Benchmarking RNA sequencing for more accurate alternative splicing analysis
RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...
MitoClipSplice – machine learning improves RNA sequencing analysis of mitochondrial RNA processing
Mitochondria are best known for producing energy for cells, but they also contain their own DNA and produce their own RNA molecules. These mitochondrial RNAs must be carefully processed before they can function properly. Errors in this processing have ...
ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing
Long-read RNA sequencing has made it possible for researchers to study complete RNA molecules instead of assembling them from many short fragments. This provides a much clearer picture of how genes produce different RNA isoforms through alternative splicing. However, ...
Combining AI and RNA analysis improves detection of disease-causing splicing variants
Modern genome and exome sequencing can identify thousands of genetic variants, including many located within introns, the stretches of DNA that do not directly code for proteins. While these regions were once thought to be unimportant, researchers now know ...
Generative modeling for RNA splicing prediction and design
Combining RNA sequencing data with generative AI, TrASPr+BOS predicts and designs tissue-specific splicing outcomes, helping researchers explore gene regulation and potential RNA therapeutics...
HELIX – a scalable model for predicting context-dependent regulation of RNA splicing and isoform usage
RNA molecules do not always remain in the same form after they are transcribed from DNA. Before messenger RNA (mRNA) is used to produce proteins, cells can rearrange segments of RNA through a process called alternative splicing. This allows ...
FUSILLI -long-read fusion detection
B-cell acute lymphoblastic leukemia, or B-ALL, is a blood cancer that affects developing immune cells called B cells. Many cases are driven by fusion oncogenes, which form when pieces of different genes become incorrectly joined together. Detecting these fusions ...
SCOTCH – isoform-level characterization of gene expression through long-read single-cell RNA sequencing
Single-cell RNA sequencing helps researchers understand which genes are active in individual cells. However, many traditional methods rely on short sequencing reads, which can make it difficult to tell which full-length RNA isoforms are present. Isoforms are different RNA ...
A long-read RNA sequencing and polysome profiling framework reveals transposable element-driven transcript diversity
More than half of the human genome is made up of transposable elements, often called “jumping genes.” These sequences are usually inactive, but in cancer they can become active again and interfere with normal gene regulation. Understanding how ...
CHOP researchers develop versatile and low-cost technology for targeted long-read RNA sequencing
The easy-to-implement technology reduces the per-reaction cost of target capture by 2-3 orders of magnitude, as compared to standard commercial solutions In a development that could accelerate the discovery of new diagnostics and treatments, researchers at Children’s Hospital of ...
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