integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory
COPE: an accurate k -mer-based pair-end reads connection tool to facilitate genome assembly
CLEVER: clique-enumerating variant finder
FetalQuant : deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma
Comparing clustering and pre-processing in taxonomy analysis
Extra-binomial variation approach for analysis of pooled DNA sequencing data
Post-translational modifications induce significant yet not extreme changes to protein structure
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays
MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
Efficient methods for identifying mutated driver pathways in cancer
A novel missense-mutation-related feature extraction scheme for ‘driver’ mutation identification
A linear programming model for protein inference problem in shotgun proteomics
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text
Biologistics—Diffusion coefficients for complete proteome of Escherichia coli
Mendel-GPU: haplotyping and genotype imputation on graphics processing units
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P -values
Phylogenetics, likelihood, evolution and complexity
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
DLRS: gene tree evolution in light of a species tree
CSB: a Python framework for structural bioinformatics
SAPIN: A framework for the structural analysis of protein interaction networks
NetworkView : 3D display and analysis of protein·RNA interaction networks
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations
An RNA Mapping DataBase for curating RNA structure mapping experiments
ImgLib2—generic image processing in Java