Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the...
Read More »A mew machine learning-based framework for mapping uncertainty analysis in RNA-Seq read alignment and gene expression estimation
One of the main benefits of using modern RNA-Sequencing (RNA-Seq) technology is the more accurate gene expression estimations compared with previous generations of expression data, such as the microarray. However, numerous issues can result...
Read More »Using supervised learning methods for gene selection in RNA-Seq case-control studies
Whole transcriptome studies typically yield large amounts of data, with expression values for all genes or transcripts of the genome. The search for genes...
Read More »LncFinder – an integrated platform for long non-coding RNA identification
Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances ...
Read More »LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data
Recently, long noncoding RNA molecules (lncRNA) captured widespread attentions for its critical roles in diverse biological process and important implications in variety of human diseases and cancers...
Read More »ScISOr-Seq – single-cell isoform RNA sequencing
Full-length isoform sequencing has advanced our knowledge of isoform biology. However, apart from applying full-length isoform sequencing to very few single cells, isoform sequencing has been limited...
Read More »Identification of transcribed protein coding sequence remnants within lincRNAs
Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences. Importantly, such elements are known to be tissue-specifically expressed and to play a widespread role in gene regulation...
Read More »StarSeeker – an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule
MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals. MicroRNA biogenesis involves the enzymatic processing of a primary RNA transcript. The final step is the production of a duplex...
Read More »Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies
The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Non-specific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation...
Read More »Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically...
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