AI Center ::Dr Peter D Karp

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Dr Peter D Karp

Director, Bioinformatics Research Group
Artificial Intelligence Center

SRI International
Room AE206
333 Ravenswood Avenue
Menlo Park, CA 94025-3493
USA

Phone: (650) 859-4358
Fax: (650) 859-3735

Email:

Current Projects

	BioCyc Database Collection 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, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
	EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism 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.
	MetaCyc: Metabolic Pathway Database The MetaCyc metabolic pathway database contains pathways from over 150 different organisms. MetaCyc describes metabolic pathways, reactions, enzymes, and substrate compounds. The MetaCyc data were gathered from a variety of literature and on-line sources, and contain citations to the source of each pathway.
	Pathway Tools Pathway Tools consists of two sets of tools: the Editors and Pathologic. The Editors are specialized for editing a pathway/genome database. Pathologic helps create a new pathway/genome database containing pathways predicted from an annotated genome (typically as a Genbank entry) and the MetaCyc database.

Software

Grasper: An Interactive Network Editor and Graphical Database
Grasper is a system for viewing and manipulating graph-structured information, and for building graph-based user interfaces for application programs.

Selected Publications

The following publications are selected by the author. They are listed in reverse chronological order.

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Caspi, R. and Foerster, H. and Fulcher, C.A. and Hopkinson, R. and Ingraham, J. and Kaipa, P. and Krummenacker, M. and Paley, S. and Pick, J. and Rhee, S.Y. and Tissier, C. and Zhang, P. and Karp, P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes.. Nucleic Acids Research, vol. 34, pp. D511-D516, Jan 2006. [PDF, Details]
Keseler, I.M. and Collado-Vides, J. and Gama-Castro, S. and Ingraham, J. and Paley, S. and Paulsen, I.T. and Peralta-Gil, M. and Karp, P.D. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research, vol. 33, pp. D334-D337, Jan 2005. [PDF, Details]
P. Larsson, P.C.F. Oyston, P. Chain, M.C. Chu, M. Duffield, H.K. Fuxelius, E. Garcia, G. H�lltorp, D. Johansson, K.E. Isherwood, P.D. Karp, E. Larsson, Y. Liu, S. Michell, J. Prior, R. Prior, S. Malfatti, A. Sj�stedt, K. Svensson, N. Thompson, L. Vergez, J.K. Wagg, B.W. Wren, L.E. Lindler, S.G.E. Andersson, M. Forsman, and R.W. Titball. The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nature Genetics, vol. 37, pp. 153-9, 2005. [Details]
Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M. and Karp, P.D. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology, vol. 6, no. R2, 2004. [Details]
Karp, P.D. and Paley, S. and Romero, P. The Pathway Tools Software. Bioinformatics, vol. 18, pp. S225-S232, 2002. [Details]
Karp, P.D. Pathway Databases: A Case Study in Computational Symbolic Theories. Science, vol. 293, pp. 2040-4, 2001. [Details]

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