There are a great many computational biology tools and resources available online. Below are some of the more useful tools that I either currently use or have used in the past.
Genome Databases
- Ensembl
- Mouse Genome Informatics
- UCSC Genome Bioinformatics
- International Cancer Genome Consortium data portal
- HUGO Gene Nomenclature Committee
- My Cancer Genome
Metabolome Databases
Pathway Databases
Ontologies
- Browse ontologies – Ontology Lookup Service (OLS)
Expression analysis resources
- GeneSpring GX (Agilent Technologies)
- Custom CDF (Brainarray)
- Ingenuity Pathways Analysis (Ingenuity Systems)
- DAVID Bioinformatics Resources 2008 (NIAID)
- BioGPS (GNF)
- WikiGenes
- GenePattern (Broad Institute)
- TM4 (Dana-Farber Cancer Institute)
- Gene Sifter (Geospiza)
- In silico Transcriptomics Online (GeneSapiens)
- Oncogenomics (NCI)
GeneSet Analysis
- Gene Set Enrichment Analysis (GSEA)
- ToppGene (Anil Jegga, Cincinnati Children’s Hospital)
- GATACA (Bruce Aronow, Cincinnati Children’s Hospital)
- WebGestalt (Bing Zhang, Vanderbuilt)
Next Generation Sequencing
Microarray repositories
- Gene Expression Omnibus (NCBI)
- Oncomine (Compendia Bioscience)
- Stanford Microarray Database
- Array Express (EMBL-EBI)
Biomarker resources
- Secreted Protein Database (Peking University)
- Infectious Disease Biomarker Database (IDBD) (Korea Institute of Health)
Biological Pathways
Protein interaction databases
- Human Protein Reference Database (HPRD)
- IntAct (EMBL-EBI)
- BioGRID
- Human Interactome Map (HiMAP)
- mint