The evolution of nitrogen fixation in cyanobacteria
An effective statistical evaluation of ChIPseq dataset similarity
PHACTS, a computational approach to classifying the lifestyle of phages
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Transformations for the compression of FASTQ quality scores of next-generation sequencing data
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs
SNP calling using genotype model selection on high-throughput sequencing data
Application of canonical correlation analysis for identifying viral integration preferences
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
Predicting folding free energy changes upon single point mutations
Interactome–transcriptome integration for predicting distant metastasis in breast cancer
SSuMMo : rapid analysis, comparison and visualization of microbial communities
influx_s : increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments
Modeling community-wide molecular networks of multicellular systems
De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae
Mining and evaluation of molecular relationships in literature
Roundup 2.0 : enabling comparative genomics for over 1800 genomes
CHROMATRA : a Galaxy tool for visualizing genome-wide chromatin signatures
A scalable and portable framework for massively parallel variable selection in genetic association studies
FX : an RNA-Seq analysis tool on the cloud
AnnTools : a comprehensive and versatile annotation toolkit for genomic variants
nEASE : a method for gene ontology subclassification of high-throughput gene expression data
IMA : an R package for high-throughput analysis of Illumina's 450K Infinium methylation data
StochSens—matlab package for sensitivity analysis of stochastic chemical systems
NetSeed : a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment
MetExtract : a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research
Mining and integration of pathway diagrams from imaging data
medpie : an information extraction package for medical message board posts
COPICAT : a software system for predicting interactions between proteins and chemical compounds
IMID : integrated molecular interaction database
BESC knowledgebase public portal†
GROMACS molecule & liquid database