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Researchers from the Beijing Forestry University have developed a clustering mixture model to discover distinct groups of genes expressed du...

RNA-Seq allows the identification of intronic causative mutations missed by the usual filtering of Whole Exome Sequencing - A team led by researchers at Universitat Pompeu Fabra performed whole-exome sequencing (WES) and blood cell transcriptome by RNA-Seq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. They detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L…

derfinder – identify, visualize, and interpret differentially expressed regions - Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. Previously, researchers at Johns Hopkins Bloomberg School of Public Health introduced an intermediate approach called differentially expressed...

Removing technical noise from single cell RNA-Seq data - Single-cell RNA-seq is a promising technology with broad applications and discerning biological noise from technical noise is critical for correctly interpreting the data (Jaitin, et al., 2014). Recently, statistical methods are developed to model the technical noise from spike-in ERCC molecules, whose concentrations are presumably same across...

FunPat – function-based pattern analysis on RNA-seq time series data - Dynamic expression data, nowadays obtained using high-throughput RNA sequencing, are essential to monitor transient gene expression changes and to study the dynamics of their transcriptional activity in the cell or response to stimuli. Several methods for data selection, clustering and functional analysis are available; however, these...

Tailor – a computational framework for detecting non-templated tailing of small silencing RNAs - Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently…

A regression-based differential expression detection algorithm for studies with ultra-low sample size - Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly…

Normalization and Differential Expression in RNA-Seq - Sandrine Dudoit, talks to the Toronto Bioinformatics User Group about Normalization and Differential Expression in RNA-Seq. Find out more about TorBUG at http://www.torbug.org.