-dependent m2G in multiple RNA types](https://www.rna-seqblog.com/phoxi-seq-detecting-enzyme-dependent-m2g-in-multiple-rna-types/) - RNA is more than just a messenger carrying genetic instructions—it undergoes complex modifications that can significantly influence its function and, ultimately, human health. One of the key players in this process is a group of enzymes known as RNA-modifying enzymes, which chemically alter RNA molecules in specific ways. These modifications are crucial for proper cellular
- [Team develops a single-nucleus resolution atlas of white adipose tissue in different depots](https://www.rna-seqblog.com/team-develops-a-single-nucleus-resolution-atlas-of-white-adipose-tissue-in-different-depots/) - Adipose tissue is an important regulator of metabolism and energy homeostasis in the human body. It is usually classified into two distinct categories: white adipose tissue (WAT) and brown adipose tissue (BAT). WAT is widely distributed throughout the body of mammals, and based on their anatomical distribution, can be divided into subcutaneous adipose tissue (SAT),
- [Belgian scientists create a scRNA-seq atlas of the multiple myeloma immune microenvironment across disease stages](https://www.rna-seqblog.com/belgian-scientists-create-a-scrna-seq-atlas-of-the-multiple-myeloma-immune-microenvironment-across-disease-stages/) - Multiple Myeloma (MM) is an incurable blood cancer, leading to weakened immunity, bone damage, and other serious health issues. The high relapse rates following initial treatments, make the search for novel immunotherapies urgent. However, the effectiveness of these therapies often depends on a functional immune microenvironment in MM patients. Researchers from VIB and VUB now
- [KIT researchers discover novel cell type that controls the formation and growth of new blood vessels](https://www.rna-seqblog.com/kit-researchers-discover-novel-cell-type-that-controls-the-formation-and-growth-of-new-blood-vessels/) - Image of active pioneer cell (center of image). Green indicates endothelial cell nucleus, grey the outline of the blood vessels. (Photo: Zoological Institute, KIT) Cardiovascular diseases, including stroke and myocardial infarction, are the world’s leading causes of mortality, accounting for over 18 million deaths a year. A team of KIT researchers has now identified a
- [BaSSSh-seq - unveiling biofilm bacterial diversity with single-cell insights](https://www.rna-seqblog.com/basssh-seq-unveiling-biofilm-bacterial-diversity-with-single-cell-insights/) - Bacteria have evolved remarkable ways to survive and thrive in hostile environments. One of their most impressive strategies is forming biofilms—dense, multi-layered communities where bacteria live together, clinging to surfaces, and producing a protective matrix. These biofilms allow bacteria to resist antibiotics and evade the immune system, making them a significant challenge in treating infections.
- [ConDecon - clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data](https://www.rna-seqblog.com/condecon-clustering-independent-estimation-of-cell-abundances-in-bulk-tissues-using-single-cell-rna-seq-data/) - Understanding the complex world of cells within tissues has taken a leap forward with the advent of single-cell RNA sequencing (scRNA-seq). This powerful technique allows researchers to analyze the gene activity of individual cells, offering a detailed map of the diverse cell states that make up biological tissues. However, when researchers study tissues at the
- [Researchers use RNA sequencing to uncover genetic links in atherosclerotic plaques and predict cardiovascular risk](https://www.rna-seqblog.com/researchers-use-rna-sequencing-to-uncover-genetic-links-in-atherosclerotic-plaques-and-predict-cardiovascular-risk/) - In a new study published in the European Heart Journal, researchers at Karolinska Institutet show that genetic traits influence the cellular composition of atherosclerotic plaques, which over time will affect the risk of such lesions to cause a stroke or heart attack. The new knowledge can be used to improve the risk assessment and treatment
- [Online Course - A Practical Introduction to NGS Data Analysis (December 9-11, 2024)](https://www.rna-seqblog.com/online-course-a-practical-introduction-to-ngs-data-analysis-december-9-11-2024/) - When? December 9-11, 2024 9 am - 5 pm (CEST UTC+2) Where? Online Link? Website Advance your research. Understand NGS and analyze sequenced data yourself. In a nutshell Learn the essential computing skills for NGS bioinformatics Understand NGS technology, algorithms and data formats Use bioinformatics tools for handling sequencing data Perform first downstream analyses for studying genetic variation
- [Single-Cell RNA-Seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells](https://www.rna-seqblog.com/single-cell-rna-seq-of-the-developing-cardiac-outflow-tract-reveals-convergent-development-of-the-vascular-smooth-muscle-cells/) - Introduction Cardiac outflow tract (OFT) is a major hotspot for congenital heart diseases (CHDs). OFT malformations require surgical repair once diagnosed and usually have a poor prognosis, However, the etiology for most of this severe class of CHDs remains unknown. A thorough understanding of the cellular diversity, transitions, and regulatory networks of normal OFT development
- [Genome Research publishes a special issue on long-read DNA and RNA sequencing applications in Biology and Medicine](https://www.rna-seqblog.com/genome-research-publishes-a-special-issue-on-long-read-dna-and-rna-sequencing-applications-in-biology-and-medicine/) - Genome Research (https://genome.org) publishes a special issue highlighting advances in long-read sequencing applications in biology and medicine. In this first of two Special Issues guest-edited by Dr. Ana Conesa, Dr. Alexander Hoischen, and Dr. Fritz Sedlazeck, Genome Research publishes a diverse collection of research and review articles highlighting novel applications and developments in long-read sequencing (LRS). Papers in this issue
- [Mapping 1.6 million gut cells to find new ways to treat disease](https://www.rna-seqblog.com/mapping-1-6-million-gut-cells-to-find-new-ways-to-treat-disease/) - By combining 25 datasets, researchers have created the largest cohesive cell atlas of the human gut and uncovered a new way that stomach cells may play a role in Inflammatory Bowel Disease. The most comprehensive cell map of the human gut to date has been created by combining spatial and single-cell data from 1.6 million
- [scPair - Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases](https://www.rna-seqblog.com/scpair-boosting-single-cell-multimodal-analysis-by-leveraging-implicit-feature-selection-and-single-cell-atlases/) - Multimodal single-cell assays are revolutionizing how we study biology by allowing researchers to analyze multiple features from the same cell. Imagine being able to see not only the instructions encoded in DNA but also how those instructions are executed in the form of RNA molecules, all within a single cell. This capability helps scientists understand
- [DIISCO - a new method for analyzing dynamic intercellular interactions in cancer](https://www.rna-seqblog.com/diisco-a-new-method-for-analyzing-dynamic-intercellular-interactions-in-cancer/) - A new paper from Elham Azizi’s lab at Columbia University in the City of New York and collaborators has been accepted in Genome Research, marking a significant advancement in the study of dynamic single-cell interactions. The study led by Cameron Park and Shouvik Mani introduces a tool called DIISCO, that aims to improve our understanding of how
- [AI tool ‘sees’ cancer gene expression in biopsy images](https://www.rna-seqblog.com/ai-tool-sees-cancer-gene-expression-in-biopsy-images/) - Researchers used artificial intelligence to predict the activity of thousands of genes in tumors based on routinely collected images of tumor biopsies. It could guide treatment without costly genomic tests. A new AI program, SEQUOIA, can analyze a microscopy image from a tumor biopsy (left, purple) and rapidly determine what genes are likely turned on
- [Single-cell RNA sequencing reveals how marine worms regenerate lost body parts](https://www.rna-seqblog.com/single-cell-rna-sequencing-reveals-how-marine-worms-regenerate-lost-body-parts/) - The return of cells to a stem cell-like state as the key to regeneration Many living organisms are able to regenerate damaged or lost tissue, but why some are particularly good at this and others are not is not fully understood. Molecular biologists Alexander Stockinger, Leonie Adelmann and Florian Raible from the Max Perutz Labs
- [Single-cell RNA sequencing reveals immune dysfunction increases cancer risk in obese populations](https://www.rna-seqblog.com/single-cell-rna-sequencing-reveals-immune-dysfunction-increases-cancer-risk-in-obese-populations/) - Ryan Teague, Ph.D., professor of molecular microbiology and immunology at Saint Louis University’s School of Medicine, and his team are now trying to uncover the exact mechanism underlying the metabolic dysfunctions associated with obesity that directly impact T-cell function. Researchers at Saint Louis University’s School of Medicine say T-cell dysfunction is leading to an increased
- [Lexogen launches streamlined, large-scale RNA-Seq service for blood samples](https://www.rna-seqblog.com/lexogen-launches-streamlined-large-scale-rna-seq-service-for-blood-samples/) - Lexogen, a pioneer in NGS Services, has launched a streamlined Blood RNA-Seq Service to expedite drug discovery from whole blood or biofluids. Lexogen’s established blood transcriptomics solutions, including CORALL for Blood and QuantSeq for Blood, offer efficient globin removal and robust workflows for comprehensive whole transcriptome sequencing and cost-effective gene expression profiling from blood. At Lexogen NGS Services, the proprietary
- [scRNA-Seq reveals neurons that change our understanding of how the brain handles hunger](https://www.rna-seqblog.com/scrna-seq-reveals-neurons-that-change-our-understanding-of-how-the-brain-handles-hunger/) - “Hunger” neurons expressing the AGRP gene (red), alongside newly-discovered “satiety” neurons expressing the BNC2 gene (green). As you’re deciding whether to eat one more potato chip, a pitched battle takes place in your brain. One group of neurons promotes hunger while another induces satiety. How quickly one group gains the upper hand determines how likely
- [Circular logic: understanding RNA’s strangest form yet](https://www.rna-seqblog.com/circular-logic-understanding-rnas-strangest-form-yet/) - From Nature By Amber Dance Circular RNAs are prevalent, mysterious and fascinating, but their study requires great care. RNA can adopt many configurations in the cell (artist’s illustration).Credit: Christoph Burgsted/Science Photo Library/Getty Over the past few decades, RNA’s place in biology has transformed from being a mere intermediate between DNA and protein to a fascinating molecule
- [Transcriptome-wide analysis of the 5′ Cap status of RNA and RNA sequencing](https://www.rna-seqblog.com/transcriptome-wide-analysis-of-the-5′-cap-status-of-rna-and-rna-sequencing/) - Messenger RNA (mRNA) is essential for transferring genetic instructions from DNA to the cellular machinery that produces proteins...
- [Concurrent DNA and RNA sequencing detect more actionable variants in NSCLC](https://www.rna-seqblog.com/concurrent-dna-and-rna-sequencing-detect-more-actionable-variants-in-nsclc/) - Concurrent RNA and DNA sequencing revealed 15.3% more patients with actionable variants than DNA sequencing alone...
- [Deciphering gene expression patterns using large-scale transcriptomic data](https://www.rna-seqblog.com/deciphering-gene-expression-patterns-using-large-scale-transcriptomic-data/) - Gene expression, the process by which genes are activated to produce proteins, is a cornerstone of understanding cellular function and disease mechanisms. However, gene expression varies unpredictably across genders, ethnic groups, and health conditions, making it challenging to pinpoint which genes are most important for diagnosing diseases like cancer or understanding their progression. In a
- [International canine gene research database accelerates biomedical research](https://www.rna-seqblog.com/international-canine-gene-research-database-accelerates-biomedical-research/) - A new database covering over 100 different canine tissues can significantly enhance our understanding of hereditary diseases and provide valuable information for health research in both dogs and humans. The International DoGA Consortium has achieved a significant milestone in genetics research by creating a comprehensive canine promoter and gene expression atlas. The atlas is a
- [ELATUS - uncovering functional lncRNAs by scRNA-seq](https://www.rna-seqblog.com/elatus-uncovering-functional-lncrnas-by-scrna-seq/) - Long non-coding RNAs, or lncRNAs, are an important part of our genetic code, but they aren’t as well understood as other parts of our DNA, like protein-coding genes. While protein-coding genes carry instructions to build proteins, lncRNAs don’t make proteins directly. Instead, they control how genes are expressed and have a hand in many cellular
- [Genomic Testing Cooperative unveils “GTC Interpret,” a groundbreaking web-based platform for partner labs to access analyzed sequencing data and finalize reports](https://www.rna-seqblog.com/genomic-testing-cooperative-unveils-gtc-interpret-a-groundbreaking-web-based-platform-for-partner-labs-to-access-analyzed-sequencing-data-and-finalize-reports/) - Genomic Testing Cooperative (GTC), a leader in advanced genomic testing, announced the launch of GTC Interpret, a new web-based platform designed to provide Co-Op member laboratories and partner labs seamless online access to fully analyze genomic data with sophisticated reporting tools. With GTC Interpret, users can now access a wealth of detailed genomic information, all generated
- [Publication trends of single cell RNA sequencing research](https://www.rna-seqblog.com/publication-trends-of-single-cell-rna-sequencing-research/) - From Parse Biosciences Cells profiled in each publication double every year. Experimental size is growing at a break-neck pace, demanding increased attention on experimental design and technology selection. Today’s prevailing methods for single cell RNA sequencing (scRNA-seq) analysis still rely on specialized hardware. Since 2015, these methods have been widely used, allowing tens of thousands
- [SPoTLIghT - integrating histopathology and transcriptomics for spatial tumor microenvironment profiling](https://www.rna-seqblog.com/spotlight-integrating-histopathology-and-transcriptomics-for-spatial-tumor-microenvironment-profiling/) - Cancer research is increasingly focused on understanding the tumor microenvironment (TME) — the community of cells that surround and interact with cancer cells within a tumor. The TME plays a significant role in how tumors grow and respond to treatments. But studying this environment isn’t straightforward, and understanding its complex architecture at a cellular level
- [Single-cell RNA-sequencing analysis of immune and mesenchymal cell crosstalk in the developing enthesis](https://www.rna-seqblog.com/single-cell-rna-sequencing-analysis-of-immune-and-mesenchymal-cell-crosstalk-in-the-developing-enthesis/) - Autoimmunity plays a major role in several painful conditions, including enthesopathies, which affect the enthesis, the area where tendons and ligaments attach to bones. These conditions involve complex immune responses, with immune cells like B cells, macrophages, and T cells infiltrating tissues and causing inflammation. Recent research has been focusing on better understanding how these
- [Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma](https://www.rna-seqblog.com/single-cell-rna-seq-reveals-the-transcriptional-program-underlying-tumor-progression-and-metastasis-in-neuroblastoma/) - Neuroblastoma (NB), the most prevalent extracranial solid tumor in children, poses a significant therapeutic challenge due to its metastasis and high heterogeneity. A recent study at Tianjin Medical University leveraging single-cell RNA sequencing (scRNA-seq) has uncovered vital molecular mechanisms underlying NB’s progression and metastasis, shedding light on potential therapeutic targets. The research analyzed primary tumors
- [PacBio unveils the Vega System, a new sequencing platform bringing HiFi to the benchtop](https://www.rna-seqblog.com/pacbio-unveils-the-vega-system-a-new-sequencing-platform-bringing-hifi-to-the-benchtop/) - PacBio, developer of the world’s most advanced sequencing technologies, today announced the Vega™ system, the company’s first benchtop long-read sequencing platform. Vega delivers all the functionality of the Revio system, PacBio’s high-throughput long-read sequencer, into a compact, lower-throughput benchtop platform. Offering exceptional data accuracy with HiFi technology, fast turnaround time, and a U.S. list price of $169,000, Vega
- [Overcoming bioinformatics skill gaps in single-cell research](https://www.rna-seqblog.com/overcoming-bioinformatics-skill-gaps-in-single-cell-research/) - From Nygen Analytics This article addresses the bioinformatics skill gap in single-cell research, highlighting challenges faced by wet-lab scientists in analyzing scRNA-seq data. It explores solutions to make data analysis more accessible to researchers without extensive computational expertise. The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized biological research by allowing scientists to explore gene
- [MST-m6A - a novel multi-scale transformer-based framework for prediction of m6A modification sites](https://www.rna-seqblog.com/mst-m6a-a-novel-multi-scale-transformer-based-framework-for-prediction-of-m6a-modification-sites/) - In recent years, scientists have found that cells use small chemical “tags” on RNA molecules to regulate a wide range of biological functions. One of the most common tags in eukaryotic cells (like our own cells) is called N6-methyladenosine, or m6A. This chemical modification doesn’t alter the genetic code itself but acts as a type
- [scGraphformer - unveiling cellular heterogeneity and interactions in scRNA-seq data using a scalable graph transformer network](https://www.rna-seqblog.com/scgraphformer-unveiling-cellular-heterogeneity-and-interactions-in-scrna-seq-data-using-a-scalable-graph-transformer-network/) - Single-cell RNA sequencing (scRNA-seq) has become a cornerstone tool in modern biology, allowing researchers to examine gene expression at the individual cell level. This powerful technique uncovers the vast diversity of cell types and states that exist within tissues, helping scientists understand biological processes in much greater detail. However, accurately classifying these cells and understanding
- [The evolution from DNA-based to RNA-based genomic analysis in renal cell carcinoma](https://www.rna-seqblog.com/the-evolution-from-dna-based-to-rna-based-genomic-analysis-in-renal-cell-carcinoma/) -  Zachary Klaassen speaks with Pedro Barata about a publication examining transcription profiles in renal cell carcinoma. The discussion explores the evolution from DNA-based to RNA-based genomic analysis in RCC, focusing on their study of over 600 patients' gene expression signatures across different RCC subtypes. Dr. Barata emphasizes that non-clear cell RCC comprises biologically distinct
- [MGI Tech Partners with Human Cell Atlas to expand single cell RNA sequencing and spatial transcriptomics access](https://www.rna-seqblog.com/mgi-tech-partners-with-human-cell-atlas-to-expand-single-cell-rna-sequencing-and-spatial-transcriptomics-access/) - MGI Tech, a company committed to building core tools and technologies that drive innovation in life science, today announced a commercial partnership with Human Cell Atlas (HCA) consortium to further accelerate the human cell mapping initiative. Aimed to facilitate the wider adoption of single cell sequencing and spatial transcriptomics technologies globally, MGI will expand access
- [BostonGene to present RNA Sequencing and AI advancements in tumor microenvironment profiling and precision oncology at SITC 2024](https://www.rna-seqblog.com/bostongene-to-present-rna-sequencing-and-ai-advancements-in-tumor-microenvironment-profiling-and-precision-oncology-at-sitc-2024/) - Six studies highlight advancements in AI-powered tumor microenvironment profiling, genomic analysis, biomarker identification, immune-related adverse event prediction and novel drug targets, paving the way for precision oncology BostonGene, a leading provider of AI-driven molecular and immune...
