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Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Background: MicroRNAs (miRNAs) are small RNA molecules (̃22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. …

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and compare small RNA profiles …

bcbioRNASeq: R package for bcbio RNA-seq analysis

RNA-seq analysis involves multiple steps from processing raw sequencing data to identifying, organizing, annotating, and reporting differentially expressed genes. bcbio is an open source, community-maintained framework providing automated and …

Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140

Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with …

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop …

Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution

LLC It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the …

Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

We empirically examined the strengths and weaknesses of two human genome-wide DNA methylation platforms: rapid multiplexed reduced representation bisulfite sequencing and Illumina's Infinium BeadChip. Rapid multiplexed reduced representation …

Viewing RNA-seq data on the entire human genome

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a …

Genomic analyses identify molecular subtypes of pancreatic cancer

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-beta, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA …

Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.

MOTIVATION: Most computational tools for small non-coding RNAs (sRNA) sequencing data analysis focus in microRNAs (miRNAs), overlooking other types of sRNAs that show multi-mapping hits. Here, we have developed a pipeline to non-redundantly quantify …