Data Analysis

De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, ...

The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for ...

Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. Researchers at the University of Wisconsin-Madison have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell ...

MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. The mirEX 2.0 web portal provides ...

Detecting and quantifying isoforms from RNA-seq data is an important but challenging task. The problem is often ill-posed, particularly at low coverage. One promising direction is to exploit several samples simultaneously. A team led by researchers at MINES ParisTech have ...

A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to ...

With the recent advent of RNA-seq technology the proteomics community has begun to generate sample-specific protein databases for peptide and protein identification, an approach we call proteomics informed by transcriptomics (PIT). This approach has gained a lot of interest, particularly ...

Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have ...

Fusion genes are chimeric results originated from previous separate genes with aberrant functions. The resulting protein products may lead to abnormal status of expression levels, functions and action sites, which in return may cause the abnormal proliferation of cells and ...

from Bits of DNA by Lior Pachter Today my student Harold Pimentel released the beta version of his new RNA-Seq analysis method and software program called sleuth. A sleuth for RNA-Seq begins with the quantification of samples with kallisto, and together a sleuth ...