iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data
Scaffolding low quality genomes using orthologous protein sequences
Stability analysis of phylogenetic trees
Defining and predicting structurally conserved regions in protein superfamilies
An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees
A Lasso multi-marker mixed model for association mapping with population structure correction
Density parameter estimation for finding clusters of homologous proteins—tracing actinobacterial pathogenicity lifestyles
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
Drug–target interaction prediction by learning from local information and neighbors
An effective framework for reconstructing gene regulatory networks from genetical genomics data
Non-redundant compendium of human ncRNA genes in GeneCards
HD-CNV: hotspot detector for copy number variants
VAGUE: a graphical user interface for the Velvet assembler
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads
DOOSS: a tool for visual analysis of data overlaid on secondary structures
Intron-centric estimation of alternative splicing from RNA-seq data
High-throughput microbial population genomics using the Cortex variation assembler
Largenet2: an object-oriented programming library for simulating large adaptive networks
NetCAD: a network analysis tool for coronary artery disease-associated PPI network
mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass
Bioclipse-R: integrating management and visualization of life science data with statistical analysis
An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values
PTID: an integrated web resource and computational tool for agrochemical discovery
NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse
ImgLib2—generic image processing in Java