BioSigNet-RR, from Arizona State University, is an inference-based approach to representing signaling networks: http://www.public.asu.edu/~cbaral/biosignet.
CIS (Compound Importance Sampling), from the Hebrew University of Jerusalem, scans regulatory regions for putative binding sites to construct a genome-wide regulatory network: http://compbio.cs.huji.ac.il/CIS/.
DECON, from Carnegie Mellon University, combines budding index and gene expression data to deconvolve expression profiles: http://www.cs.cmu.edu/~zivbj/decon/decon.html.
DSS (Data Sources Selection), from the Laboratory of Informatics Research at CNRS, is an algorithm that takes a user’s query and preferences into account to provide a list of sources to address a biological query: http://lri.fr/~cohen/dss/dss.html.
HaploBlock, from Technion University, uses high-density haplotype or genotype data top perform linkage disequilibrium: http://bioinfo.cs.technion.ac.il/haploblock/.
HyBrow (Hypothesis Browser), from the Huck Institute for Life Sciences at Penn State University, uses a hypothesis ontology to design and evaluate hypotheses: http://www.hybrow.org.
IMGT/JunctionAnalysis, from the Institute of Human Genetics at CNRS, analyzes immunoglobulin and T-cell receptor junctions: http://imgt.cines.fr.
*MUSCLE, from Robert Edgar, is a multiple sequence alignment program that can align 5,000 sequences of 350 bases in seven minutes on a desktop PC: http://www.drive5.com/muscle.
Netmotsa, from the Institute for Systems Biology, uses a probabilistic model to predict protein-protein interactions based on protein sequence information and observed physical interactions: http://sf.net/projects/netmotsa.
NLProt, from Columbia University, extracts protein names from the scientific literature: http://cubic.bioc.columbia.edu/services/nlprot/.
*PROBCONS, from Stanford, is a multiple sequence alignment program: http://probcons.stanford.edu.
PSILC (Pseudogene Inference from Loss of Constraint), from the Wellcome Trust Sanger Institute, distinguishes pseudogenes from functional genes: http://www.sanger.ac.uk/Software/PSILC.
SCOPEC, from Inpharmatica, is a database of catalytic domains: http://www.enzome.com.
TIDE (Terra Incognita Discovery Endeavor), from the Weizmann Institute, assigns gene identities for human ESTs: http://genecards.weizmann.ac.il/TIDE/.
Traitmap, from RIKEN, is a database of genetic mapping charts for human, mouse, and Arabidopsis: http://omicspace.riken.jp/gps/
*Co-winners of best paper for ISMB 2004.