Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
Prediction of protein functional residues from sequence by probability density estimation
Beyond the ‘best’ match: machine learning annotation of protein sequences by integration of different sources of information
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Structural search and retrieval using a tableau representation of protein folding patterns
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions
Observation of multiple folding pathways of β-hairpin trpzip2 from independent continuous folding trajectories
Genome-wide co-expression based prediction of differential expressions
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Using repeated measurements to validate hierarchical gene clusters
An assessment of the uses of homologous interactions
Interpool: interpreting smart-pooling results
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
GENESIS: genome evolution scenarios
SOAP: short oligonucleotide alignment program
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations
Jenti: an efficient tool for mining complex inbred genealogies
Jane: suggesting journals, finding experts
HCGene: a software tool to support the hierarchical classification of genes
TagFinder for the quantitative analysis of gas chromatography—mass spectrometry (GC-MS)-based metabolite profiling experiments
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours