RNA-Seq Blog Transcriptome Research & Industry News
Gene fusion is a chromosomal rearrangement event which plays a significant role in cancer due to the oncogenic potential of the chimeric protein generated through fusions. The chimeric protein produced as a result of fusion of genes often possesses oncogenic ...
Read More »CirComPara – A Multi-Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA-seq Data
Circular RNAs (circRNAs) are generated by backsplicing of immature RNA forming covalently closed loops of intron/exon RNA molecules. Pervasiveness, evolutionary conservation, massive and regulated expression, and posttranscriptional regulatory roles of circRNAs in eukaryotes have been...
Read More »VDJPuzzle – B-cell receptor reconstruction from single-cell RNA-seq
The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic...
Read More »Improving the value of public RNA-seq expression data by phenotype prediction
Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled...
Read More »CEMiTool – gene co-expression network analysis
The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions. ...
Read More »Discovering circRNA-microRNA interactions from CLIP-Seq and RNA-Seq data
Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechanisms and functions of most of circRNAs remain largely unknown. In this chapter, ...
Read More »UClncR – Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Long non-coding RNA (lncRNA) is a large class of gene transcripts with regulatory functions discovered in recent years. Many more are expected to be...
Read More »ChopStitch – exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data
Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques...
Read More »RolyPoly – inferring relevant cell types for complex traits using single-cell gene expression
Previous studies have prioritized trait-relevant cell types by looking for an enrichment of genome-wide association study (GWAS) signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell ...
Read More »Identification of Non-coding RNAs by High-Throughput Sequencing
Non-coding RNA transcripts, such as long non-coding RNAs, miRNAs, siRNAs, and transposon-originating transcripts, are involved in the regulation of RNA stability, protein translation, and/or the modulation of chromatin states. RNA-Seq can be used to catalog this diversity of novel transcripts ...
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