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The BioCyc Database Collection is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
BsubCyc is a model-organism database that describes the genome and the biochemical machinery of Bacillus subtilis. The long-term goal of the project is to describe the molecular catalog of the B. subtilis cell and the functions of each of its molecular parts, to facilitate a system-level understanding of B. subtilis.
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli. The long-term goal of the project is to describe the 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.
The following are in reverse chronological order of publication.
Showing most recent 5 out of 8 [View All]
7. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res, vol. 40, no. D1, pp. D742-D753, 2012. [PDF, Details]
Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., and Karp, P.D. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Adics Research, vol. 39, pp. D583-90, 2011. [PDF, Details]
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.. Brief Bioinform., vol. 11, no. 1, pp. 40-79, Jan 2010. [PDF, Details]
Hu, J.C. and Karp, P.D. and Keseler, I.M. and Krummenacker, M. and Siegele, D.A. What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology, vol. 17, no. 7, pp. 269-278, July 2009. [Details]
Keseler, I.M. and Bonavides-Martinez, C. and Collado-Vides, J. and Gama-Castro, S. and Gunsalus, R.P. and Johnson, D.A. and Krummenacker, M., and Nolan, L.M. and Paley, S. and Paulsen, I.T. and Peralta-Gil, M. and Santos-Zavaleta, A. and Shearer, A.G. and Karp, P.D. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Research, vol. 37, pp. D464-D470, Jan 2009. [PDF, Details]