P
Peter D. Karp
Researcher at SRI International
Publications - 188
Citations - 27079
Peter D. Karp is an academic researcher from SRI International. The author has contributed to research in topics: EcoCyc & Metabolic network. The author has an hindex of 63, co-authored 183 publications receiving 24737 citations. Previous affiliations of Peter D. Karp include University of North Carolina at Chapel Hill & Artificial Intelligence Center.
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Journal ArticleDOI
The complete genome sequence of the gastric pathogen Helicobacter pylori
Jean-F. Tomb,Owen White,Anthony R. Kerlavage,Rebecca A. Clayton,Granger G. Sutton,Robert D. Fleischmann,Karen A. Ketchum,Hans-Peter Klenk,Steven R. Gill,Brian Dougherty,Karen E. Nelson,John Quackenbush,Lixin Zhou,Ewen F. Kirkness,Scott N. Peterson,Brendan J. Loftus,Delwood Richardson,Robert J. Dodson,Hanif Khalak,Anna Glodek,Keith McKenney,Lisa M. Fitzegerald,Norman H. Lee,Mark Raymond Adams,Erin Hickey,Douglas E. Berg,Jeanine D. Gocayne,Teresa Utterback,Jeremy Peterson,Jenny M. Kelley,Matthew D. Cotton,J. Weidman,Claire Fujii,Cheryl Bowman,Larry Watthey,Erik Wallin,William S. Hayes,Mark Borodovsky,Peter D. Karp,Hamilton O. Smith,Claire M. Fraser,J. Craig Venter +41 more
TL;DR: Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification, and consistent with its restricted niche, it has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity.
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi,Richard Billington,Luciana Ferrer,Hartmut Foerster,Carol A. Fulcher,Ingrid M. Keseler,Anamika Kothari,Markus Krummenacker,Mario Latendresse,Lukas A. Mueller,Quang Ong,Suzanne M. Paley,Pallavi Subhraveti,Daniel Weaver,Peter D. Karp +14 more
TL;DR: The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.
Journal ArticleDOI
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Adam M. Feist,Christopher S. Henry,Jennifer L. Reed,Markus Krummenacker,Andrew R. Joyce,Peter D. Karp,Linda J. Broadbelt,Vassily Hatzimanikatis,Bernhard O. Palsson +8 more
TL;DR: An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 with increased scope and computational capability is presented, expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.
Journal ArticleDOI
The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58
Derek W. Wood,João C. Setubal,Rajinder Kaul,Dave E. Monks,João Paulo Kitajima,Vagner K. Okura,Yang Zhou,Lishan Chen,Gwendolyn E. Wood,Nalvo F. Almeida,Lisa Woo,Yuching Chen,Ian T. Paulsen,Jonathan A. Eisen,Peter D. Karp,Donald Bovee,Peter Chapman,James B. Clendenning,Glenda Deatherage,Will Gillet,Charles E. Grant,Tatyana Kutyavin,Ruth Levy,Meng-Jin Li,Erin K. McClelland,Anthony Palmieri,Christopher K. Raymond,Gregory Rouse,Channakhone Saenphimmachak,Zaining Wu,Pedro Romero,David E. Gordon,Shiping Zhang,Heayun Yoo,Yumin Tao,Phyllis Biddle,Mark Timothy Jung,William Krespan,Michael Perry,Bill Gordon-Kamm,Li Liao,Sun Kim,Carol A. Hendrick,Zuo-Yu Zhao,Maureen Dolan,Forrest Chumley,Scott V. Tingey,Jean-Francois Tomb,Milton P. Gordon,Maynard V. Olson,Eugene W. Nester +50 more
TL;DR: The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids that suggest a recent evolutionary divergence.
Journal ArticleDOI
EcoCyc: a comprehensive database resource for Escherichia coli
Ingrid M. Keseler,Julio Collado-Vides,Socorro Gama-Castro,John L. Ingraham,Suzanne M. Paley,Ian T. Paulsen,Martín Peralta-Gil,Peter D. Karp +7 more
TL;DR: The EcoCyc database contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions.