Characterization of the SOS meta-regulon in the human gut microbiome
Subclonal variant calling with multiple samples and prior knowledge
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
Prediction of nuclear export signals using weighted regular expressions (Wregex)
Exploring genome characteristics and sequence quality without a reference
InterProScan 5: genome-scale protein function classification
Evolutionary footprint of coevolving positions in genes
Evolutionary solution for the RNA design problem
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
Characterizing cancer subtypes as attractors of Hopfield networks
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
CGAT: computational genomics analysis toolkit
estMOI: estimating multiplicity of infection using parasite deep sequencing data
CGARS: cancer genome analysis by rank sums
PanGP: A tool for quickly analyzing bacterial pan-genome profile
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
PhyloJIVE: Integrating biodiversity data with the Tree of Life
jmodeltest.org : selection of nucleotide substitution models on the cloud
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
MAGIC: access portal to a cross-platform gene expression compendium for maize
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
netClass: an R-package for network based, integrative biomarker signature discovery
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data
Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
INCA: a computational platform for isotopically non-stationary metabolic flux analysis
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
The EBI RDF platform: linked open data for the life sciences
Ontodog: a web-based ontology community view generation tool