Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced...
Read More »How RNA sequencing innovations help scientists tackle the complexity of the transcriptome
Short-read sequencing can be a bit like trying to reconstruct paragraphs of text word by word—a daunting process. By contrast, long-read sequencing
Read More »FreePSI – an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for ...
Read More »Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Novel single-cell transcriptome sequencing assays allow researchers to measure gene expression levels at the resolution of single cells and offer the unprecendented opportunity to investigate at the molecular level fundamental biological questions, such as stem cell differentiation or the discovery ...
Read More »scRNA-Seq identifies of molecular markers for preoptic sleep neurons
In humans and other mammalian species, lesions in the preoptic area of the hypothalamus cause profound sleep impairment, indicating a crucial role of the preoptic area in sleep generation. However, the underlying circuit mechanism remains poorly understood. Electrophysiological recordings and ...
Read More »There is significant heterogeneity in the performance of RNA-Seq workflows to identify differentially expressed genes
RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of tools available for each of the three major processing steps: read alignment, expression ...
Read More »A more refined equine transcriptome
Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially ...
Read More »systemPipeR – NGS workflow and report generation environment
Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology, as it requires complex multi-step processing ...
Read More »Single-cell RNA sequencing reveals human brain houses diverse populations of neurons
A team of researchers has developed the first scalable method to identify different subtypes of neurons in the human brain. The research lays the groundwork for “mapping” the gene activity in the human brain and could help provide a better ...
Read More »Study lays groundwork for arthritis prevention
Joint injury can lead to post-traumatic osteoarthritis (PTOA). In fact, about half of all people who rupture the anterior cruciate ligament (ACL) in their knee will develop PTOA within 10 to 20 years of the injury. But the molecular and ...
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