Peter D. Karp

Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi, Peter D. Karp: A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinformatics 14: 112 (2013)

Steven Eker, Markus Krummenacker, Alexander Glennon Shearer, Ashish Tiwari, Ingrid M. Keseler, Carolyn L. Talcott, Peter D. Karp: Computing minimal nutrient sets from metabolic networks via linear constraint solving. BMC Bioinformatics 14: 114 (2013)

Ingrid M. Keseler, Amanda Mackie, Martín Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol A. Fulcher, Araceli M. Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Imke Schröder, Alexander Glennon Shearer, Pallavi Subhraveti, Michael Travers, Deepika Weerasinghe, Verena Weiss, Julio Collado-Vides, Robert P. Gunsalus, Ian T. Paulsen, Peter D. Karp: EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Research 41(Database-Issue): 605-612 (2013)

Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp: Construction and completion of flux balance models from pathway databases. Bioinformatics 28(3): 388-396 (2012)

Suzanne M. Paley, Mario Latendresse, Peter D. Karp: Regulatory network operations in the Pathway Tools software. BMC Bioinformatics 13: 243 (2012)

Ron Caspi, Tomer Altman, Kate Dreher, Carol A. Fulcher, Pallavi Subhraveti, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Anuradha Pujar, Alexander Glennon Shearer, Michael Travers, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 40(Database-Issue): 742-753 (2012)

Luciana Ferrer, Alexander Glennon Shearer, Peter D. Karp: Discovering novel subsystems using comparative genomics. Bioinformatics 27(18): 2478-2485 (2011)

Mario Latendresse, Peter D. Karp: Web-Based Metabolic Network Visualization with a Zooming User Interface. BMC Bioinformatics 12: 176 (2011)

Ingrid M. Keseler, Julio Collado-Vides, Alberto Santos-Zavaleta, Martín Peralta-Gil, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martínez, Suzanne M. Paley, Markus Krummenacker, Tomer Altman, Pallavi Kaipa, Aaron Spaulding, John Pacheco, Mario Latendresse, Carol A. Fulcher, Malabika Sarker, Alexander Glennon Shearer, Amanda Mackie, Ian T. Paulsen, Robert P. Gunsalus, Peter D. Karp: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Research 39(Database-Issue): 583-590 (2011)

Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Mario Latendresse, Joseph M. Dale, Thomas J. Lee, Pallavi Kaipa, Fred Gilham, Aaron Spaulding, Liviu Popescu, Tomer Altman, Ian T. Paulsen, Ingrid M. Keseler, Ron Caspi: Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics 11(1): 40-79 (2010)

Joseph M. Dale, Liviu Popescu, Peter D. Karp: Machine learning methods for metabolic pathway prediction. BMC Bioinformatics 11: 15 (2010)

Luciana Ferrer, Joseph M. Dale, Peter D. Karp: A systematic study of genome context methods: calibration, normalization and combination. BMC Bioinformatics 11: 493 (2010)

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne M. Paley, Liviu Popescu, Anuradha Pujar, Alexander Glennon Shearer, Peifen Zhang, Peter D. Karp: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 38(Database-Issue): 473-479 (2010)

Peter D. Karp: Databases and Algorithms for Pathway Bioinformatics. HEALTHINF 2010: 5

Peter D. Karp: Development of Large Scientific Knowledge Bases. ICAART (1) 2010: 23

Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides, Socorro Gama-Castro, Robert P. Gunsalus, D. Aaron Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Alberto D. Santos-Zavaleta, Alexander Glennon Shearer, Peter D. Karp: EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Research 37(Database-Issue): 464-470 (2009)

Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Yon Rhee, Alexander Glennon Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, Peter D. Karp: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 36(Database-Issue): 623-631 (2008)

Peter D. Karp, Thomas J. Lee, Valerie Wagner: BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. DILS 2008: 5-7

Thomas J. Lee, Ian T. Paulsen, Peter D. Karp: Annotation-based inference of transporter function. ISMB 2008: 259-267

Yannick Pouliot, Peter D. Karp: A survey of orphan enzyme activities. BMC Bioinformatics 8 (2007)

Michelle L. Green, Peter D. Karp: Using genome-context data to identify specific types of functional associations in pathway/genome databases. ISMB/ECCB (Supplement of Bioinformatics) 2007: 205-211

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides: The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics 7: 5 (2006)

Thomas J. Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David W. J. Stringer-Calvert, Jessica D. Tenenbaum, Peter D. Karp: BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics 7: 170 (2006)

Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne M. Paley, John Pick, Seung Yon Rhee, Christophe Tissier, Peifen Zhang, Peter D. Karp: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 34(Database-Issue): 511-516 (2006)

Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp: Querying and computing with BioCyc databases. Bioinformatics 21(16): 3454-3455 (2005)

Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33(Database-Issue): 334-337 (2005)

Pedro Romero, Peter D. Karp: Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics 20(5): 709-717 (2004)

Michelle L. Green, Peter D. Karp: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5: 76 (2004)

Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne M. Paley, Martha Arnaud, John Pick, Seung Yon Rhee, Peter D. Karp: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 32(Database-Issue): 438-442 (2004)

Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang: An Evidence Ontology for Use in Pathway/Genome Databases. Pacific Symposium on Biocomputing 2004: 190-201

Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman: Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics 19(2): 241-248 (2003)

Peter D. Karp: What Database Management System(s) Should Be Employed in Bioinformatics Applications? OMICS 7(1): 35-36 (2003)

