bogdan's blog

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.

Towards computational prediction of microRNA function and activity

Towards computational prediction of microRNA function and activity - While it has been established that microRNAs (miRNAs) play key roles throughout development and are dysregulated in many human pathologies, the specific processes and pathways regulated by individual miRNAs are mostly unknown.

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes - Motivation: Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory region such as transcriptional enhancers.

Genome-wide functional element detection using pairwise statistical alignment outperforms multi-genome footprinting techniques

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques - Motivation: Comparative genomic sequence analysis is a powerful approach for identifying putative functional elements in silico.