- [RNA Sequencing reveals shared gene expression patterns between Alzheimer’s disease and alcohol use disorder](https://www.rna-seqblog.com/rna-sequencing-reveals-shared-gene-expression-patterns-between-alzheimers-disease-and-alcohol-use-disorder/) - By examining RNA in hundreds of thousands of individual brain cells, Scripps Research scientists further support that alcohol use disorder could accelerate Alzheimer’s disease progression, paving the way for future targeted treatments. Researchers characterized the gene expression of more than 100,000 individual cells from brains of humans with Alzheimer’s disease and compared the patterns to
- [RealSeq Biosciences announces strategic service agreement with Tropic to advance agricultural genomics](https://www.rna-seqblog.com/realseq-biosciences-announces-strategic-service-agreement-with-tropic-to-advance-agricultural-genomics/) - RealSeq Biosciences, a leader in next-generation RNA-fragmentomics and liquid biopsy diagnostics, today announced a strategic service agreement with Tropic, an innovative biotechnology company focused on enhancing agricultural productivity and sustainability. The agreement aims to leverage...
- [RNA Institute study explores cellular response to Zika Virus infection](https://www.rna-seqblog.com/rna-institute-study-explores-cellular-response-to-zika-virus-infection/) - Developing new drugs to treat and prevent viral infections requires a precise understanding of how the virus takes hold and how the host cells respond. In a new study published in the Journal of Virology, University at Albany researchers investigated how the human body fights off Zika virus at the cellular level. Their findings illuminate new potential intervention
- [Leveraging a comprehensive unbiased RNAseq database to characterize human monocyte-derived macrophage gene expression profiles](https://www.rna-seqblog.com/leveraging-a-comprehensive-unbiased-rnaseq-database-to-characterize-human-monocyte-derived-macrophage-gene-expression-profiles/) - Macrophages are crucial players in our immune system, known for their ability to adapt to various challenges our bodies face, such as infections. These cells can change their state, known as “polarization,” in response to different signals from their environment, allowing them to perform diverse functions. Researchers often simulate these polarization states in laboratory settings
- [REDalign - accurate RNA structural alignment using residual encoder-decoder network](https://www.rna-seqblog.com/redalign-accurate-rna-structural-alignment-using-residual-encoder-decoder-network/) - RNA molecules are essential for various biological processes, and studying them helps scientists understand how cells function. A key part of this research involves examining the “secondary structures” of RNA, which are specific shapes RNA molecules fold into due to bonds between their building blocks. These shapes often reveal the molecule’s function, so scientists look
- [RNA sequencing and flow cytometry reveal the breadth of breast cell types](https://www.rna-seqblog.com/rna-sequencing-and-flow-cytometry-reveal-the-breadth-of-breast-cell-types/) - UNM Cancer Center scientist publishes a comprehensive analysis of breast cell types to better understand how breast cancers start, grow and spread October is Breast Cancer Awareness Month, and fittingly, University of New Mexico Comprehensive Cancer Center biologist Curt Hines, PhD, has published a pair of papers that comprehensively describe the twelve major types of
- [ReadStore: NGS Data Management Simplified](https://www.rna-seqblog.com/readstore-ngs-data-management-simplified/) - Managing NGS datasets and experimental metadata is often a major bottleneck in computational genomics. ReadStore is here to simplify this process, providing scientists and data analysts with a streamlined platform to manage, annotate, and access NGS datasets alongside essential experimental metadata. With ReadStore, teams can leverage a flexible database integrated into an intuitive web app,
- [Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15,2024)](https://www.rna-seqblog.com/online-workshop-bioinformatics-pipeline-development-with-nextflow-november-13-152024/) - How to manage your own data analysis pipelines using workflow management systems When? November 13-15, 2024 Where? Online Link? Website Streamline your research through the development of reproducible analysis pipelines In a nutshell Learn the fundamental best-practices of bioinformatic pipeline development Understand how workflow management systems can accelerate your research Use state-of-the-art, open source software to make complex analyses routine Perform your
- [Takara Bio Europe Expands Existing Gothenburg Site to Offer Custom Enzyme Manufacturing](https://www.rna-seqblog.com/takara-bio-europe-expands-existing-gothenburg-site-to-offer-custom-enzyme-manufacturing/) - [Gothenburg, Sweden] – 28 October 2024 – Takara Bio Europe is pleased to announce the expansion of its Gothenburg facility with the addition of a custom manufacturing lab, which came into operation on October 1st. This new facility will serve the molecular biology needs of academic researchers, diagnostic labs, and biotech companies across Europe, the
- [Parse Launches GigaLab to scale single cell sequencing to billions of cells annually](https://www.rna-seqblog.com/parse-launches-gigalab-to-scale-single-cell-sequencing-to-billions-of-cells-annually/) - Demonstrates capabilities with 10 million cells and 1,000+ samples in a single run Parse Biosciences, a leading provider of accessible and scalable single cell sequencing solutions, today announced the launch of the Parse GigaLab™ to scale single cell sequencing to billions of cells per year. The GigaLab leverages Parse’s Evercode™ single cell technology with a scaled
- [Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation](https://www.rna-seqblog.com/leveraging-deep-single-soma-rna-sequencing-to-explore-the-neural-basis-of-human-somatosensation/) - Our ability to feel sensations like touch, pain, and temperature relies on a group of specialized nerve cells called dorsal root ganglion (DRG) neurons. These neurons play a key role in how our body senses and responds to different stimuli. However, understanding the specific functions of individual DRG neurons has been challenging because we didn’t
- [Remix Therapeutics reveals unprecedented insights into RNA alternative splicing regulation through RNA sequencing](https://www.rna-seqblog.com/remix-therapeutics-reveals-unprecedented-insights-into-rna-alternative-splicing-regulation-through-rna-sequencing/) - Remix Therapeutics (Remix), a clinical-stage biotechnology company developing small molecule therapies to modulate RNA processing and address underlying drivers of disease, today announced the publication of a collaborative research study with Prof. Juan Valcárcel at the Center for Genomic Regulation in Barcelona, Spain in the prestigious journal Science. The research article, titled “Transcriptome-wide splicing network reveals specialized regulatory functions
- [scHetG - Structure-preserved integration of scRNA-seq data using heterogeneous graph neural network](https://www.rna-seqblog.com/schetg-structure-preserved-integration-of-scrna-seq-data-using-heterogeneous-graph-neural-network/) - Single-cell RNA sequencing (scRNA-seq) is a powerful technique that allows scientists to study individual cells and their gene activity. This method has revolutionized our understanding of cell states and how different cells behave in various environments. However, when researchers conduct experiments in different batches or settings, it can be challenging to combine the data from
- [A benchmark of RNA-seq data normalization methods for transcriptome mapping](https://www.rna-seqblog.com/a-benchmark-of-rna-seq-data-normalization-methods-for-transcriptome-mapping/) - Metabolism is the set of life-sustaining chemical reactions in organisms that allows them to grow, reproduce, maintain their structures, and respond to their environments. To study how these metabolic processes change in different conditions, scientists use genome-scale metabolic models (GEMs). GEMs are like comprehensive blueprints that list all the metabolic genes and the reactions they
- [Validating RNA sequencing predictions - Quantum-Si showcases next-generation protein sequencing](https://www.rna-seqblog.com/validating-rna-sequencing-predictions-quantum-si-showcases-next-generation-protein-sequencing/) - Quantum-Si, The Protein Sequencing Company™, today announced its attendance at the 2024 American Society of Human Genetics (ASHG) Annual Meeting, where it will host a sponsored talk on the role of Next-Generation Protein Sequencing (NGPS) in advancing genomics research. The presentation, titled “From Prediction to Protein: Validating Transcriptomics Data with Quantum-Si’s Next-Generation Protein Sequencing Technology,”
- [UC San Diego researchers explore genetic vulnerability to substance use disorders with RNA sequencing](https://www.rna-seqblog.com/uc-san-diego-researchers-explore-genetic-vulnerability-to-substance-use-disorders-with-rna-sequencing/) - The human amygdala (pictured in orange) plays an important role in addiction. Researchers at the Center for Genetics, Genomics, and Epigenetics of Substance Use Disorders in Outbred Rats study genes in the amygdalas of heterogeneous stock (HS) rats as a model for understanding why some people are more susceptible to substance use disorders than others.
- [Understanding aging through the lens of single-cell RNA sequencing](https://www.rna-seqblog.com/understanding-aging-through-the-lens-of-single-cell-rna-sequencing/) - Aging is a natural process that affects all living organisms, but understanding how it occurs at a molecular level has been a complex challenge for scientists. Recently, researchers have used a powerful technique called single-cell RNA sequencing (scRNA-seq) to study the genes active in aging cells. While this technology has allowed scientists to gather valuable
- [ZINBStein - shrinkage estimation of gene interaction networks in single-cell RNA sequencing data](https://www.rna-seqblog.com/zinbstein-shrinkage-estimation-of-gene-interaction-networks-in-single-cell-rna-sequencing-data/) - Understanding how genes interact with one another is crucial for unraveling the complexities of biological processes. Think of gene interaction networks as complex webs where genes (the nodes) are connected by various interactions (the edges). These interactions can involve how genes regulate each other, how their protein products interact, or how they participate in metabolic
- [Seq-Scope - repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics](https://www.rna-seqblog.com/seq-scope-repurposing-illumina-sequencing-flow-cells-for-high-resolution-spatial-transcriptomics/) - Spatial transcriptomics (ST) is reshaping how scientists study gene expression in tissues. Traditional methods like immunostaining and RNA in situ hybridization focus on a limited number of genes, which restricts researchers’ ability to get a complete picture of what’s happening in a tissue sample at the molecular level. ST, however, allows scientists to explore the
- [The roots of fear - unraveling the amygdala with insights from single-cell RNA sequencing on anxiety and depression disorders](https://www.rna-seqblog.com/the-roots-of-fear-unraveling-the-amygdala-with-insights-from-single-cell-rna-sequencing-on-anxiety-and-depression-disorders/) - Treating anxiety, depression and other disorders may depend on the amygdala, a part of the brain that controls strong emotional reactions, especially fear. But a deep understanding of this structure has been lacking. Now scientists at the University of California, Davis have identified new clusters of cells with differing patterns of gene expression in the
- [Novel colon cancer subtype identifier based on RNA splicing](https://www.rna-seqblog.com/novel-colon-cancer-subtype-identifier-based-on-rna-splicing/) - Researchers have discovered an alternative way to classify distinct types of colon cancer, making the information more valuable to patients and their doctors as they consider treatment. A team at Wilmot Cancer Institute collaborated with a German company, Indivumed...
- [GRUpred-m5U - a robust deep learning approach for identification of RNA 5-methyluridine sites](https://www.rna-seqblog.com/grupred-m5u-a-robust-deep-learning-approach-for-identification-of-rna-5-methyluridine-sites/) - RNA molecules play crucial roles in various processes, including gene expression, protein synthesis, and cellular function. One significant aspect of RNA research is understanding how modifications to RNA can influence these processes. One such modification is known as...
- [QUIC-seq - quick ultra-affordable high-throughput convenient RNA sequencing](https://www.rna-seqblog.com/quic-seq-quick-ultra-affordable-high-throughput-convenient-rna-sequencing/) - Understanding how genes function and regulate biological processes requires accurate measurement of transcript levels, which represent how much of a specific RNA molecule is present in a cell. Various techniques have been developed to analyze these transcript levels, with transcriptome sequencing being one of the most prominent methods. A standard RNA sequencing (RNA-seq) experiment involves
- [Wobble Genomics' new tech demonstrates the power of RNA sequencing in identifying rare RNA transcript variants](https://www.rna-seqblog.com/wobble-genomics-new-tech-demonstrates-the-power-of-rna-sequencing-in-identifying-rare-rna-transcript-variants/) - Wobble Genomics, a healthcare and biotechnology company at the forefront of long-read RNA sequencing, will present data today demonstrating that its technology can detect rare full-length RNA transcript variants not picked up by other methods. Wobble’s technology utilised full-length RNA transcripts as biomarkers to achieve early-stage breast cancer detection with 80% sensitivity at 95% specificity.
