AI Center ::Suzanne Paley

	Search \| Contact \| SRI Home

AIC Home > People > Suzanne Paley

Suzanne Paley

Computer Scientist
Artificial Intelligence Center

SRI International
Room EK203
333 Ravenswood Avenue
Menlo Park, CA 94025-3493
USA

Phone: (650) 859-5904
Fax: (650) 859-3735

Email:

Home Page: http://www.ai.sri.com/~paley

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 hundreds of 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.

Publications

The following are in reverse chronological order of publication.

Showing most recent 5 out of 26 [View All]

Caspi R, Foerster H, Fulcher C. A, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S. Y, Shearer A. G, Tissier C, Walk T. C, Zhang P, Karp P. D. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research, vol. 36, pp. D623-D631, 2007. [PDF, Details]
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]
Krummenacker, M., Paley, S., Mueller, L., Yan, T., and Karp, P.D. Querying and Computing with BioCyc Databases. Bioinformatics, vol. 21, pp. 3454-5, 2005. [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]
Zhang, P., Foerster, H., Tissier, C.P., Mueller, L., Paley, S., Karp,. MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Resarch. Plant Physiol, vol. 138, no. 1, pp. 27�37, 2005. [Details]

SRI International
©2008 SRI International, 333 RavenswoodAvenue, Menlo Park, CA 94025-3493
SRI International is a nonprofit corporation. Privacy policy