ORCID Profile
0000-0001-8780-7664
Current Organisations
Boston University
,
Universidad Nacional Autónoma de México
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Publisher: Oxford University Press (OUP)
Date: 26-11-2007
DOI: 10.1093/NAR/GKM740
Publisher: Oxford University Press (OUP)
Date: 2009
DOI: 10.1093/NAR/GKN751
Publisher: Oxford University Press (OUP)
Date: 17-12-2004
DOI: 10.1093/NAR/GKI108
Publisher: American Society for Microbiology
Date: 09-05-2014
DOI: 10.1128/ECOSALPLUS.ESP-0009-2013
Abstract: EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli . EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli . The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.
Publisher: Oxford University Press (OUP)
Date: 07-11-2012
DOI: 10.1093/NAR/GKS1027
Publisher: American Society for Microbiology
Date: 08-02-2018
DOI: 10.1128/ECOSALPLUS.ESP-0006-2018
Abstract: EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli . EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli . The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed via EcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
Publisher: Oxford University Press (OUP)
Date: 21-11-2010
DOI: 10.1093/NAR/GKQ1143
Publisher: Oxford University Press (OUP)
Date: 28-11-2016
DOI: 10.1093/NAR/GKW1003
No related grants have been discovered for Julio Collado-Vides.