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PAR: a PARallel and distributed job crusher

PAR: a PARallel and distributed job crusher - Summary: Bioinformaticians are tackling increasingly computation-intensive tasks. In the meantime, workstations are shifting towards multi-core architectures and even massively multi-core may be the norm soon.

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

The binding site distance test score: a robust method for the assessment of predicted protein binding sites - Motivation: We propose a novel method for scoring the accuracy of protein binding site predictions—the Binding-site Distance Test (BDT) score.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks - Summary: SpotXplore is a plugin for Cytoscape for extraction and visualization of differentially expressed subnetworks (hotspots) from gene networks.

BioRuby: bioinformatics software for the Ruby programming language

BioRuby: bioinformatics software for the Ruby programming language - Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language.

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing - Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data - Deep sequencing of RNAs (RNA-seq) has been a useful tool to characterize and quantify transcriptomes.

Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures - Comparing independent high-throughput gene-expression experiments can generate hypotheses about which gene-expression programs are shared between particular biological processes.

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