- [Memento - method of moments framework for differential expression analysis of single-cell RNA sequencing data](https://www.rna-seqblog.com/memento-method-of-moments-framework-for-differential-expression-analysis-of-single-cell-rna-sequencing-data/) - Single-cell RNA sequencing (scRNA-seq) is a powerful technique that allows scientists to study how genes are expressed in individual cells. This approach helps us understand how cells behave under different conditions—whether they’re fighting infections, responding to treatments, or affected by genetic changes. However, analyzing scRNA-seq data isn’t straightforward because there can be a lot of
- [LoDEI - a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data](https://www.rna-seqblog.com/lodei-a-robust-and-sensitive-tool-to-detect-transcriptome-wide-differential-a-to-i-editing-in-rna-seq-data/) - RNA editing is a vital biological process that involves modifying RNA molecules after they are created from DNA. One of the most well-known types of RNA editing is called adenosine-to-inosine (A-to-I) editing, which is facilitated by enzymes known as adenosine deaminases, particularly ADAR. This process is important for various biological functions and has significant implications
- [Sample multiplexing for retinal single-cell RNA-sequencing](https://www.rna-seqblog.com/sample-multiplexing-for-retinal-single-cell-rna-sequencing/) - Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying gene expression at the cellular level. However, it can be tricky to analyze rare cell populations, especially when working with tiny, hard-to-find groups of cells. Researchers often face the challenge of collecting enough rare cells for reliable data. Traditionally, scientists enrich the target cells from
- [Single-nucleus transcriptomics identifies new classes of fat cells](https://www.rna-seqblog.com/single-nucleus-transcriptomics-identifies-new-classes-of-fat-cells/) - Adipose tissue, commonly known as body fat, plays a vital role in our body’s ability to manage energy and regulate temperature. Recent research has discovered that certain fat cells, specifically beige adipocytes, can recruit other types of fat cells that use chemical energy to produce heat. This process can happen through two main pathways: one
- [UAlbany chemist receives federal support to advance tool for complete RNA sequencing](https://www.rna-seqblog.com/ualbany-chemist-receives-federal-support-to-advance-tool-for-complete-rna-sequencing/) - University at Albany’s Shenglong Zhang, associate professor in the Department of Chemistry and the RNA Institute, has received two Small Business Technology Transfer (STTR) grants from the National Institutes of Health totaling over $620,000. The grants were jointly awarded to the University and UAlbany spinoff company DirectSeq Biosciences, Inc., which Zhang has directed as founder and president since November 2022.
- [Circular RNA: understanding its applications in therapeutics](https://www.rna-seqblog.com/circular-rna-understanding-its-applications-in-therapeutics/) - Introduction to Circular RNA Research surrounding ribonucleic acid (RNA) has fueled countless advancements in medical science, genomics, and biology in general. It plays a vital role in many fields of study, including disease prevention and species conservation. Since its inception, RNA sequencing (RNA-Seq) has been pivotal in further advancing our understanding of how RNA works
- [Festival of Genomics & Biodata](https://www.rna-seqblog.com/festival-of-genomics-biodata/) - Registration for The Festival of Genomics & Biodata in London is now open! Join us on Wednesday 29th January – Thursday 30th January 2025 in London for inspirational speakers, the latest research and clinical breakthroughs, cutting-edge technology and incredible networking opportunities. Free for 90% of attendees, the Festival is designed to help you return to
- [m6ATM - a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data](https://www.rna-seqblog.com/m6atm-a-deep-learning-framework-for-demystifying-the-m6a-epitranscriptome-with-nanopore-long-read-rna-seq-data/) - N6-methyladenosine (m6A) is a chemical modification found in messenger RNA (mRNA), and it has gained attention since its discovery...
- [A brief guide to analyzing expression quantitative trait loci](https://www.rna-seqblog.com/a-brief-guide-to-analyzing-expression-quantitative-trait-loci/) - Molecular quantitative trait loci (molQTL) mapping is a powerful tool that helps scientists understand how genetic variations can affect the molecular processes inside cells, shedding light on the underlying causes of diseases and complex traits. One of the most common types of molQTL is expression quantitative trait loci (eQTL), which focuses on how certain genetic
- [PacBio Onso™ Short Read Sequencing Instrument Joins 10x Genomics Compatible Partner Program](https://www.rna-seqblog.com/pacbio-onso-short-read-sequencing-instrument-joins-10x-genomics-compatible-partner-program/) - PacBio, a leading developer of high-quality, highly accurate genomic sequencing solutions, today announced the inclusion of the Onso short-read sequencing platform in the 10x Genomics Compatible Partner Program. The 10x Genomics Compatible Partner Program recognizes instruments and workflows compatible with 10x Genomics’ products and applications, thereby broadening the range of sequencing solutions available to researchers
- [LABEL-seq - multiplexed profiling of intracellular protein abundance, activity, interactions and druggability](https://www.rna-seqblog.com/label-seq-multiplexed-profiling-of-intracellular-protein-abundance-activity-interactions-and-druggability/) - Understanding how proteins work inside our cells is key to figuring out disease mechanisms and developing new treatments. A recent study at the University of Washington introduces LABEL-seq, a novel tool that makes it easier to study large numbers of protein variants simultaneously, helping scientists understand how tiny changes in proteins can impact their function
- [scCaT - an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing](https://www.rna-seqblog.com/sccat-an-explainable-capsulating-architecture-for-sepsis-diagnosis-transferring-from-single-cell-rna-sequencing/) - Sepsis is a serious medical condition that occurs when the body has an extreme response to an infection. This reaction can lead to damage to the organs and, unfortunately, high rates of death, especially in critically ill patients in intensive care units. Diagnosing sepsis quickly and accurately is crucial, but current methods often struggle due
- [PROFIT-seq - real-time and programmable transcriptome sequencing](https://www.rna-seqblog.com/profit-seq-real-time-and-programmable-transcriptome-sequencing/) - The eukaryotic transcriptome is incredibly complex, with many types of RNA molecules—including messenger RNAs (mRNAs), non-coding RNAs, and circular RNAs—interacting within cells...
- [Single-cell RNA-sequencing provides cellular roadmap reveals new paths to treating inflammatory bowel disease](https://www.rna-seqblog.com/single-cell-rna-sequencing-provides-cellular-roadmap-reveals-new-paths-to-treating-inflammatory-bowel-disease/) - In a world first, researchers at the Kennedy Institute, Oxford have mapped the cellular dynamics following treatment with the most commonly used advanced therapy in autoimmune diseases. They have discovered why some patients benefit from this therapy while others do not, potentially paving the way for new therapies. Autoimmune diseases such as inflammatory bowel diseases
- [NeoGenomics Receives New York State Approval for NGS Solid Tumor Test](https://www.rna-seqblog.com/neogenomics-receives-new-york-state-approval-for-ngs-solid-tumor-test/) - NeoGenomics, a leading oncology testing services company, today announced that the New York State Department of Health (NYSDOH) has granted the company conditional approval for its Neo Comprehensive Solid Tumor assay and NeoTYPE® DNA & RNA Lung, allowing for immediate commercial access in the state of New York. These next-generation sequencing (NGS) tests deliver better diagnostic value and cost-effectiveness than
- [New Methods for RNA Modification Detection and Structure Probing](https://www.rna-seqblog.com/upcoming-webinar-new-methods-for-rna-modification-detection-and-structure-probing/) - Webinar – now available on demand - Recent advancements in next-generation sequencing technologies have provided powerful tools for RNA modification detection, yet these methods often lack the sensitivity and specificity needed to capture the full spectrum...
- [RNA sequencing unlocks new insights into DFSP treatment with patient-derived organoids](https://www.rna-seqblog.com/rna-sequencing-unlocks-new-insights-into-dfsp-treatment-with-patient-derived-organoids/) - Dermatofibrosarcoma protuberans (DFSP) is a rare skin sarcoma known for its high recurrence rates, making treatment particularly challenging. While surgery remains the standard option, it often leads to scarring and other complications. Current in vitro models struggle to capture the complexity of the skin tumor environment, especially the role of immune cells. These limitations highlight
- [Why the future of personalized medicine will require new machine learning tools and methods for analyzing single cell omics data](https://www.rna-seqblog.com/why-the-future-of-personalized-medicine-will-require-new-machine-learning-tools-and-methods-for-analyzing-single-cell-omics-data/) - While not everything in this world improves with age, technologies tend to get better and cheaper over time. This is good news for the sciences. Moore’s oft-cited law describes how the number of transistors that can be squeezed onto an integrated circuit doubles approximately every two years, with attendant improvements in processing power and little
- [Single-cell sequencing of python RNA uncovers conserved regenerative mechanisms in humans](https://www.rna-seqblog.com/single-cell-sequencing-of-python-rna-uncovers-conserved-regenerative-mechanisms-in-humans/) - UT Arlington research on pythons provides insights into human diseases like diabetes and cancer High-resolution, single-cell sequencing of python RNA uncovers conserved regenerative mechanisms in humans All animals possess some capacity for repairing and replacing the lining of their intestines, a process called intestinal regeneration. In mammals, including humans, this constant but relatively minor turnover
- [Postdoc position available - RNA-seq analyst](https://www.rna-seqblog.com/postdoc-position-available-rna-seq-analyst/) - Applications are invited for appointment as a Post-doctoral Fellow in Single Cell and Spatial Omics for two years, with the possibility of renewal subject to funding availability and satisfactory performance...
- [Enhancing RNA-seq analysis by addressing all co-existing biases](https://www.rna-seqblog.com/enhancing-rna-seq-analysis-by-addressing-all-co-existing-biases/) - RNA sequencing (RNA-seq) helps scientists study which genes are active in cells by reading the RNA molecules they produce. However, RNA-seq data often contains biases—errors that arise from sample preparation or sequencing technology. These biases can skew the results, making it harder for researchers to accurately interpret gene activity. To solve this problem, scientists at
- [scTWAS Atlas - an integrative knowledgebase of single-cell transcriptome-wide association studies](https://www.rna-seqblog.com/sctwas-atlas-an-integrative-knowledgebase-of-single-cell-transcriptome-wide-association-studies/) - Single-cell transcriptome-wide association studies (scTWAS) bring a more precise way of studying gene-trait associations. Traditional TWAS approaches often struggle with the complexity of cell-type heterogeneity, meaning it can be hard to tell which specific cell types are driving observed genetic associations. scTWAS solves this issue by analyzing genetic data at the single-cell level, helping researchers
- [Bridging the gap – enhancing and unifying bone RNA-seq data](https://www.rna-seqblog.com/bridging-the-gap-enhancing-and-unifying-bone-rna-seq-data/) - Single-cell RNA sequencing, or scRNA-seq, has revolutionized the way scientists study cells, by grouping them based on similar gene expression. Although several scRNA-seq studies have explored bone physiology, they often lacked sufficient data on some cell populations and reached divergent conclusions, assigning different names to similar cell clusters. These discrepancies hinder research efforts and complicate
- [SELF-Former - multi-scale gene filtration transformer for single-cell spatial reconstruction](https://www.rna-seqblog.com/self-former-multi-scale-gene-filtration-transformer-for-single-cell-spatial-reconstruction/) - Scientists have developed incredible tools to study how genes are expressed in individual cells, giving us insight into the complex workings of tissues. Two key technologies are single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). However, one big challenge has been combining these two approaches to understand not only what genes are active but where

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## Tags

- [$1000 genome](https://www.rna-seqblog.com/tag/1000-genome/)
- [1000 genomes](https://www.rna-seqblog.com/tag/1000-genomes/)
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- [a to i editing](https://www.rna-seqblog.com/tag/a-to-i-editing/)
