Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters...
Read More »circRNAprofiler – an R-based computational framework for the downstream analysis of circular RNAs
Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream...
Read More »FusionHub – A unified web platform for annotation and visualization of gene fusion events in human cancer
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 »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 »Considerations and complications of mapping small RNA high-throughput data to transposable elements
High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, ...
Read More »miRquant 2.0 – an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data
Small non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse ...
Read More »FEELnc – a tool for long non-coding RNA annotation
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be ...
Read More »Analysis of Annotation and Differential Expression Methods used in RNA-Seq Studies
Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to ...
Read More »RNA-Seq enables a complete reannotation of the Arabidopsis thaliana reference genome
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, ...
Read More »Mapping eQTLs With RNA-Seq reveals a more comprehensive set of eQTLs and illuminates underlying molecular consequence missed by microarrays
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. Researchers from ...
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