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Dr Peter D Karp

Dr Peter D Karp

Director, Bioinformatics Research Group
Artificial Intelligence Center

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

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


Biography and Interests

Honors and Awards

Research Interests

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.

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.


EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism

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: Metabolic Pathway Database

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

Pathway Tools

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: An Interactive Network Editor and Graphical Database

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.
[View All 165 Publications]

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