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- [abrf](https://www.rna-seqblog.com/tag/abrf/)
- [acute lymphoblastic leukemia](https://www.rna-seqblog.com/tag/acute-lymphoblastic-leukemia/)
- [adipogenesis](https://www.rna-seqblog.com/tag/adipogenesis/)
- [Adriatic sturgeon](https://www.rna-seqblog.com/tag/adriatic-sturgeon/)
- [Advanced Analytical](https://www.rna-seqblog.com/tag/advanced-analytical/)
- [affymetrix](https://www.rna-seqblog.com/tag/affymetrix/)
- [Affymetrix Human Exon](https://www.rna-seqblog.com/tag/affymetrix-human-exon/)
- [Affymetrix microarray](https://www.rna-seqblog.com/tag/affymetrix-microarray/)
- [agbt](https://www.rna-seqblog.com/tag/agbt/)
- [Agilent](https://www.rna-seqblog.com/tag/agilent/)
- [Agilent Technologies](https://www.rna-seqblog.com/tag/agilent-technologies/)
- [Albert Einstein College of Medicine](https://www.rna-seqblog.com/tag/albert-einstein-college-of-medicine/)
- [alignment algorithm](https://www.rna-seqblog.com/tag/alignment-algorithm/)
- [allele frequencies](https://www.rna-seqblog.com/tag/allele-frequencies/)
- [allele frequency](https://www.rna-seqblog.com/tag/allele-frequency/)
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- [allelic expression](https://www.rna-seqblog.com/tag/allelic-expression/)
- [altanalyze](https://www.rna-seqblog.com/tag/altanalyze/)
- [alternatice splicing](https://www.rna-seqblog.com/tag/alternatice-splicing/)
- [alternative splice](https://www.rna-seqblog.com/tag/alternative-splice/)
- [alternative splicing](https://www.rna-seqblog.com/tag/alternative-splicing/)
- [Alternative Splicing Events](https://www.rna-seqblog.com/tag/alternative-splicing-events/)
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- [biological replicates](https://www.rna-seqblog.com/tag/biological-replicates/)
- [biological variation](https://www.rna-seqblog.com/tag/biological-variation/)
- [Biomarker Discovery](https://www.rna-seqblog.com/tag/biomarker-discovery/)
- [Biomarkers](https://www.rna-seqblog.com/tag/biomarkers/)
- [Bioo Scientific](https://www.rna-seqblog.com/tag/bioo-scientific/)
- [bladder cancer](https://www.rna-seqblog.com/tag/bladder-cancer/)
- [BMC Bioinformatics](https://www.rna-seqblog.com/tag/bmc-bioinformatics/)
- [Boston University School of Medicine](https://www.rna-seqblog.com/tag/boston-university-school-of-medicine/)
- [bowtie](https://www.rna-seqblog.com/tag/bowtie/)
- [Bowtie 2](https://www.rna-seqblog.com/tag/bowtie-2/)
- [breast cancer](https://www.rna-seqblog.com/tag/breast-cancer/)
- [BRIC-seq](https://www.rna-seqblog.com/tag/bric-seq/)
- [broad institute](https://www.rna-seqblog.com/tag/broad-institute/)
- [Brown University](https://www.rna-seqblog.com/tag/brown-university/)
- [bwa](https://www.rna-seqblog.com/tag/bwa/)
- [c. elegans](https://www.rna-seqblog.com/tag/c-elegans/)
- [C1 Single-Cell Auto Prep System](https://www.rna-seqblog.com/tag/c1-single-cell-auto-prep-system/)
- [Caenorhabditis elegans](https://www.rna-seqblog.com/tag/caenorhabditis-elegans/)
- [Cambridge Healthtech Institute](https://www.rna-seqblog.com/tag/cambridge-healthtech-institute/)
- [Campylobacter jejuni](https://www.rna-seqblog.com/tag/campylobacter-jejuni/)
- [cancer](https://www.rna-seqblog.com/tag/cancer/)
- [Cancer Genome Atlas](https://www.rna-seqblog.com/tag/cancer-genome-atlas/)
- [cancer transcriptome](https://www.rna-seqblog.com/tag/cancer-transcriptome/)
- [Candida albicans](https://www.rna-seqblog.com/tag/candida-albicans/)
- [CaptureSeq](https://www.rna-seqblog.com/tag/captureseq/)
- [Carnegie Mellon University](https://www.rna-seqblog.com/tag/carnegie-mellon-university/)
- [Case Western Reserve University](https://www.rna-seqblog.com/tag/case-western-reserve-university/)
- [Case Western Reserve University School of Medicine](https://www.rna-seqblog.com/tag/case-western-reserve-university-school-of-medicine/)
- [cDNA](https://www.rna-seqblog.com/tag/cdna/)
- [cDNA libraries](https://www.rna-seqblog.com/tag/cdna-libraries/)
- [cDNA microarrays](https://www.rna-seqblog.com/tag/cdna-microarrays/)
- [cdna sequencing](https://www.rna-seqblog.com/tag/cdna-sequencing/)
- [cDNA synthesis](https://www.rna-seqblog.com/tag/cdna-synthesis/)
- [CEL-Seq](https://www.rna-seqblog.com/tag/cel-seq/)
- [Cell](https://www.rna-seqblog.com/tag/cell/)
- [cellular heterogeneity](https://www.rna-seqblog.com/tag/cellular-heterogeneity/)
- [CEM](https://www.rna-seqblog.com/tag/cem/)
- [CeMM Research Center for Molecular Medicine](https://www.rna-seqblog.com/tag/cemm-research-center-for-molecular-medicine/)
- [Centre for Genomic Regulation](https://www.rna-seqblog.com/tag/centre-for-genomic-regulation/)
- [Chalmers University of Technology](https://www.rna-seqblog.com/tag/chalmers-university-of-technology/)
- [chimeras](https://www.rna-seqblog.com/tag/chimeras/)
- [chimerascan](https://www.rna-seqblog.com/tag/chimerascan/)
- [Chimeric transcripts](https://www.rna-seqblog.com/tag/chimeric-transcripts/)
- [Chinese Academy of Sciences](https://www.rna-seqblog.com/tag/chinese-academy-of-sciences/)
- [chip-seq](https://www.rna-seqblog.com/tag/chip-seq/)
- [chromosome rearrangements](https://www.rna-seqblog.com/tag/chromosome-rearrangements/)
- [chronic lymphocytic leukemia](https://www.rna-seqblog.com/tag/chronic-lymphocytic-leukemia/)
- [Cincinnati Children's Hospital Medical Center](https://www.rna-seqblog.com/tag/cincinnati-childrens-hospital-medical-center/)
- [classification](https://www.rna-seqblog.com/tag/classification/)
- [clc bio](https://www.rna-seqblog.com/tag/clc-bio/)
- [clc genomics workbench](https://www.rna-seqblog.com/tag/clc-genomics-workbench/)
- [Clontech Laboratories](https://www.rna-seqblog.com/tag/clontech-laboratories/)
- [cloud computing](https://www.rna-seqblog.com/tag/cloud-computing/)
- [clustering gene expression](https://www.rna-seqblog.com/tag/clustering-gene-expression/)
- [coexpression networks](https://www.rna-seqblog.com/tag/coexpression-networks/)
- [cofactor genomics](https://www.rna-seqblog.com/tag/cofactor-genomics/)
- [Cold Spring Harbor Laboratory](https://www.rna-seqblog.com/tag/cold-spring-harbor-laboratory/)
- [colon cancer](https://www.rna-seqblog.com/tag/colon-cancer/)
- [Comparative genomics](https://www.rna-seqblog.com/tag/comparative-genomics/)
- [comparative transcriptomics](https://www.rna-seqblog.com/tag/comparative-transcriptomics/)
- [Complete Genomics](https://www.rna-seqblog.com/tag/complete-genomics/)
- [Computational Biologist](https://www.rna-seqblog.com/tag/computational-biologist/)
- [Computational Biology](https://www.rna-seqblog.com/tag/computational-biology/)
- [Conference](https://www.rna-seqblog.com/tag/conference/)
- [contextmap](https://www.rna-seqblog.com/tag/contextmap/)
- [coral](https://www.rna-seqblog.com/tag/coral/)
- [Crassostrea gigas](https://www.rna-seqblog.com/tag/crassostrea-gigas/)
- [crRNA](https://www.rna-seqblog.com/tag/crrna/)
- [cuffdiff](https://www.rna-seqblog.com/tag/cuffdiff/)
- [cufflinks](https://www.rna-seqblog.com/tag/cufflinks/)
- [cummerbund](https://www.rna-seqblog.com/tag/cummerbund/)
- [cyanobacteria](https://www.rna-seqblog.com/tag/cyanobacteria/)
- [Cytokinin](https://www.rna-seqblog.com/tag/cytokinin/)
- [dana farber](https://www.rna-seqblog.com/tag/dana-farber/)
- [danio rerio](https://www.rna-seqblog.com/tag/danio-rerio/)
- [data analysis pipeline](https://www.rna-seqblog.com/tag/data-analysis-pipeline/)
- [data analysis software](https://www.rna-seqblog.com/tag/data-analysis-software/)
- [data analysis tools](https://www.rna-seqblog.com/tag/data-analysis-tools/)
- [database](https://www.rna-seqblog.com/tag/database/)
- [Database Issue](https://www.rna-seqblog.com/tag/database-issue/)
- [Davis](https://www.rna-seqblog.com/tag/davis/)
- [de novo assembly](https://www.rna-seqblog.com/tag/de-novo-assembly/)
- [deep sequencing](https://www.rna-seqblog.com/tag/deep-sequencing/)
- [Deepwater Horizon](https://www.rna-seqblog.com/tag/deepwater-horizon/)
- [degradome](https://www.rna-seqblog.com/tag/degradome/)
- [degradome sequencing](https://www.rna-seqblog.com/tag/degradome-sequencing/)
- [deseq](https://www.rna-seqblog.com/tag/deseq/)
- [dexseq](https://www.rna-seqblog.com/tag/dexseq/)
- [DGE](https://www.rna-seqblog.com/tag/dge/)
- [Dicer](https://www.rna-seqblog.com/tag/dicer/)
- [differential analysis](https://www.rna-seqblog.com/tag/differential-analysis/)
- [differential expression](https://www.rna-seqblog.com/tag/differential-expression/)
- [Differential expression analysis](https://www.rna-seqblog.com/tag/differential-expression-analysis/)
- [differential gene expression](https://www.rna-seqblog.com/tag/differential-gene-expression/)
- [DiffSplice](https://www.rna-seqblog.com/tag/diffsplice/)
- [digital gene expression](https://www.rna-seqblog.com/tag/digital-gene-expression/)
- [dna microarrays](https://www.rna-seqblog.com/tag/dna-microarrays/)
- [dna sequencing](https://www.rna-seqblog.com/tag/dna-sequencing/)
- [dnastar](https://www.rna-seqblog.com/tag/dnastar/)
- [DOE Joint Genome Institute](https://www.rna-seqblog.com/tag/doe-joint-genome-institute/)
- [DP-seq](https://www.rna-seqblog.com/tag/dp-seq/)
- [drosophila](https://www.rna-seqblog.com/tag/drosophila/)
- [drosophila melanogaster](https://www.rna-seqblog.com/tag/drosophila-melanogaster/)
- [drought stress](https://www.rna-seqblog.com/tag/drought-stress/)
- [DSGseq](https://www.rna-seqblog.com/tag/dsgseq/)
- [dual rna-seq](https://www.rna-seqblog.com/tag/dual-rna-seq/)
- [Duplex-specific nuclease](https://www.rna-seqblog.com/tag/duplex-specific-nuclease/)
- [e coli](https://www.rna-seqblog.com/tag/e-coli/)
- [East China Normal University](https://www.rna-seqblog.com/tag/east-china-normal-university/)
- [EBI](https://www.rna-seqblog.com/tag/ebi/)
- [ebseq](https://www.rna-seqblog.com/tag/ebseq/)
- [edgeR](https://www.rna-seqblog.com/tag/edger/)
- [EMBL](https://www.rna-seqblog.com/tag/embl/)
- [embl-ebi](https://www.rna-seqblog.com/tag/embl-ebi/)
- [embryonic stem cells](https://www.rna-seqblog.com/tag/embryonic-stem-cells/)
- [Empirical Bayes](https://www.rna-seqblog.com/tag/empirical-bayes/)
- [encode](https://www.rna-seqblog.com/tag/encode/)
- [ensembl](https://www.rna-seqblog.com/tag/ensembl/)
- [entomology](https://www.rna-seqblog.com/tag/entomology/)
- [Epicentre](https://www.rna-seqblog.com/tag/epicentre/)
- [epigenetics](https://www.rna-seqblog.com/tag/epigenetics/)
- [epigenome](https://www.rna-seqblog.com/tag/epigenome/)
- [eQTL Mapping](https://www.rna-seqblog.com/tag/eqtl-mapping/)
- [eqtls](https://www.rna-seqblog.com/tag/eqtls/)
- [error correction](https://www.rna-seqblog.com/tag/error-correction/)
- [Escherichia coli](https://www.rna-seqblog.com/tag/escherichia-coli/)
- [estrogen receptor](https://www.rna-seqblog.com/tag/estrogen-receptor/)
- [European Molecular Biology Laboratory](https://www.rna-seqblog.com/tag/european-molecular-biology-laboratory/)
- [Evolution](https://www.rna-seqblog.com/tag/evolution/)
- [evolutionary relationships](https://www.rna-seqblog.com/tag/evolutionary-relationships/)
- [exome sequencing](https://www.rna-seqblog.com/tag/exome-sequencing/)
- [exon array](https://www.rna-seqblog.com/tag/exon-array/)
- [exon microarrays](https://www.rna-seqblog.com/tag/exon-microarrays/)
- [exons](https://www.rna-seqblog.com/tag/exons/)
- [exosome rna](https://www.rna-seqblog.com/tag/exosome-rna/)
- [exosomes](https://www.rna-seqblog.com/tag/exosomes/)
- [experimental biology](https://www.rna-seqblog.com/tag/experimental-biology/)
- [experimental design](https://www.rna-seqblog.com/tag/experimental-design/)
- [eXpress](https://www.rna-seqblog.com/tag/express/)
- [expression](https://www.rna-seqblog.com/tag/expression/)
- [expression analysis](https://www.rna-seqblog.com/tag/expression-analysis/)
- [Expression and Quantification](https://www.rna-seqblog.com/tag/expression-and-quantification/)
- [expression level](https://www.rna-seqblog.com/tag/expression-level/)
- [expression levels](https://www.rna-seqblog.com/tag/expression-levels/)
- [expression profiling](https://www.rna-seqblog.com/tag/expression-profiling/)
- [expression quantification](https://www.rna-seqblog.com/tag/expression-quantification/)
- [External RNA Control Consortium](https://www.rna-seqblog.com/tag/external-rna-control-consortium/)
- [fda](https://www.rna-seqblog.com/tag/fda/)
- [FDM](https://www.rna-seqblog.com/tag/fdm/)
- [FFPE samples](https://www.rna-seqblog.com/tag/ffpe-samples/)
- [Fluidigm](https://www.rna-seqblog.com/tag/fluidigm/)
- [flybase](https://www.rna-seqblog.com/tag/flybase/)
- [Foundation Medicine](https://www.rna-seqblog.com/tag/foundation-medicine/)
- [FPKM](https://www.rna-seqblog.com/tag/fpkm/)
- [Fred Hutchinson Cancer Research Center](https://www.rna-seqblog.com/tag/fred-hutchinson-cancer-research-center/)
- [Fudan University](https://www.rna-seqblog.com/tag/fudan-university/)
- [Functional Genomics Center Zurich](https://www.rna-seqblog.com/tag/functional-genomics-center-zurich/)
- [fusion gene](https://www.rna-seqblog.com/tag/fusion-gene/)
- [fusion transcripts](https://www.rna-seqblog.com/tag/fusion-transcripts/)
- [fusionhunter](https://www.rna-seqblog.com/tag/fusionhunter/)
- [galaxy](https://www.rna-seqblog.com/tag/galaxy/)
- [Galaxy platform](https://www.rna-seqblog.com/tag/galaxy-platform/)
- [gen fusions](https://www.rna-seqblog.com/tag/gen-fusions/)
- [gencode](https://www.rna-seqblog.com/tag/gencode/)
- [gene annotation](https://www.rna-seqblog.com/tag/gene-annotation/)
- [gene atlas](https://www.rna-seqblog.com/tag/gene-atlas/)
