333 Ravenswood Avenue
Menlo Park, CA 94025-3493
Phone: (650) 859-4358
Fax: (650) 859-3735
Honors and Awards
Dr. Karp’s research interests include metabolic-pathway bioinformatics, systems biology, and metabolic engineering. He is the bioinformatics architect of the BioCyc collection of Pathway/Genome Databases that includes EcoCyc, HumanCyc, and MetaCyc. He has developed algorithms for prediction of metabolic pathways from sequenced genomes, for visualization of individual pathways and entire metabolic maps, and for generation of metabolic models from pathway databases. He is interested in extending these modeling techniques from individual organisms to communities of interacting microorganisms. His interests also include biological databases and ontologies, and interoperation of bioinformatics databases.
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.
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of Escherichia 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. EcoCyc integrates information from more than 30,000 scientific publications.
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2500 pathways from more than 2800 different organisms (circa 2012). The MetaCyc data were curated from more than 50,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.
Pathway Tools is a systems biology software system that supports several use cases: development of organism-specific database that integrate many bioinformatics datatypes, from genomes to pathways; Development of metabolic-flux models using flux-balance analysis; scientific visualization, web publishing, and querying of organism-specific databases; analysis of omics datasets; and Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons.
Grasper is a system for viewing and manipulating graph-structured information, and for building graph-based user interfaces for application programs.
The following publications are selected by the author. They are listed in reverse chronological order.
[View All 165 Publications]
Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.. Nucleic Acids Res, vol. 44, no. D1, pp. D471-D480, 2016. [Details]
"Karp P.D., Latendresse M., Paley S.M., Krummenacker Q., Billington R., Kothari D., Lee T., Subhraveti P., Spaulding A., Fulcher C., Keseler I.M., Caspi R.". "Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology". 2015. [Details]
Weaver S., Keseler I. M., Mackie A., Paulsen I. T., Karp" P. D. A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Systems Biology, vol. 8, p. 79, 2014. [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. Pathway Databases: A Case Study in Computational Symbolic Theories. Science, vol. 293, pp. 2040-4, 2001. [Details]