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

On the UW-Madison campus

E. coli related resources

General E. coli information

What the Heck is an E. coli? Jack Brown's introduction to the bug in question
The E. coli Chronicles: A Magical Friendship Rachel Salemi's educational comic book
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
The FDA's Foodborne Pathogenic Microorganisms and Natural Toxins Handbook,
aka The Bad Bug Book (Second Edition)
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
PAIDB the Pathogenicity Island Database: pathogenicity islands and antimicrobial resistance islands
The Genesis of Pathogenic E. coli -- a creationist take on pathogens

Databases and data collections (mostly 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
- MG1655 Metabolic map poster PDF
CyberCell database (CCDB) quantitative genomic, proteomic, and metabolomic data on E. coli
PortEco data resource for the bacterial model organism, Escherichia coli (formerly EcoliHub)
EchoBASE an integrated post-genomic database for E. coli
coliBASE a genome resource for the E. coli research community
RegulonDB E. coli K-12 transcriptional regulatory network
transportDB predicted cytoplasmic membrane transport proteins
E. coli Gene Expression Database (GenExpDB) at Oklahoma State University
Bacteriome.org -- A database of E. coli protein-protein interactions
PEC profiling of the E. coli chromosome
ECMDB the Escherichia coli Metabolome Database: the genome and metabolome of E. coli K-12
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
ECODAB Escherichia coli O-antigen Database
LTEE the E. coli Long-term Experimental Evolution project
The E. coli Student Portal -- a microbiology education site for E. coli, developed at the University of California Los Angeles

The lighter side of E. coli

Glass Microbiology Luke Jerram's eerily beautiful sculptures
Rogan Brown - Paper Sculptures Rogan Brown's exquisite hand cut paper microbes and pathogens
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 [also see Microbe Music]
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

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
Bacterial Genomes Wellcome Trust Sanger Institute
PATRIC Pathosystems Resource Integration Center, a Bacterial Bioinformatics Resource Center
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:
- 505 Salmonella enterica genomes and associated metabolic pathways
- 40 Shigella flexneri genomes and associated metabolic pathways
KEGG Kyoto Encyclopedia of Genes and Genomes
MicrobesOnline an integrated portal for comparative and functional genomics
BacMap an Interactive Atlas for Exploring Bacterial Genomes
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 **
DEG: Database of Essential Genes from the Centre of Bioinformatics, Tianjin University
NIH Human Microbiome Project

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