- [gene expression](https://www.rna-seqblog.com/tag/gene-expression/)
- [gene expression quantification](https://www.rna-seqblog.com/tag/gene-expression-quantification/)
- [gene finding](https://www.rna-seqblog.com/tag/gene-finding/)
- [gene fusion](https://www.rna-seqblog.com/tag/gene-fusion/)
- [gene fusions](https://www.rna-seqblog.com/tag/gene-fusions/)
- [gene ontology](https://www.rna-seqblog.com/tag/gene-ontology/)
- [gene prediction](https://www.rna-seqblog.com/tag/gene-prediction/)
- [gene set analysis](https://www.rna-seqblog.com/tag/gene-set-analysis/)
- [gene set enrichment](https://www.rna-seqblog.com/tag/gene-set-enrichment/)
- [Gene set enrichment analysis](https://www.rna-seqblog.com/tag/gene-set-enrichment-analysis/)
- [gene-expression profiling](https://www.rna-seqblog.com/tag/gene-expression-profiling/)
- [Genentech](https://www.rna-seqblog.com/tag/genentech/)
- [genepattern](https://www.rna-seqblog.com/tag/genepattern/)
- [genetic engineering news](https://www.rna-seqblog.com/tag/genetic-engineering-news/)
- [Genohub](https://www.rna-seqblog.com/tag/genohub/)
- [genome](https://www.rna-seqblog.com/tag/genome/)
- [genome annotation](https://www.rna-seqblog.com/tag/genome-annotation/)
- [Genome Biol](https://www.rna-seqblog.com/tag/genome-biol/)
- [genome browser](https://www.rna-seqblog.com/tag/genome-browser/)
- [Genome Institute of Singapore](https://www.rna-seqblog.com/tag/genome-institute-of-singapore/)
- [genome-guided](https://www.rna-seqblog.com/tag/genome-guided/)
- [genome-guided assembly](https://www.rna-seqblog.com/tag/genome-guided-assembly/)
- [genomequest](https://www.rna-seqblog.com/tag/genomequest/)
- [GenomeSpace](https://www.rna-seqblog.com/tag/genomespace/)
- [genomic coordinates](https://www.rna-seqblog.com/tag/genomic-coordinates/)
- [genomic health](https://www.rna-seqblog.com/tag/genomic-health/)
- [genomic sequences](https://www.rna-seqblog.com/tag/genomic-sequences/)
- [genomics](https://www.rna-seqblog.com/tag/genomics/)
- [Genomics Proteomics Bioinformatics](https://www.rna-seqblog.com/tag/genomics-proteomics-bioinformatics/)
- [Genotype-Tissue Expression project](https://www.rna-seqblog.com/tag/genotype-tissue-expression-project/)
- [genotyping](https://www.rna-seqblog.com/tag/genotyping/)
- [George Washington University](https://www.rna-seqblog.com/tag/george-washington-university/)
- [Georgia State University](https://www.rna-seqblog.com/tag/georgia-state-university/)
- [github](https://www.rna-seqblog.com/tag/github/)
- [glycine max](https://www.rna-seqblog.com/tag/glycine-max/)
- [Golden Helix](https://www.rna-seqblog.com/tag/golden-helix/)
- [goseq](https://www.rna-seqblog.com/tag/goseq/)
- [grant program](https://www.rna-seqblog.com/tag/grant-program/)
- [granulosa cell](https://www.rna-seqblog.com/tag/granulosa-cell/)
- [GSA](https://www.rna-seqblog.com/tag/gsa/)
- [GTEx](https://www.rna-seqblog.com/tag/gtex/)
- [GWAS](https://www.rna-seqblog.com/tag/gwas/)
- [Harvard Medical School](https://www.rna-seqblog.com/tag/harvard-medical-school/)
- [helicos biosciences](https://www.rna-seqblog.com/tag/helicos-biosciences/)
- [her2](https://www.rna-seqblog.com/tag/her2/)
- [hESCs](https://www.rna-seqblog.com/tag/hescs/)
- [Hevea brasiliensis](https://www.rna-seqblog.com/tag/hevea-brasiliensis/)
- [Hierarchical Bayesian Model](https://www.rna-seqblog.com/tag/hierarchical-bayesian-model/)
- [high-throughput sequencing](https://www.rna-seqblog.com/tag/high-throughput-sequencing/)
- [HiSeq](https://www.rna-seqblog.com/tag/hiseq/)
- [hiseq 2500](https://www.rna-seqblog.com/tag/hiseq-2500/)
- [HIV](https://www.rna-seqblog.com/tag/hiv/)
- [HLA typing](https://www.rna-seqblog.com/tag/hla-typing/)
- [Hordeum vulgare](https://www.rna-seqblog.com/tag/hordeum-vulgare/)
- [HTS-KIN](https://www.rna-seqblog.com/tag/hts-kin/)
- [HTSeq](https://www.rna-seqblog.com/tag/htseq/)
- [htsstation](https://www.rna-seqblog.com/tag/htsstation/)
- [human bodymap](https://www.rna-seqblog.com/tag/human-bodymap/)
- [Icahn School of Medicine at Mount Sinai](https://www.rna-seqblog.com/tag/icahn-school-of-medicine-at-mount-sinai/)
- [igb](https://www.rna-seqblog.com/tag/igb/)
- [igv](https://www.rna-seqblog.com/tag/igv/)
- [illumina](https://www.rna-seqblog.com/tag/illumina/)
- [Illumina HiSeq](https://www.rna-seqblog.com/tag/illumina-hiseq/)
- [illumina rna-seq](https://www.rna-seqblog.com/tag/illumina-rna-seq/)
- [immune cells](https://www.rna-seqblog.com/tag/immune-cells/)
- [in situ](https://www.rna-seqblog.com/tag/in-situ/)
- [in situ sequencing](https://www.rna-seqblog.com/tag/in-situ-sequencing/)
- [Inc](https://www.rna-seqblog.com/tag/inc/)
- [Ingenity Systems](https://www.rna-seqblog.com/tag/ingenity-systems/)
- [ingenuity](https://www.rna-seqblog.com/tag/ingenuity/)
- [INRA](https://www.rna-seqblog.com/tag/inra/)
- [Institut Pasteur](https://www.rna-seqblog.com/tag/institut-pasteur/)
- [institute for systems biology](https://www.rna-seqblog.com/tag/institute-for-systems-biology/)
- [integrated genome browser](https://www.rna-seqblog.com/tag/integrated-genome-browser/)
- [internship](https://www.rna-seqblog.com/tag/internship/)
- [interpretation](https://www.rna-seqblog.com/tag/interpretation/)
- [introns](https://www.rna-seqblog.com/tag/introns/)
- [ion torrent](https://www.rna-seqblog.com/tag/ion-torrent/)
- [Iowa State University](https://www.rna-seqblog.com/tag/iowa-state-university/)
- [iplant](https://www.rna-seqblog.com/tag/iplant/)
- [iPlant Collaborative](https://www.rna-seqblog.com/tag/iplant-collaborative/)
- [iReckon](https://www.rna-seqblog.com/tag/ireckon/)
- [ireport](https://www.rna-seqblog.com/tag/ireport/)
- [isoem](https://www.rna-seqblog.com/tag/isoem/)
- [isoform](https://www.rna-seqblog.com/tag/isoform/)
- [isoform abundance](https://www.rna-seqblog.com/tag/isoform-abundance/)
- [isoform discovery](https://www.rna-seqblog.com/tag/isoform-discovery/)
- [isoform expression](https://www.rna-seqblog.com/tag/isoform-expression/)
- [Isoform Identification](https://www.rna-seqblog.com/tag/isoform-identification/)
- [Isoform Quantification](https://www.rna-seqblog.com/tag/isoform-quantification/)
- [isoforms](https://www.rna-seqblog.com/tag/isoforms/)
- [isolasso](https://www.rna-seqblog.com/tag/isolasso/)
- [isomir](https://www.rna-seqblog.com/tag/isomir/)
- [isomirs](https://www.rna-seqblog.com/tag/isomirs/)
- [job](https://www.rna-seqblog.com/tag/job/)
- [jobs](https://www.rna-seqblog.com/tag/jobs/)
- [Johns Hopkins School of Medicine](https://www.rna-seqblog.com/tag/johns-hopkins-school-of-medicine/)
- [Johns Hopkins University School of Medicine](https://www.rna-seqblog.com/tag/johns-hopkins-university-school-of-medicine/)
- [Johnson & Johnson](https://www.rna-seqblog.com/tag/johnson-johnson/)
- [junction mapping](https://www.rna-seqblog.com/tag/junction-mapping/)
- [Kansas State University](https://www.rna-seqblog.com/tag/kansas-state-university/)
- [Karolinska Institute](https://www.rna-seqblog.com/tag/karolinska-institute/)
- [Karolinska Institutet](https://www.rna-seqblog.com/tag/karolinska-institutet/)
- [KEGG](https://www.rna-seqblog.com/tag/kegg/)
- [kidney disease](https://www.rna-seqblog.com/tag/kidney-disease/)
- [kissplice](https://www.rna-seqblog.com/tag/kissplice/)
- [LC Sciences](https://www.rna-seqblog.com/tag/lc-sciences/)
- [Lexogen](https://www.rna-seqblog.com/tag/lexogen/)
- [library construction](https://www.rna-seqblog.com/tag/library-construction/)
- [library prep](https://www.rna-seqblog.com/tag/library-prep/)
- [library preparation](https://www.rna-seqblog.com/tag/library-preparation/)
- [life technologies](https://www.rna-seqblog.com/tag/life-technologies/)
- [limb regeneration](https://www.rna-seqblog.com/tag/limb-regeneration/)
- [lincRNA](https://www.rna-seqblog.com/tag/lincrna/)
- [lincRNAs](https://www.rna-seqblog.com/tag/lincrnas/)
- [lncrna](https://www.rna-seqblog.com/tag/lncrna/)
- [lncRNAs](https://www.rna-seqblog.com/tag/lncrnas/)
- [long intergenic non-coding RNA](https://www.rna-seqblog.com/tag/long-intergenic-non-coding-rna/)
- [long non-coding rna](https://www.rna-seqblog.com/tag/long-non-coding-rna/)
- [long non-coding RNAs](https://www.rna-seqblog.com/tag/long-non-coding-rnas/)
- [long noncoding RNA](https://www.rna-seqblog.com/tag/long-noncoding-rna/)
- [long-noncoding RNAs](https://www.rna-seqblog.com/tag/long-noncoding-rnas/)
- [Ludwig Institute for Cancer Research](https://www.rna-seqblog.com/tag/ludwig-institute-for-cancer-research/)
- [Ludwig-Maximilians-University](https://www.rna-seqblog.com/tag/ludwig-maximilians-university/)
- [lung cancer](https://www.rna-seqblog.com/tag/lung-cancer/)
- [Maastricht University](https://www.rna-seqblog.com/tag/maastricht-university/)
- [maize](https://www.rna-seqblog.com/tag/maize/)
- [mapping](https://www.rna-seqblog.com/tag/mapping/)
- [mapping tools](https://www.rna-seqblog.com/tag/mapping-tools-2/)
- [mapreduce](https://www.rna-seqblog.com/tag/mapreduce/)
- [maps](https://www.rna-seqblog.com/tag/maps/)
- [mapsplice](https://www.rna-seqblog.com/tag/mapsplice/)
- [Massachusetts General Hospital](https://www.rna-seqblog.com/tag/massachusetts-general-hospital/)
- [massively parallel sequencing](https://www.rna-seqblog.com/tag/massively-parallel-sequencing/)
- [MATS](https://www.rna-seqblog.com/tag/mats/)
- [Max Planck Institute for Molecular Genetics](https://www.rna-seqblog.com/tag/max-planck-institute-for-molecular-genetics/)
- [md anderson](https://www.rna-seqblog.com/tag/md-anderson/)
- [MD Anderson cancer Center](https://www.rna-seqblog.com/tag/md-anderson-cancer-center/)
- [Medical University of Vienna](https://www.rna-seqblog.com/tag/medical-university-of-vienna/)
- [melanoma](https://www.rna-seqblog.com/tag/melanoma/)
- [Metagenomic](https://www.rna-seqblog.com/tag/metagenomic/)
- [metaRNASeq](https://www.rna-seqblog.com/tag/metarnaseq/)
- [metastasis](https://www.rna-seqblog.com/tag/metastasis/)
- [metatranscriptomics](https://www.rna-seqblog.com/tag/metatranscriptomics/)
- [methods mol biol](https://www.rna-seqblog.com/tag/methods-mol-biol/)
- [methylation](https://www.rna-seqblog.com/tag/methylation/)
- [Michael Smith Genome Sciences Centre](https://www.rna-seqblog.com/tag/michael-smith-genome-sciences-centre/)
- [Michigan State University](https://www.rna-seqblog.com/tag/michigan-state-university/)
- [microarray](https://www.rna-seqblog.com/tag/microarray/)
- [microarrays](https://www.rna-seqblog.com/tag/microarrays/)
- [microbial](https://www.rna-seqblog.com/tag/microbial/)
- [microbial transcriptomes](https://www.rna-seqblog.com/tag/microbial-transcriptomes/)
- [microrna](https://www.rna-seqblog.com/tag/microrna/)
- [microrna prediction](https://www.rna-seqblog.com/tag/microrna-prediction/)
- [microrna sequencing](https://www.rna-seqblog.com/tag/microrna-sequencing/)
- [microrna-seq](https://www.rna-seqblog.com/tag/microrna-seq/)
- [MicroRNAs](https://www.rna-seqblog.com/tag/micrornas/)
- [Minnesota Supercomputing Institute](https://www.rna-seqblog.com/tag/minnesota-supercomputing-institute/)
- [mirbase](https://www.rna-seqblog.com/tag/mirbase/)
- [mirdeep](https://www.rna-seqblog.com/tag/mirdeep/)
- [mirexpress](https://www.rna-seqblog.com/tag/mirexpress/)
- [mirna](https://www.rna-seqblog.com/tag/mirna/)
- [miRNA biogenesis](https://www.rna-seqblog.com/tag/mirna-biogenesis/)
- [miRNA discovery](https://www.rna-seqblog.com/tag/mirna-discovery/)
- [mirna expression](https://www.rna-seqblog.com/tag/mirna-expression/)
- [mirna prediction](https://www.rna-seqblog.com/tag/mirna-prediction/)
- [miRNA sequencing](https://www.rna-seqblog.com/tag/mirna-sequencing/)
- [mirna targets](https://www.rna-seqblog.com/tag/mirna-targets/)
- [mirnas](https://www.rna-seqblog.com/tag/mirnas/)
- [mirnest](https://www.rna-seqblog.com/tag/mirnest/)
- [miseq](https://www.rna-seqblog.com/tag/miseq/)
- [miso](https://www.rna-seqblog.com/tag/miso/)
- [mitochondria](https://www.rna-seqblog.com/tag/mitochondria/)
- [modencode](https://www.rna-seqblog.com/tag/modencode/)
- [Monash University](https://www.rna-seqblog.com/tag/monash-university/)
- [Morgridge Institute for Research](https://www.rna-seqblog.com/tag/morgridge-institute-for-research/)
- [mosquito](https://www.rna-seqblog.com/tag/mosquito/)
- [mouse brain](https://www.rna-seqblog.com/tag/mouse-brain/)
- [mrna](https://www.rna-seqblog.com/tag/mrna/)
- [mRNA isoforms](https://www.rna-seqblog.com/tag/mrna-isoforms/)
- [mrna sequencing](https://www.rna-seqblog.com/tag/mrna-sequencing/)
- [multiplex](https://www.rna-seqblog.com/tag/multiplex/)
- [Mycobacterium tuberculosis](https://www.rna-seqblog.com/tag/mycobacterium-tuberculosis/)
- [nanoparticles](https://www.rna-seqblog.com/tag/nanoparticles/)
- [Nanyang Technological University](https://www.rna-seqblog.com/tag/nanyang-technological-university/)
- [Nat Biotechnol](https://www.rna-seqblog.com/tag/nat-biotechnol/)
- [National Human Genome Research Institute](https://www.rna-seqblog.com/tag/national-human-genome-research-institute/)
- [National Institute of Environmental Health Sciences](https://www.rna-seqblog.com/tag/national-institute-of-environmental-health-sciences/)
- [nature](https://www.rna-seqblog.com/tag/nature/)
- [nature biotechnology](https://www.rna-seqblog.com/tag/nature-biotechnology/)
- [nature methods](https://www.rna-seqblog.com/tag/nature-methods/)
- [ncrna](https://www.rna-seqblog.com/tag/ncrna/)
- [Negative Binomial](https://www.rna-seqblog.com/tag/negative-binomial/)
- [nescent academy](https://www.rna-seqblog.com/tag/nescent-academy/)
