Bioinformatics software for biologists in the genomics era
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
Fast model-based protein homology detection without alignment
STOP: searching for transcription factor motifs using gene expression
Nucleotide composition string selection in HIV-1 subtyping using whole genomes
Persistent voids: a new structural metric for membrane fusion
Assortative mixing in Protein Contact Networks and protein folding kinetics
Assessment of survival prediction models based on microarray data
Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms
Biological network mapping and source signal deduction
Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
T-Pile—a package for thermodynamic calculations for biomolecules
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations
Recombination-filtered genomic datasets by information maximization
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing
Genetdes: automatic design of transcriptional networks
Stochastic simulation GUI for biochemical networks
MutationFinder: a high-performance system for extracting point mutation mentions from text
DoriC: a database of oriC regions in bacterial genomes
OBO to OWL: a protégé OWL tab to read/save OBO ontologies