title: The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
abstract: EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.
authors.forename: Amanda
authors.initials: A
authors.lastname: Mackie
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Billington
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Carol
authors.initials: C
authors.lastname: Fulcher
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Anamika
authors.initials: A
authors.lastname: Kothari
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Quang
authors.initials: Q
authors.lastname: Ong
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Martin
authors.initials: M
authors.lastname: Peralta-Gil
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Subhraveti
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: David A
authors.initials: DA
authors.lastname: Velázquez-Ramírez
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Paulsen
authors.affiliation: SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA pkarp@ai.sri.com.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004734:Energy Metabolism; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D053858:Metabolic Networks and Pathways; D015398:Signal Transduction; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D064878:Web Browser
chemical_list: D029968:Escherichia coli Proteins; D014157:Transcription Factors