- [Network Flows](https://www.rna-seqblog.com/tag/network-flows/)
- [neuroscience](https://www.rna-seqblog.com/tag/neuroscience/)
- [New Mexico State University](https://www.rna-seqblog.com/tag/new-mexico-state-university/)
- [news](https://www.rna-seqblog.com/tag/news-2/)
- [Next Generation Sequencing Core](https://www.rna-seqblog.com/tag/next-generation-sequencing-core/)
- [next-gen sequencing](https://www.rna-seqblog.com/tag/next-gen-sequencing/)
- [next-generation sequencing](https://www.rna-seqblog.com/tag/next-generation-sequencing/)
- [Nextera](https://www.rna-seqblog.com/tag/nextera/)
- [NEXTflex](https://www.rna-seqblog.com/tag/nextflex/)
- [ngs](https://www.rna-seqblog.com/tag/ngs/)
- [NHGRI](https://www.rna-seqblog.com/tag/nhgri/)
- [NHPRTR](https://www.rna-seqblog.com/tag/nhprtr/)
- [NIAID](https://www.rna-seqblog.com/tag/niaid/)
- [NIEHS](https://www.rna-seqblog.com/tag/niehs/)
- [nih](https://www.rna-seqblog.com/tag/nih/)
- [NIMH](https://www.rna-seqblog.com/tag/nimh/)
- [nist](https://www.rna-seqblog.com/tag/nist/)
- [noiseq](https://www.rna-seqblog.com/tag/noiseq/)
- [non-coding rna](https://www.rna-seqblog.com/tag/non-coding-rna/)
- [non-coding RNAs](https://www.rna-seqblog.com/tag/non-coding-rnas/)
- [non-human primate reference transcriptome resource](https://www.rna-seqblog.com/tag/non-human-primate-reference-transcriptome-resource/)
- [noncoding rna](https://www.rna-seqblog.com/tag/noncoding-rna/)
- [Norgen Biotek](https://www.rna-seqblog.com/tag/norgen-biotek/)
- [normalization](https://www.rna-seqblog.com/tag/normalization/)
- [novartis](https://www.rna-seqblog.com/tag/novartis/)
- [novel transcripts](https://www.rna-seqblog.com/tag/novel-transcripts/)
- [novoalign](https://www.rna-seqblog.com/tag/novoalign/)
- [nucleic acids research](https://www.rna-seqblog.com/tag/nucleic-acids-research/)
- [NuGEN](https://www.rna-seqblog.com/tag/nugen/)
- [NuGEN Technologies](https://www.rna-seqblog.com/tag/nugen-technologies/)
- [number of reads](https://www.rna-seqblog.com/tag/number-of-reads/)
- [NYU school of medicine](https://www.rna-seqblog.com/tag/nyu-school-of-medicine/)
- [OGT](https://www.rna-seqblog.com/tag/ogt/)
- [omiRas](https://www.rna-seqblog.com/tag/omiras/)
- [oqtans](https://www.rna-seqblog.com/tag/oqtans/)
- [oryza sativa](https://www.rna-seqblog.com/tag/oryza-sativa/)
- [Otogenetics](https://www.rna-seqblog.com/tag/otogenetics/)
- [oxford](https://www.rna-seqblog.com/tag/oxford/)
- [Oxford Gene Technologies](https://www.rna-seqblog.com/tag/oxford-gene-technologies/)
- [p-value](https://www.rna-seqblog.com/tag/p-value/)
- [pacbio](https://www.rna-seqblog.com/tag/pacbio/)
- [pacific biosciences](https://www.rna-seqblog.com/tag/pacific-biosciences/)
- [paired-end](https://www.rna-seqblog.com/tag/paired-end/)
- [paired-end rna-seq](https://www.rna-seqblog.com/tag/paired-end-rna-seq/)
- [paired-end RNA-Seq data](https://www.rna-seqblog.com/tag/paired-end-rna-seq-data/)
- [paired-end tag sequencing](https://www.rna-seqblog.com/tag/paired-end-tag-sequencing/)
- [PARE](https://www.rna-seqblog.com/tag/pare/)
- [partek](https://www.rna-seqblog.com/tag/partek/)
- [patch-clamp](https://www.rna-seqblog.com/tag/patch-clamp/)
- [patent](https://www.rna-seqblog.com/tag/patent/)
- [pathogens](https://www.rna-seqblog.com/tag/pathogens/)
- [pathway analysis](https://www.rna-seqblog.com/tag/pathway-analysis-2/)
- [pathways](https://www.rna-seqblog.com/tag/pathways/)
- [pattern](https://www.rna-seqblog.com/tag/pattern/)
- [pcr](https://www.rna-seqblog.com/tag/pcr/)
- [perkin elmer](https://www.rna-seqblog.com/tag/perkin-elmer/)
- [pfizer](https://www.rna-seqblog.com/tag/pfizer/)
- [PGM](https://www.rna-seqblog.com/tag/pgm/)
- [pipeline](https://www.rna-seqblog.com/tag/pipeline/)
- [planarian](https://www.rna-seqblog.com/tag/planarian/)
- [plant & animal genomes](https://www.rna-seqblog.com/tag/plant-animal-genomes/)
- [plant and animal genomes](https://www.rna-seqblog.com/tag/plant-and-animal-genomes/)
- [plants](https://www.rna-seqblog.com/tag/plants/)
- [PLoS ONE](https://www.rna-seqblog.com/tag/plos-one/)
- [PNAS](https://www.rna-seqblog.com/tag/pnas/)
- [poisson](https://www.rna-seqblog.com/tag/poisson/)
- [Poisson distribution](https://www.rna-seqblog.com/tag/poisson-distribution/)
- [poll results](https://www.rna-seqblog.com/tag/poll-results/)
- [post-transcriptional regulation](https://www.rna-seqblog.com/tag/post-transcriptional-regulation/)
- [Postdoctoral Position](https://www.rna-seqblog.com/tag/postdoctoral-position/)
- [poster](https://www.rna-seqblog.com/tag/poster/)
- [pre-miRNA](https://www.rna-seqblog.com/tag/pre-mirna/)
- [PREBS](https://www.rna-seqblog.com/tag/prebs/)
- [predicting long non-coding RNAs](https://www.rna-seqblog.com/tag/predicting-long-non-coding-rnas/)
- [prostate cancer](https://www.rna-seqblog.com/tag/prostate-cancer/)
- [Protein Abundance](https://www.rna-seqblog.com/tag/protein-abundance/)
- [protein expression](https://www.rna-seqblog.com/tag/protein-expression/)
- [proteomics](https://www.rna-seqblog.com/tag/proteomics/)
- [pseudogenes](https://www.rna-seqblog.com/tag/pseudogenes/)
- [Pseudomonas aeruginosa](https://www.rna-seqblog.com/tag/pseudomonas-aeruginosa/)
- [Purdue University](https://www.rna-seqblog.com/tag/purdue-university/)
- [pyrosequencing](https://www.rna-seqblog.com/tag/pyrosequencing/)
- [qiagen](https://www.rna-seqblog.com/tag/qiagen/)
- [qpcr](https://www.rna-seqblog.com/tag/qpcr/)
- [qrt-pcr](https://www.rna-seqblog.com/tag/qrt-pcr/)
- [quantification](https://www.rna-seqblog.com/tag/quantification/)
- [Quantitative Transcriptomics](https://www.rna-seqblog.com/tag/quantitative-transcriptomics/)
- [Quartz-Seq](https://www.rna-seqblog.com/tag/quartz-seq/)
- [Quasi-likelihood](https://www.rna-seqblog.com/tag/quasi-likelihood/)
- [R package](https://www.rna-seqblog.com/tag/r-package/)
- [read length](https://www.rna-seqblog.com/tag/read-length/)
- [read mapping](https://www.rna-seqblog.com/tag/read-mapping/)
- [recount](https://www.rna-seqblog.com/tag/recount/)
- [reference genome](https://www.rna-seqblog.com/tag/reference-genome/)
- [reference transcriptome](https://www.rna-seqblog.com/tag/reference-transcriptome/)
- [Reproducibility](https://www.rna-seqblog.com/tag/reproducibility/)
- [research and markets](https://www.rna-seqblog.com/tag/research-and-markets/)
- [ribosomal depletion](https://www.rna-seqblog.com/tag/ribosomal-depletion/)
- [Ribosomal RNA](https://www.rna-seqblog.com/tag/ribosomal-rna/)
- [ribosomal RNA depletion](https://www.rna-seqblog.com/tag/ribosomal-rna-depletion/)
- [rice](https://www.rna-seqblog.com/tag/rice/)
- [RIKEN](https://www.rna-seqblog.com/tag/riken/)
- [RIP-seq](https://www.rna-seqblog.com/tag/rip-seq/)
- [Riverside](https://www.rna-seqblog.com/tag/riverside/)
- [rna](https://www.rna-seqblog.com/tag/rna/)
- [rna analysis](https://www.rna-seqblog.com/tag/rna-analysis/)
- [rna captureseq](https://www.rna-seqblog.com/tag/rna-captureseq/)
- [RNA decay](https://www.rna-seqblog.com/tag/rna-decay/)
- [RNA degradation](https://www.rna-seqblog.com/tag/rna-degradation/)
- [rna editing](https://www.rna-seqblog.com/tag/rna-editing/)
- [rna expression](https://www.rna-seqblog.com/tag/rna-expression/)
- [RNA isolation](https://www.rna-seqblog.com/tag/rna-isolation/)
- [RNA preservation](https://www.rna-seqblog.com/tag/rna-preservation/)
- [rna processing](https://www.rna-seqblog.com/tag/rna-processing/)
- [rna profiling](https://www.rna-seqblog.com/tag/rna-profiling/)
- [rna sequence](https://www.rna-seqblog.com/tag/rna-sequence/)
- [rna sequence analysis](https://www.rna-seqblog.com/tag/rna-sequence-analysis/)
- [rna sequencing](https://www.rna-seqblog.com/tag/rna-sequencing/)
- [RNA Sequencing Data](https://www.rna-seqblog.com/tag/rna-sequencing-data/)
- [rna sequencing service](https://www.rna-seqblog.com/tag/rna-sequencing-service/)
- [rna splicing](https://www.rna-seqblog.com/tag/rna-splicing/)
- [RNA stability](https://www.rna-seqblog.com/tag/rna-stability/)
- [rna structure](https://www.rna-seqblog.com/tag/rna-structure/)
- [RNA transcripts](https://www.rna-seqblog.com/tag/rna-transcripts/)
- [RNA-binding proteins](https://www.rna-seqblog.com/tag/rna-binding-proteins/)
- [RNA-Seq](https://www.rna-seqblog.com/tag/rna-seq/)
- [RNA-Seq analysis](https://www.rna-seqblog.com/tag/rna-seq-analysis/)
- [RNA-seq analysis pipeline](https://www.rna-seqblog.com/tag/rna-seq-analysis-pipeline/)
- [RNA-Seq assembly](https://www.rna-seqblog.com/tag/rna-seq-assembly/)
- [rna-seq blog](https://www.rna-seqblog.com/tag/rna-seq-blog/)
- [rna-seq data analysis](https://www.rna-seqblog.com/tag/rna-seq-data-analysis/)
- [rna-seq data sets](https://www.rna-seqblog.com/tag/rna-seq-data-sets/)
- [rna-seq europe](https://www.rna-seqblog.com/tag/rna-seq-europe/)
- [RNA-seq experimental design](https://www.rna-seqblog.com/tag/rna-seq-experimental-design/)
- [rna-seq jobs](https://www.rna-seqblog.com/tag/rna-seq-jobs/)
- [RNA-Seq libraries](https://www.rna-seqblog.com/tag/rna-seq-libraries/)
- [rna-seq pipeline](https://www.rna-seqblog.com/tag/rna-seq-pipeline/)
- [RNA-Seq Quantification](https://www.rna-seqblog.com/tag/rna-seq-quantification/)
- [rna-seq simulator](https://www.rna-seqblog.com/tag/rna-seq-simulator/)
- [RNA-Seq Summit](https://www.rna-seqblog.com/tag/rna-seq-summit/)
- [rna-seq workshop](https://www.rna-seqblog.com/tag/rna-seq-workshop/)
- [rna-seqc](https://www.rna-seqblog.com/tag/rna-seqc/)
- [rnaseq](https://www.rna-seqblog.com/tag/rnaseq/)
- [roche](https://www.rna-seqblog.com/tag/roche/)
- [rockefeller university](https://www.rna-seqblog.com/tag/rockefeller-university/)
- [Rockhopper](https://www.rna-seqblog.com/tag/rockhopper/)
- [rpkm](https://www.rna-seqblog.com/tag/rpkm/)
- [rRNA](https://www.rna-seqblog.com/tag/rrna/)
- [rRNA depletion](https://www.rna-seqblog.com/tag/rrna-depletion/)
- [rsem](https://www.rna-seqblog.com/tag/rsem/)
- [rseqc](https://www.rna-seqblog.com/tag/rseqc/)
- [rubber tree](https://www.rna-seqblog.com/tag/rubber-tree/)
- [Rubicon Genomics](https://www.rna-seqblog.com/tag/rubicon-genomics/)
- [Sailfish](https://www.rna-seqblog.com/tag/sailfish/)
- [Salk Institute](https://www.rna-seqblog.com/tag/salk-institute/)
- [Salmonella enterica](https://www.rna-seqblog.com/tag/salmonella-enterica/)
- [sample size](https://www.rna-seqblog.com/tag/sample-size/)
- [sanger](https://www.rna-seqblog.com/tag/sanger/)
- [SB Genomics](https://www.rna-seqblog.com/tag/sb-genomics/)
- [sbir](https://www.rna-seqblog.com/tag/sbir/)
- [schizophrenia](https://www.rna-seqblog.com/tag/schizophrenia/)
- [scripture](https://www.rna-seqblog.com/tag/scripture/)
- [SEECER](https://www.rna-seqblog.com/tag/seecer/)
- [seminar](https://www.rna-seqblog.com/tag/seminar/)
- [SENIOR BIOINFORMATICS SPECIALIST](https://www.rna-seqblog.com/tag/senior-bioinformatics-specialist/)
- [SeqGSEA](https://www.rna-seqblog.com/tag/seqgsea/)
- [seqmonk](https://www.rna-seqblog.com/tag/seqmonk/)
- [Sequence Alignment](https://www.rna-seqblog.com/tag/sequence-alignment/)
- [sequence database](https://www.rna-seqblog.com/tag/sequence-database/)
- [sequencing](https://www.rna-seqblog.com/tag/sequencing/)
- [sequencing bias](https://www.rna-seqblog.com/tag/sequencing-bias/)
- [sequencing depth](https://www.rna-seqblog.com/tag/sequencing-depth/)
- [sequencing library](https://www.rna-seqblog.com/tag/sequencing-library/)
- [sequencing rna](https://www.rna-seqblog.com/tag/sequencing-rna/)
- [sequencing technologies](https://www.rna-seqblog.com/tag/sequencing-technologies/)
- [sequencing technology](https://www.rna-seqblog.com/tag/sequencing-technology/)
- [SevenBridges Genomics](https://www.rna-seqblog.com/tag/sevenbridges-genomics/)
- [sex chromosome](https://www.rna-seqblog.com/tag/sex-chromosome/)
- [Shannon Entropy](https://www.rna-seqblog.com/tag/shannon-entropy/)
- [short read sequencing](https://www.rna-seqblog.com/tag/short-read-sequencing/)
- [Simon Fraser University](https://www.rna-seqblog.com/tag/simon-fraser-university/)
- [Singapore Immunology Network](https://www.rna-seqblog.com/tag/singapore-immunology-network/)
- [single molecule sequencing](https://www.rna-seqblog.com/tag/single-molecule-sequencing/)
- [single nucleotide variant](https://www.rna-seqblog.com/tag/single-nucleotide-variant/)
- [Single-cell](https://www.rna-seqblog.com/tag/single-cell/)
- [single-cell genomics](https://www.rna-seqblog.com/tag/single-cell-genomics/)
- [Single-cell RNA sequencing](https://www.rna-seqblog.com/tag/single-cell-rna-sequencing/)
- [single-cell rna-seq](https://www.rna-seqblog.com/tag/single-cell-rna-seq/)
- [single-cell sequencing](https://www.rna-seqblog.com/tag/single-cell-sequencing/)
- [single-nucleotide polymorphisms](https://www.rna-seqblog.com/tag/single-nucleotide-polymorphisms/)
- [Sloan-Kettering Institute](https://www.rna-seqblog.com/tag/sloan-kettering-institute/)
- [small rna](https://www.rna-seqblog.com/tag/small-rna/)
- [small rna sequencing](https://www.rna-seqblog.com/tag/small-rna-sequencing/)
- [Small RNA-seq](https://www.rna-seqblog.com/tag/small-rna-seq/)
- [small rnas](https://www.rna-seqblog.com/tag/small-rnas/)
- [smart-seq](https://www.rna-seqblog.com/tag/smart-seq/)
- [SnowShoes-FTD](https://www.rna-seqblog.com/tag/snowshoes-ftd/)
- [SNP](https://www.rna-seqblog.com/tag/snp/)
- [SNPs](https://www.rna-seqblog.com/tag/snps/)
- [SOAPdenovo-Trans](https://www.rna-seqblog.com/tag/soapdenovo-trans/)
- [society for Neuroscience](https://www.rna-seqblog.com/tag/society-for-neuroscience/)
