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Resources on the Internet
Here we historically provided links to research resources beyond our lab. Many have become invalid over the years; broken links are periodically fixed or deleted, but no wholesale update is anticipated. We are open to suggestions for additional links.
On the UW-Madison campus
E. coli related resources
Other Enterobacterial genome projects
Microarray and Functional Genomics
On the UW-Madison campus
- UW Biotechnology Center
- Laboratory of Genetics
- Genome Evolution Laboratory (Nicole Perna's lab)
- J.F. Crow Institute for the Study of Evolution
- Department of Bacteriology
- Department of Biochemistry
- Department of Biomolecular Chemistry
- Department of Chemical and Biological Engineering
- Department of Chemistry
- Department of Medical Microbiology & Immunology
- Department of Soil Science
- School of Pharmacy
- School of Veterinary Medicine
E. coli related resources
General E. coli information
- What the Heck is an E. coli? Jack Brown's introduction to the bug in question
- Escherichia coli | Wikipedia entry from the free encyclopedia
- Escherichia coli | EOL entry from the Encyclopedia of Life
- Escherichia | MicrobeWiki entry from the student-edited microbiology resource
- EcoSal Plus online reference covering virtually all aspects of E. coli, Salmonella, and other members of the family Enterobacteriaceae (subscription required)
- Standing on the Shoulders of a Tiny Giant Brooke Anderson's guest post about the history of E. coli as a model organism, for the blog Small Things Considered
- Bacteria: Escherichia coli entry from Seres modélicos: Entre la naturaleza y el laboratorio (Model Organisms: Between nature and laboratory), an exhibition created by the Higher Council for Scientific Research (CSIC). [in Spanish]
Pathogenic E. coli
- Pathogenic E. coli chapter from Todar's Online Textbook of Bacteriology
- E. coli | CDC general information from the Centers for Disease Control and Prevention
- E. coli | FoodSafety.gov general information from the U.S. Food & Drug Administration
- Bad Bug Book: Foodborne Pathogenic Microorganisms and Natural Toxins Handbook
- E. coli | EPA basic information about E. coli in water sources from the Environmental Protection Agency
- E. coli | NIAID research from the National Institute of Allergy and Infectious Diseases
- E. coli Reference Center at Penn State: largest repository for E. coli strains in America
- STEC Center a reference center to facilitate the study of of Shiga toxin-producing E. coli
- EcMLST a multilocus sequence typing (MLST) database for pathogenic E. coli
- E. coli O157:H7 and Salmonella typhimurium DT104: the role of animals
- PAIDB the Pathogenicity Island Database: pathogenicity islands and antimicrobial resistance islands
Databases and data collections (mostly E. coli K-12)
- IECA the International E. coli Alliance's database portal
- EcoGene the comprehensive data resource structural and functional annotation of E. coli K-12
- CGSC the Coli Genetic Stock Center at Yale University
- E. coli Strain NBRP Japanese National BioResource Project for strains, clones, cloning vectors and more
- EcoCyc the bioinformatics database describing the genome and biochemical machinery of E. coli K-12
- MG1655 Genome poster PDF (approx 42"x73")
- MG1655 Metabolic map poster PDF (approx 42"x73")
- PortEco data resource for the bacterial model organism, Escherichia coli (formerly EcoliHub)
- GenoBase functional genomic analysis of E. coli in Japan
- EchoBASE an integrated post-genomic database for E. coli
- ECDC the E. coli Database Collection
- RegulonDB E. coli K-12 transcriptional regulatory network
- transportDB predicted cytoplasmic membrane transport proteins
- PEC profiling of the E. coli chromosome
- ECMDB the Escherichia coli Metabolome Database: the genome and metabolome of E. coli K-12
- PrFEcT-Predict a database of computational resources for multiple proteomes
- EcoProDB the E. coli protein database, integrating 2-D gel data with other resources
- E. coli | Zhang Lab Genome-wide protein structure & function modeling
- ECCE the E. coli cell envelope protein data collection
- proteases of E. coli
- E. coli transcription factor binding sites
- repeated sequences short repeated palindromes in enterobacteria
- ECODAB Escherichia coli O-antigen Database
- ECOR Strains the Escherichia coli Reference Collection of natural isolates
- LTEE the E. coli Long-term Experimental Evolution project
- ** GenProtEc, an E. coli genome and proteome database at MBL, has been retired **
The lighter side of E. coli
- Glass Microbiolgy Luke Jerram's eerily beautiful sculptures
- Science ^ Art Zachary Copfer's "bacteriographs"
- Model Organisms :: E coli part of a short series by Velica, on deviantART
- E. Coli "To Drool" "bummer pop" album issued on the Triple X label in 1996
- Giantmicrobes, Inc. plush E. coli, among others
- @real_e_coli the Twitter account of the self-styled President E. coli, the first Bacterial-American President
- Foretold in Alphabetics E. coli O157:H7 and the Bible Code
Other Enterobacterial genome projects (aka the Deluge)
Keeping track of the multitude of other genome projects has become a Sisyphean task; there are well over 1000 completed or ongoing sequencing projects for strains of E. coli alone. In addition to a few enterobacterial projects, here are links to major microbial sequencing centers, multi-organism databases, and related resources.
- salmonella.org
- AToL: Enterobacteriaceae project to sequence Type strains of the family Enterobacteriaceae
- GOLD the Genomes OnLine Database
- Microbial Genome Projects Genome Information Research Center, Osaka Univ
- Bacterial Genomes Wellcome Trust Sanger Institute
- Genomes: Microorganisms The Genome Institute, Washington University
- PATRIC Pathosystems Resource Integration Center, a Bacterial Bioinformatics Resource Center
- xBASE a comprehensive resource for comparative bacterial genomics
- GenoList an integrated environment for the analysis of microbial genomes
- JGI Genome Portal DOE's Joint Genome Institute
- Microbial Genomes at NCBI public data from prokaryotic genome sequencing projects
- BioCyc pathway/genome databases; EcoCyc and other organism entry pages:
- KEGG Kyoto Encyclopedia of Genes and Genomes
- MicrobesOnline an integrated portal for comparative and functional genomics
- Genome Atlas Database from Technical University of Denmark's Center for Biological Sequence Analysis
- BacMap interactive Bacterial Genome Atlas
- UCSC Microbial Genome Browser a microbe-specific version of the popular visualization tool
- ASAP a systematic annotation package for community analysis of genomes
- IMG DOE's Integrated Microbial Genomes ** account needed as of January 7, 2014 **
- ** JCVI's Comprehensive Microbial Resource (CMR) is no longer supported and has been taken offline **
Microarray and Functional Genomics
- MIAME Minimal Information About Microarray Experiment
- SMD Stanford Microarray Database
- ArrayExpress a database of functional genomics experiments