Peter D. Karp: Pathway Bioinformatics. CSB 2003: 27

Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero: Genome, Pathway, and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2003: 101-103

Suzanne M. Paley, Peter D. Karp: Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics 18(5): 715-724 (2002)

Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, Alida Pellegrini-Toole, César Bonavides-Martínez, Socorro Gama-Castro: The EcoCyc Database. Nucleic Acids Research 30(1): 56-58 (2002)

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole: The MetaCyc Database. Nucleic Acids Research 30(1): 59-61 (2002)

Peter D. Karp, Suzanne M. Paley, Pedro Romero: The Pathway Tools software. ISMB 2002: 225-232

Peter D. Karp, Pedro Romero, Eric P. Neumann: Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2002: 398-399

Peter D. Karp, Suzanne M. Paley, Jingchun Zhu: Database verification studies of SWISS-PROT and GenBank. Bioinformatics 17(6): 526-532 (2001)

Peter D. Karp, Eric P. Neumann, Pedro Romero: Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2001: 420-421

Pedro Romero, Peter D. Karp: Nutrition-Related Analysis of Pathway/Genome Databases. Pacific Symposium on Biocomputing 2001: 470-482

Peter D. Karp: An ontology for biological function based on molecular interactions. Bioinformatics 16(3): 269-285 (2000)

Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-Toole: The EcoCyc and MetaCyc databases. Nucleic Acids Research 28(1): 56-59 (2000)

Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou: An Evaluation of Ontology Exchange Languages for Bioinformatics. ISMB 2000: 239-250

Peter D. Karp, Vinay K. Chaudhri, Suzanne M. Paley: A Collaborative Environment for Authoring Large Knowledge Bases. J. Intell. Inf. Syst. 13(3): 155-194 (1999)

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker: Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Research 27(1): 55-58 (1999)

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker: EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Research 26(1): 50-53 (1998)

Vinay K. Chaudhri, Adam Farquhar, Richard Fikes, Peter D. Karp, James Rice: OKBC: A Programmatic Foundation for Knowledge Base Interoperability. AAAI/IAAI 1998: 600-607

Ronald G. Forsythe Jr., Peter D. Karp, Michael L. Mavrovouniotis: Estimation of equilibrium constants using automated group contribution methods. Computer Applications in the Biosciences 13(5): 537-543 (1997)

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker: EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism. Nucleic Acids Research 25(1): 43-51 (1997)

Suzanne M. Paley, John D. Lowrance, Peter D. Karp: A Generic Knowledge-Base Browser and Editor. AAAI/IAAI 1997: 1045-1051

Marie desJardins, Peter D. Karp, Markus Krummenacker, Thomas J. Lee, Christos A. Ouzounis: Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. ISMB 1997: 92-99

Vinay K. Chaudhri, Peter D. Karp: Querying Schema Information. KRDB 1997: 4.1-4.6

Terry Gaasterland, Peter D. Karp, Kevin Karplus, Christos A. Ouzounis, Chris Sander, Alfonso Valencia (Eds.): Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997. AAAI 1997, isbn 1-57735-022-7

Peter D. Karp, Suzanne M. Paley: Integrated Access to Metabolic and Genomic Data. Journal of Computational Biology 3(1): 191-212 (1996)

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole: EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Research 24(1): 32-39 (1996)

Araceli M. Huerta, Julio Collado-Vides, Peter D. Karp, Kathleen Klose: Three Models of Gene Regulation in E.coli. German Conference on Bioinformatics 1996: 64-67

Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley: HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. ISMB 1996: 116-124

Peter D. Karp: A Strategy for Database Interoperation. Journal of Computational Biology 2(4): 573-586 (1995)

Peter D. Karp, Suzanne M. Paley: Knowledge Representation in the Large. IJCAI (1) 1995: 751-758

Peter D. Karp, Karen L. Myers, Thomas R. Gruber: The Generic Frame Protocol. IJCAI (1) 1995: 768-774

Peter D. Karp, Michael L. Mavrovouniotis: Representing, Analyzing, and Synthesizing Biochemical Pathways. IEEE Expert 9(2): 11-21 (1994)

Peter D. Karp, John D. Lowrance, Thomas M. Strat, David E. Wilkins: The Grasper-CL Graph Management System. Lisp and Symbolic Computation 7(4): 251-290 (1994)

Peter D. Karp, Suzanne M. Paley, Ira Greenberg: A Storage System for Scalable Knowledge Representation. CIKM 1994: 97-104

Peter D. Karp, Suzanne M. Paley: Representations of Metabolic Knowledge: Pathways. ISMB 1994: 203-211

Russ B. Altman, Douglas L. Brutlag, Peter D. Karp, Richard H. Lathrop, David B. Searls (Eds.): Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USA. AAAI 1994, isbn 0-929280-68-7

Peter D. Karp: Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology. Machine Learning 12: 89-116 (1993)

Peter D. Karp, Monica Riley: Representations of Metabolic Knowledge. ISMB 1993: 207-215

Peter D. Karp: A knowledge base of the chemical compounds of intermediary metabolism. Computer Applications in the Biosciences 8(4): 347-357 (1992)

Peter D. Karp: Artificial intelligence methods for theory representation and hypothesis formation. Computer Applications in the Biosciences 7(3): 301-308 (1991)

Peter D. Karp: Hypothesis Formation and Qualitative Reasoning in Molecular Biology. AI Magazine 11(4): 9-10 (1990)