- [SOLiD](https://www.rna-seqblog.com/tag/solid/)
- [South China University of Technology](https://www.rna-seqblog.com/tag/south-china-university-of-technology/)
- [splice junctions](https://www.rna-seqblog.com/tag/splice-junctions/)
- [splice mapping](https://www.rna-seqblog.com/tag/splice-mapping/)
- [splice variants](https://www.rna-seqblog.com/tag/splice-variants/)
- [Spliced Transcripts Alignment to a Reference](https://www.rna-seqblog.com/tag/spliced-transcripts-alignment-to-a-reference/)
- [spliceosome](https://www.rna-seqblog.com/tag/spliceosome/)
- [splicetrap](https://www.rna-seqblog.com/tag/splicetrap/)
- [splicing analysis](https://www.rna-seqblog.com/tag/splicing-analysis/)
- [splicing and junction mapping](https://www.rna-seqblog.com/tag/splicing-and-junction-mapping/)
- [Splicing factors](https://www.rna-seqblog.com/tag/splicing-factors/)
- [splicing isoforms](https://www.rna-seqblog.com/tag/splicing-isoforms/)
- [splicing regulatory elements](https://www.rna-seqblog.com/tag/splicing-regulatory-elements/)
- [sQTLs](https://www.rna-seqblog.com/tag/sqtls/)
- [sRNA](https://www.rna-seqblog.com/tag/srna/)
- [sRNAome](https://www.rna-seqblog.com/tag/srnaome/)
- [sSeq](https://www.rna-seqblog.com/tag/sseq/)
- [Stanford University](https://www.rna-seqblog.com/tag/stanford-university/)
- [Stanford University School of Medicine](https://www.rna-seqblog.com/tag/stanford-university-school-of-medicine/)
- [statistical analysis](https://www.rna-seqblog.com/tag/statistical-analysis/)
- [statistical modeling](https://www.rna-seqblog.com/tag/statistical-modeling/)
- [statistics](https://www.rna-seqblog.com/tag/statistics/)
- [Stockholm University](https://www.rna-seqblog.com/tag/stockholm-university/)
- [Stony Brook University](https://www.rna-seqblog.com/tag/stony-brook-university/)
- [Strand Scientific](https://www.rna-seqblog.com/tag/strand-scientific/)
- [strand-specific](https://www.rna-seqblog.com/tag/strand-specific/)
- [Strand-specific RNA-seq](https://www.rna-seqblog.com/tag/strand-specific-rna-seq/)
- [stranded rna-seq](https://www.rna-seqblog.com/tag/stranded-rna-seq/)
- [Striga](https://www.rna-seqblog.com/tag/striga/)
- [study design](https://www.rna-seqblog.com/tag/study-design/)
- [Subcellular RNA Sequencing](https://www.rna-seqblog.com/tag/subcellular-rna-sequencing/)
- [sugar beet](https://www.rna-seqblog.com/tag/sugar-beet/)
- [sus scrofa](https://www.rna-seqblog.com/tag/sus-scrofa/)
- [swiss institute of bioinformatics](https://www.rna-seqblog.com/tag/swiss-institute-of-bioinformatics/)
- [tamoxifen](https://www.rna-seqblog.com/tag/tamoxifen/)
- [target prediction](https://www.rna-seqblog.com/tag/target-prediction/)
- [targeted sequencing](https://www.rna-seqblog.com/tag/targeted-sequencing/)
- [targetome](https://www.rna-seqblog.com/tag/targetome/)
- [TCGA](https://www.rna-seqblog.com/tag/tcga/)
- [technical variability](https://www.rna-seqblog.com/tag/technical-variability/)
- [Technion - Israel Institute of Technology](https://www.rna-seqblog.com/tag/technion-israel-institute-of-technology/)
- [template switching](https://www.rna-seqblog.com/tag/template-switching/)
- [Texas A&M University](https://www.rna-seqblog.com/tag/texas-am-university/)
- [Texas State University](https://www.rna-seqblog.com/tag/texas-state-university/)
- [the allen institute](https://www.rna-seqblog.com/tag/the-allen-institute/)
- [The Broad Institute](https://www.rna-seqblog.com/tag/the-broad-institute/)
- [The Cancer Genome Atlas](https://www.rna-seqblog.com/tag/the-cancer-genome-atlas/)
- [The Chinese University of Hong Kong](https://www.rna-seqblog.com/tag/the-chinese-university-of-hong-kong/)
- [The University of Texas MD Anderson Cancer Center](https://www.rna-seqblog.com/tag/the-university-of-texas-md-anderson-cancer-center/)
- [The University of Tokyo](https://www.rna-seqblog.com/tag/the-university-of-tokyo/)
- [Thomas Jefferson University](https://www.rna-seqblog.com/tag/thomas-jefferson-university/)
- [Tohoku University](https://www.rna-seqblog.com/tag/tohoku-university/)
- [Tokyo Institute of Technology](https://www.rna-seqblog.com/tag/tokyo-institute-of-technology/)
- [tomato](https://www.rna-seqblog.com/tag/tomato/)
- [tophat](https://www.rna-seqblog.com/tag/tophat/)
- [TopHat2](https://www.rna-seqblog.com/tag/tophat2/)
- [total RNA extraction](https://www.rna-seqblog.com/tag/total-rna-extraction/)
- [training course](https://www.rna-seqblog.com/tag/training-course/)
- [trans-abyss](https://www.rna-seqblog.com/tag/trans-abyss/)
- [transcript abundance](https://www.rna-seqblog.com/tag/transcript-abundance/)
- [transcript assembly](https://www.rna-seqblog.com/tag/transcript-assembly/)
- [transcript detection](https://www.rna-seqblog.com/tag/transcript-detection/)
- [transcript discovery](https://www.rna-seqblog.com/tag/transcript-discovery/)
- [Transcript isoform](https://www.rna-seqblog.com/tag/transcript-isoform/)
- [transcript variants](https://www.rna-seqblog.com/tag/transcript-variants/)
- [transcription factor binding sites](https://www.rna-seqblog.com/tag/transcription-factor-binding-sites/)
- [transcriptional analysis](https://www.rna-seqblog.com/tag/transcriptional-analysis/)
- [transcriptional dynamics](https://www.rna-seqblog.com/tag/transcriptional-dynamics/)
- [Transcriptional profiling](https://www.rna-seqblog.com/tag/transcriptional-profiling/)
- [Transcriptional Switch](https://www.rna-seqblog.com/tag/transcriptional-switch/)
- [transcriptome](https://www.rna-seqblog.com/tag/transcriptome/)
- [transcriptome analysis](https://www.rna-seqblog.com/tag/transcriptome-analysis/)
- [transcriptome assembly](https://www.rna-seqblog.com/tag/transcriptome-assembly/)
- [transcriptome coverage](https://www.rna-seqblog.com/tag/transcriptome-coverage/)
- [transcriptome evolution](https://www.rna-seqblog.com/tag/transcriptome-evolution/)
- [Transcriptome Maps](https://www.rna-seqblog.com/tag/transcriptome-maps/)
- [transcriptome profiling](https://www.rna-seqblog.com/tag/transcriptome-profiling/)
- [transcriptome quantification](https://www.rna-seqblog.com/tag/transcriptome-quantification/)
- [transcriptome sequencing](https://www.rna-seqblog.com/tag/transcriptome-sequencing/)
- [transcriptomes](https://www.rna-seqblog.com/tag/transcriptomes/)
- [transcriptomic](https://www.rna-seqblog.com/tag/transcriptomic/)
- [transcriptomics](https://www.rna-seqblog.com/tag/transcriptomics/)
- [transcripts](https://www.rna-seqblog.com/tag/transcripts/)
- [Translational Genomics Research Institute](https://www.rna-seqblog.com/tag/translational-genomics-research-institute/)
- [trinity](https://www.rna-seqblog.com/tag/trinity/)
- [triple negative breast cancer](https://www.rna-seqblog.com/tag/triple-negative-breast-cancer/)
- [TruSeq](https://www.rna-seqblog.com/tag/truseq/)
- [Trypanosoma brucei](https://www.rna-seqblog.com/tag/trypanosoma-brucei/)
- [Tsinghua University](https://www.rna-seqblog.com/tag/tsinghua-university/)
- [Tumor Biology](https://www.rna-seqblog.com/tag/tumor-biology/)
- [tumor subpopulations](https://www.rna-seqblog.com/tag/tumor-subpopulations/)
- [tutorial](https://www.rna-seqblog.com/tag/tutorial/)
- [UC Davis](https://www.rna-seqblog.com/tag/uc-davis/)
- [UC Riverside](https://www.rna-seqblog.com/tag/uc-riverside/)
- [ucla](https://www.rna-seqblog.com/tag/ucla/)
- [ucsd](https://www.rna-seqblog.com/tag/ucsd/)
- [Université de Montréal](https://www.rna-seqblog.com/tag/universite-de-montreal/)
- [University of Arizona](https://www.rna-seqblog.com/tag/university-of-arizona/)
- [University of Bristol](https://www.rna-seqblog.com/tag/university-of-bristol/)
- [University of British Columbia](https://www.rna-seqblog.com/tag/university-of-british-columbia/)
- [University of California](https://www.rna-seqblog.com/tag/university-of-california/)
- [University of California at San Diego](https://www.rna-seqblog.com/tag/university-of-california-at-san-diego/)
- [University of California San Diego](https://www.rna-seqblog.com/tag/university-of-california-san-diego/)
- [University of California Santa Cruz](https://www.rna-seqblog.com/tag/university-of-california-santa-cruz/)
- [university of cambridge](https://www.rna-seqblog.com/tag/university-of-cambridge/)
- [University of Chicago](https://www.rna-seqblog.com/tag/university-of-chicago/)
- [University of Colorado](https://www.rna-seqblog.com/tag/university-of-colorado/)
- [University of Connecticut](https://www.rna-seqblog.com/tag/university-of-connecticut/)
- [University of Delaware](https://www.rna-seqblog.com/tag/university-of-delaware/)
- [University of Edinburgh](https://www.rna-seqblog.com/tag/university-of-edinburgh/)
- [University of Frankfurt am Main](https://www.rna-seqblog.com/tag/university-of-frankfurt-am-main/)
- [University of Freiburg](https://www.rna-seqblog.com/tag/university-of-freiburg/)
- [University of Illinois](https://www.rna-seqblog.com/tag/university-of-illinois/)
- [University of Leipzig](https://www.rna-seqblog.com/tag/university-of-leipzig/)
- [University of Maryland](https://www.rna-seqblog.com/tag/university-of-maryland/)
- [University of Massachusetts Medical School](https://www.rna-seqblog.com/tag/university-of-massachusetts-medical-school/)
- [University of Michigan](https://www.rna-seqblog.com/tag/university-of-michigan/)
- [University of Missouri](https://www.rna-seqblog.com/tag/university-of-missouri/)
- [University of North Carolina](https://www.rna-seqblog.com/tag/university-of-north-carolina/)
- [University of North Carolina at Chapel Hill](https://www.rna-seqblog.com/tag/university-of-north-carolina-at-chapel-hill/)
- [University of Padova](https://www.rna-seqblog.com/tag/university-of-padova/)
- [University of Pennsylvania](https://www.rna-seqblog.com/tag/university-of-pennsylvania/)
- [University of Queensland](https://www.rna-seqblog.com/tag/university-of-queensland/)
- [University of São Paulo](https://www.rna-seqblog.com/tag/university-of-sao-paulo/)
- [University of Texas at San Antonio](https://www.rna-seqblog.com/tag/university-of-texas-at-san-antonio/)
- [University of Texas MD Anderson Cancer Center](https://www.rna-seqblog.com/tag/university-of-texas-md-anderson-cancer-center/)
- [University of Tokyo](https://www.rna-seqblog.com/tag/university-of-tokyo/)
- [University of Tübingen](https://www.rna-seqblog.com/tag/university-of-tubingen/)
- [University of Utah](https://www.rna-seqblog.com/tag/university-of-utah/)
- [University of Virginia](https://www.rna-seqblog.com/tag/university-of-virginia/)
- [university of wisconsin](https://www.rna-seqblog.com/tag/university-of-wisconsin/)
- [University of Würzburg](https://www.rna-seqblog.com/tag/university-of-wurzburg/)
- [untranslated region](https://www.rna-seqblog.com/tag/untranslated-region/)
- [Uppsala University](https://www.rna-seqblog.com/tag/uppsala-university/)
- [USC](https://www.rna-seqblog.com/tag/usc/)
- [Vanderbilt University](https://www.rna-seqblog.com/tag/vanderbilt-university/)
- [Vanderbilt University School of Medicine](https://www.rna-seqblog.com/tag/vanderbilt-university-school-of-medicine/)
- [venom](https://www.rna-seqblog.com/tag/venom/)
- [vib](https://www.rna-seqblog.com/tag/vib/)
- [virus genome](https://www.rna-seqblog.com/tag/virus-genome/)
- [VOOM](https://www.rna-seqblog.com/tag/voom/)
- [Wallenberg Advanced Infrastructure for Bioinformatics](https://www.rna-seqblog.com/tag/wallenberg-advanced-infrastructure-for-bioinformatics/)
- [web-based tools](https://www.rna-seqblog.com/tag/web-based-tools/)
- [webinar](https://www.rna-seqblog.com/tag/webinar/)
- [Weizmann Institute of Science](https://www.rna-seqblog.com/tag/weizmann-institute-of-science/)
- [wgss](https://www.rna-seqblog.com/tag/wgss/)
- [wheat genome](https://www.rna-seqblog.com/tag/wheat-genome/)
- [whitehead institute](https://www.rna-seqblog.com/tag/whitehead-institute/)
- [whole transcriptome](https://www.rna-seqblog.com/tag/whole-transcriptome/)
- [whole transcriptome sequencing](https://www.rna-seqblog.com/tag/whole-transcriptome-sequencing/)
- [whole-exome sequencing](https://www.rna-seqblog.com/tag/whole-exome-sequencing/)
- [whole-genome sequencing](https://www.rna-seqblog.com/tag/whole-genome-sequencing/)
- [wormbase](https://www.rna-seqblog.com/tag/wormbase/)
- [Wuhan University](https://www.rna-seqblog.com/tag/wuhan-university/)
- [X chromosome](https://www.rna-seqblog.com/tag/x-chromosome/)
- [yale university](https://www.rna-seqblog.com/tag/yale-university/)
- [zea mays](https://www.rna-seqblog.com/tag/zea-mays/)
- [zebrafish](https://www.rna-seqblog.com/tag/zebrafish/)
- [isoform analysis](https://www.rna-seqblog.com/tag/isoform-analysis/)
- [Allopolyploid](https://www.rna-seqblog.com/tag/allopolyploid/)
- [SSP](https://www.rna-seqblog.com/tag/ssp/)
- [Classification of RNAs by Analysis of Length](https://www.rna-seqblog.com/tag/classification-of-rnas-by-analysis-of-length/)
- [Machine learning](https://www.rna-seqblog.com/tag/machine-learning/)
- [Small interfering RNAs](https://www.rna-seqblog.com/tag/small-interfering-rnas/)
- [Leiden University](https://www.rna-seqblog.com/tag/leiden-university/)
- [proteome](https://www.rna-seqblog.com/tag/proteome/)
- [mRNA splicing](https://www.rna-seqblog.com/tag/mrna-splicing/)
- [proteomic](https://www.rna-seqblog.com/tag/proteomic/)
- [transcriptomic data](https://www.rna-seqblog.com/tag/transcriptomic-data/)
- [biomarker](https://www.rna-seqblog.com/tag/biomarker/)
- [GAGE](https://www.rna-seqblog.com/tag/gage/)
- [go analysis](https://www.rna-seqblog.com/tag/go-analysis/)
