Ontological analysis of gene expression data: current tools, limitations, and open problems
JIGSAW: integration of multiple sources of evidence for gene prediction
The predictive power of the CluSTr database
MicroRNA identification based on sequence and structure alignment
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
A geometric invariant-based framework for the analysis of protein conformational space
TileMap: create chromosomal map of tiling array hybridizations
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
Integration of metabolic networks and gene expression in virtual reality
Study of coordinative gene expression at the biological process level
Resolving abbreviations to their senses in Medline
WebACT—an online companion for the Artemis Comparison Tool
BlastXtract—a new way of exploring translated searches
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness
HEGESMA: genome search meta-analysis and heterogeneity testing
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
Friend, an integrated analytical front-end application for bioinformatics
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif
GeneCruiser: a web service for the annotation of microarray data
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
simuPOP: a forward-time population genetics simulation environment
Bifurcation discovery tool
PACdb: PolyA Cleavage Site and 3′-UTR Database
DEPD: a novel database for differentially expressed proteins
SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization