Markus Krummenacker

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.
	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 7 [View All]

• Hu, J.C. and Karp, P.D. and Keseler, I.M. and Krummenacker, M. and Siegele, D.A. What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology, vol. 17, no. 7, pp. 269-278, July 2009.  [Details]

• Keseler, I.M. and Bonavides-Martinez, C. and Collado-Vides, J. and Gama-Castro, S. and Gunsalus, R.P. and Johnson, D.A. and Krummenacker, M., and Nolan, L.M. and Paley, S. and Paulsen, I.T. and Peralta-Gil, M. and Santos-Zavaleta, A. and Shearer, A.G. and Karp, P.D. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Research, vol. 37, pp. D464-D470, Jan 2009.  [PDF, Details]

• 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]

• Karp, P.D. and Keseler, I.M. and Shearer, A. and Latendresse, M. and Krummenacker, M. and Paley, S.M. and Paulsen, I. and Collado-Vides, J. and Gama-Castro, S. and Peralta-Gil, M. and Santos-Zavaleta, A. and Penaloza-Spinola, M.I. and Bonavides-Martinez, C. and Ingraham, J. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Research, vol. 35, no. 22, pp. 7577-7590, 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]