- [biotechniques](https://www.rna-seqblog.com/tag/biotechniques/)
- [5-methylcytosine RNA methylation](https://www.rna-seqblog.com/tag/5-methylcytosine-rna-methylation/)
- [RNA methylation](https://www.rna-seqblog.com/tag/rna-methylation/)
- [whole-transcriptome analysis](https://www.rna-seqblog.com/tag/whole-transcriptome-analysis/)
- [bioinformatics institute](https://www.rna-seqblog.com/tag/bioinformatics-institute/)
- [Max Planck](https://www.rna-seqblog.com/tag/max-planck/)
- [bina](https://www.rna-seqblog.com/tag/bina/)
- [GATK](https://www.rna-seqblog.com/tag/gatk/)
- [smarter stranded rna-seq](https://www.rna-seqblog.com/tag/smarter-stranded-rna-seq/)
- [SMARTer®](https://www.rna-seqblog.com/tag/smarter/)
- [splicing](https://www.rna-seqblog.com/tag/splicing/)
- [cuffdiff2](https://www.rna-seqblog.com/tag/cuffdiff2/)
- [smrt sequencing](https://www.rna-seqblog.com/tag/smrt-sequencing/)
- [spliced alignment](https://www.rna-seqblog.com/tag/spliced-alignment/)
- [false discovery rate](https://www.rna-seqblog.com/tag/false-discovery-rate/)
- [transcript reconstruction](https://www.rna-seqblog.com/tag/transcript-reconstruction/)
- [adapters](https://www.rna-seqblog.com/tag/adapters/)
- [personalized medicine](https://www.rna-seqblog.com/tag/personalized-medicine/)
- [G/C content](https://www.rna-seqblog.com/tag/gc-content/)
- [MBCluster.Seq](https://www.rna-seqblog.com/tag/mbcluster-seq/)
- [miRspring](https://www.rna-seqblog.com/tag/mirspring/)
- [miRNA-Seq](https://www.rna-seqblog.com/tag/mirna-seq/)
- [Translational Efficiency](https://www.rna-seqblog.com/tag/translational-efficiency/)
- [Regulatory Mechanism](https://www.rna-seqblog.com/tag/regulatory-mechanism/)
- [oncology](https://www.rna-seqblog.com/tag/oncology/)
- [translational research](https://www.rna-seqblog.com/tag/translational-research/)
- [Rutgers University](https://www.rna-seqblog.com/tag/rutgers-university/)
- [King’s College London](https://www.rna-seqblog.com/tag/kings-college-london/)
- [SMRT®](https://www.rna-seqblog.com/tag/smrt/)
- [small RNA libraries](https://www.rna-seqblog.com/tag/small-rna-libraries/)
- [Stephen Quake](https://www.rna-seqblog.com/tag/stephen-quake/)
- [single cell analysis](https://www.rna-seqblog.com/tag/single-cell-analysis/)
- [J. Craig Venter Institute](https://www.rna-seqblog.com/tag/j-craig-venter-institute/)
- [single nuclei](https://www.rna-seqblog.com/tag/single-nuclei/)
- [transcriptomic analysis](https://www.rna-seqblog.com/tag/transcriptomic-analysis/)
- [algorithm](https://www.rna-seqblog.com/tag/algorithm/)
- [Hierarchical](https://www.rna-seqblog.com/tag/hierarchical/)
- [differential splicing](https://www.rna-seqblog.com/tag/differential-splicing/)
- [statistical models](https://www.rna-seqblog.com/tag/statistical-models/)
- [Georgia Tech](https://www.rna-seqblog.com/tag/georgia-tech/)
- [alternative splcing](https://www.rna-seqblog.com/tag/alternative-splcing/)
- [Baylor College of Medicine](https://www.rna-seqblog.com/tag/baylor-college-of-medicine/)
- [Validation](https://www.rna-seqblog.com/tag/validation/)
- [AgroParisTech](https://www.rna-seqblog.com/tag/agroparistech/)
- [postdoc position](https://www.rna-seqblog.com/tag/postdoc-position/)
- [Fold-Change](https://www.rna-seqblog.com/tag/fold-change/)
- [Cornell University](https://www.rna-seqblog.com/tag/cornell-university/)
- [francis crick institute](https://www.rna-seqblog.com/tag/francis-crick-institute/)
- [Boston University](https://www.rna-seqblog.com/tag/boston-university/)
- [workshop](https://www.rna-seqblog.com/tag/workshop/)
- [Bioinformatician Position](https://www.rna-seqblog.com/tag/bioinformatician-position/)
- [RT-PCR](https://www.rna-seqblog.com/tag/rt-pcr/)
- [University of Turku](https://www.rna-seqblog.com/tag/university-of-turku/)
- [Limma](https://www.rna-seqblog.com/tag/limma/)
- [Cuffdiff 2](https://www.rna-seqblog.com/tag/cuffdiff-2/)
- [California Institute of Technology](https://www.rna-seqblog.com/tag/california-institute-of-technology/)
- [University of Maryland School of Medicine](https://www.rna-seqblog.com/tag/university-of-maryland-school-of-medicine/)
- [Next generation sequencing technology](https://www.rna-seqblog.com/tag/next-generation-sequencing-technology/)
- [ncRNAs](https://www.rna-seqblog.com/tag/ncrnas/)
- [Cell Line](https://www.rna-seqblog.com/tag/cell-line/)
- [prokaryotic](https://www.rna-seqblog.com/tag/prokaryotic/)
- [eukaryotic](https://www.rna-seqblog.com/tag/eukaryotic/)
- [short reads](https://www.rna-seqblog.com/tag/short-reads/)
- [genome mapping](https://www.rna-seqblog.com/tag/genome-mapping/)
- [BMC Genomics](https://www.rna-seqblog.com/tag/bmc-genomics/)
- [University of California Davis](https://www.rna-seqblog.com/tag/university-of-california-davis/)
- [John Theurer Cancer Center](https://www.rna-seqblog.com/tag/john-theurer-cancer-center/)
- [B-Cell Lymphoma](https://www.rna-seqblog.com/tag/b-cell-lymphoma/)
- [cancer treatment](https://www.rna-seqblog.com/tag/cancer-treatment/)
- [NCI](https://www.rna-seqblog.com/tag/nci/)
- [Overdispersion](https://www.rna-seqblog.com/tag/overdispersion/)
- [University of East Anglia](https://www.rna-seqblog.com/tag/university-of-east-anglia/)
- [Duke University](https://www.rna-seqblog.com/tag/duke-university/)
- [ssRNA-seq](https://www.rna-seqblog.com/tag/ssrna-seq/)
- [strand-specific RNA sequencing](https://www.rna-seqblog.com/tag/strand-specific-rna-sequencing/)
- [PennSeq](https://www.rna-seqblog.com/tag/pennseq/)
- [non-uniformity](https://www.rna-seqblog.com/tag/non-uniformity/)
- [sequencing reads](https://www.rna-seqblog.com/tag/sequencing-reads/)
- [BCM](https://www.rna-seqblog.com/tag/bcm/)
- [tissue-specific alternative splicing](https://www.rna-seqblog.com/tag/tissue-specific-alternative-splicing/)
- [isoform switching](https://www.rna-seqblog.com/tag/isoform-switching/)
- [read alignment](https://www.rna-seqblog.com/tag/read-alignment/)
- [University of Zurich](https://www.rna-seqblog.com/tag/university-of-zurich/)
- [Research Scientist](https://www.rna-seqblog.com/tag/research-scientist/)
- [Postdoctoral Researcher](https://www.rna-seqblog.com/tag/postdoctoral-researcher/)
- [RIKEN Center for Life Science Technologies](https://www.rna-seqblog.com/tag/riken-center-for-life-science-technologies/)
- [UTHSCSA](https://www.rna-seqblog.com/tag/uthscsa/)
- [exon-skipping](https://www.rna-seqblog.com/tag/exon-skipping/)
- [splice sites](https://www.rna-seqblog.com/tag/splice-sites/)
- [allele-specific](https://www.rna-seqblog.com/tag/allele-specific/)
- [Sequentia Biotech](https://www.rna-seqblog.com/tag/sequentia-biotech/)
- [Southeast University](https://www.rna-seqblog.com/tag/southeast-university/)
- [C1TM Single-Cell Auto Prep System](https://www.rna-seqblog.com/tag/c1tm-single-cell-auto-prep-system/)
- [Institute of Applied Genomics](https://www.rna-seqblog.com/tag/institute-of-applied-genomics/)
- [read trimming](https://www.rna-seqblog.com/tag/read-trimming/)
- [NGS Data Analysis](https://www.rna-seqblog.com/tag/ngs-data-analysis/)
- [W250](https://www.rna-seqblog.com/tag/w250/)
- [Distributed Genome Annotation](https://www.rna-seqblog.com/tag/distributed-genome-annotation/)
- [Extreme Scientific and Engineering Discovery Environment](https://www.rna-seqblog.com/tag/extreme-scientific-and-engineering-discovery-environment/)
- [XSEDE](https://www.rna-seqblog.com/tag/xsede/)
- [DNA Subway](https://www.rna-seqblog.com/tag/dna-subway/)
- [JBrowse](https://www.rna-seqblog.com/tag/jbrowse/)
- [expression level estimation](https://www.rna-seqblog.com/tag/expression-level-estimation/)
- [Barrow Neurological Institute](https://www.rna-seqblog.com/tag/barrow-neurological-institute/)
- [Phoenix Children's Hospital](https://www.rna-seqblog.com/tag/phoenix-childrens-hospital/)
- [National Center for Advancing Translational Sciences](https://www.rna-seqblog.com/tag/national-center-for-advancing-translational-sciences/)
- [aneurysmal subarachnoid hemorrhage](https://www.rna-seqblog.com/tag/aneurysmal-subarachnoid-hemorrhage/)
- [intraventricular hemorrhage](https://www.rna-seqblog.com/tag/intraventricular-hemorrhage/)
- [The University of Adelaide](https://www.rna-seqblog.com/tag/the-university-of-adelaide/)
- [microRNA studies](https://www.rna-seqblog.com/tag/microrna-studies/)
- [sequencing errors](https://www.rna-seqblog.com/tag/sequencing-errors/)
- [University of Porto](https://www.rna-seqblog.com/tag/university-of-porto/)
- [Evolutionary Biology](https://www.rna-seqblog.com/tag/evolutionary-biology/)
- [University Leipzig](https://www.rna-seqblog.com/tag/university-leipzig/)
- [singl cell sequencing](https://www.rna-seqblog.com/tag/singl-cell-sequencing/)
- [Peking University](https://www.rna-seqblog.com/tag/peking-university/)
- [Smart-seq2](https://www.rna-seqblog.com/tag/smart-seq2/)
- [Nature Protocols](https://www.rna-seqblog.com/tag/nature-protocols/)
- [WaferGen Bio-systems](https://www.rna-seqblog.com/tag/wafergen-bio-systems/)
- [WaferGen](https://www.rna-seqblog.com/tag/wafergen/)
- [IntegenX](https://www.rna-seqblog.com/tag/integenx/)
- [PrepX®](https://www.rna-seqblog.com/tag/prepx/)
- [Apollo 324TM](https://www.rna-seqblog.com/tag/apollo-324tm/)
- [NGS sample pre](https://www.rna-seqblog.com/tag/ngs-sample-pre/)
- [Netherlands Institute of Ecology](https://www.rna-seqblog.com/tag/netherlands-institute-of-ecology/)
- [University of Florida](https://www.rna-seqblog.com/tag/university-of-florida/)
- [mispriming](https://www.rna-seqblog.com/tag/mispriming/)
- [random hexamer](https://www.rna-seqblog.com/tag/random-hexamer/)
- [First Strand cDNA](https://www.rna-seqblog.com/tag/first-strand-cdna/)
- [ERCC spikes](https://www.rna-seqblog.com/tag/ercc-spikes/)
- [RNA-immunoprecipitation sequencing](https://www.rna-seqblog.com/tag/rna-immunoprecipitation-sequencing/)
- [Sm-associated RNAs](https://www.rna-seqblog.com/tag/sm-associated-rnas/)
- [small ribonucleoprotein](https://www.rna-seqblog.com/tag/small-ribonucleoprotein/)
- [RNP](https://www.rna-seqblog.com/tag/rnp/)
- [exome capture](https://www.rna-seqblog.com/tag/exome-capture/)
- [genome diversity](https://www.rna-seqblog.com/tag/genome-diversity/)
- [re-sequencing](https://www.rna-seqblog.com/tag/re-sequencing/)
- [plant genome](https://www.rna-seqblog.com/tag/plant-genome/)
- [animal genome](https://www.rna-seqblog.com/tag/animal-genome/)
- [PAGXXII](https://www.rna-seqblog.com/tag/pagxxii/)
- [Characterizing Variability](https://www.rna-seqblog.com/tag/characterizing-variability/)
- [footprint](https://www.rna-seqblog.com/tag/footprint/)
- [protein](https://www.rna-seqblog.com/tag/protein/)
- [UPENN](https://www.rna-seqblog.com/tag/upenn/)
- [regulatory RNA](https://www.rna-seqblog.com/tag/regulatory-rna/)
- [microgenomics](https://www.rna-seqblog.com/tag/microgenomics/)
- [Exosome](https://www.rna-seqblog.com/tag/exosome/)
- [ichael W. Pfaffl](https://www.rna-seqblog.com/tag/ichael-w-pfaffl/)
- [derfinder](https://www.rna-seqblog.com/tag/derfinder/)
- [differentially expressed regions](https://www.rna-seqblog.com/tag/differentially-expressed-regions/)
- [single-base resolution](https://www.rna-seqblog.com/tag/single-base-resolution/)
- [Johns Hopkins University](https://www.rna-seqblog.com/tag/johns-hopkins-university/)
- [monoallelic](https://www.rna-seqblog.com/tag/monoallelic/)
- [mammalian cells](https://www.rna-seqblog.com/tag/mammalian-cells/)
- [maxcounts](https://www.rna-seqblog.com/tag/maxcounts/)
- [read counts](https://www.rna-seqblog.com/tag/read-counts/)
- [Next-Generation Sequencing technologies](https://www.rna-seqblog.com/tag/next-generation-sequencing-technologies/)
- [AATI](https://www.rna-seqblog.com/tag/aati/)
- [Fragment Analyzer](https://www.rna-seqblog.com/tag/fragment-analyzer/)
- [Tufts Technology Services](https://www.rna-seqblog.com/tag/tufts-technology-services/)
- [Salmonella](https://www.rna-seqblog.com/tag/salmonella/)
- [Cell Host Microbe](https://www.rna-seqblog.com/tag/cell-host-microbe/)
- [NextSeq™ 500](https://www.rna-seqblog.com/tag/nextseq-500/)
- [HiSeq X™ Ten](https://www.rna-seqblog.com/tag/hiseq-x-ten/)
- [parseq](https://www.rna-seqblog.com/tag/parseq/)
- [transcription landscape reconstruction](https://www.rna-seqblog.com/tag/transcription-landscape-reconstruction/)
- [basepair resolution](https://www.rna-seqblog.com/tag/basepair-resolution/)
- [Monte Carlo approach](https://www.rna-seqblog.com/tag/monte-carlo-approach/)
- [Galaxy Toolshed](https://www.rna-seqblog.com/tag/galaxy-toolshed/)
- [Galaxy CloudMan](https://www.rna-seqblog.com/tag/galaxy-cloudman/)
- [Quantitative Transcriptome Analysis](https://www.rna-seqblog.com/tag/quantitative-transcriptome-analysis/)
- [Memorial Sloan-Kettering Cancer Center](https://www.rna-seqblog.com/tag/memorial-sloan-kettering-cancer-center/)
- [Northern Genomics](https://www.rna-seqblog.com/tag/northern-genomics/)
- [R/Bioconductor](https://www.rna-seqblog.com/tag/rbioconductor/)
- [bipolar](https://www.rna-seqblog.com/tag/bipolar/)
- [Psychiatry](https://www.rna-seqblog.com/tag/psychiatry/)
- [bipolar disorder](https://www.rna-seqblog.com/tag/bipolar-disorder/)
- [circadian rhythms](https://www.rna-seqblog.com/tag/circadian-rhythms/)
- [neuroplasticity](https://www.rna-seqblog.com/tag/neuroplasticity/)
- [brain transcriptome](https://www.rna-seqblog.com/tag/brain-transcriptome/)
- [RNA-Seq Data](https://www.rna-seqblog.com/tag/rna-seq-data/)
- [Gene Signatures](https://www.rna-seqblog.com/tag/gene-signatures/)