MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, …
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA
deepEA a containerized web server for interactive analysis of epitranscriptome sequencing data
RNA molecules are decorated with a variety of chemical modifications, which make up an epitranscriptome that extensively regulates gene expression and biological processes. With the recent development of high-throughput experimental technologies, …
Exploring transcriptional switches from pairwise, temporal, and population RNA-Seq data using deepTS
Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal, or other dimensions. TS has been associated with human diseases, plant development, and …
A bioinformatics framework for comprehensive assembly and functional annotation
A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, …