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 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 MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1800 pathways from more than 2200 different organisms (circa 2012). The MetaCyc data were curated from more than 33,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.
	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. Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons. Comparative analyses.

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. Halltorp, D. Johansson, K.E. Isherwood, P.D. Karp, E. Larsson, Y. Liu, S. Michell, J. Prior, R. Prior, S. Malfatti, A. Sjostedt, 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]