Peter D. Karp

	2009
57		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)
	2008
56		Peter D. Karp, Thomas J. Lee, Valerie Wagner: BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. DILS 2008: 5-7
55		Thomas J. Lee, Ian T. Paulsen, Peter D. Karp: Annotation-based inference of transporter function. ISMB 2008: 259-267
54		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)
	2007
53		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
52		Yannick Pouliot, Peter D. Karp: A survey of orphan enzyme activities. BMC Bioinformatics 8: (2007)
	2006
51		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)
50		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)
49		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)
	2005
48		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)
47		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)
	2004
46		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
45		Michelle L. Green, Peter D. Karp: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5: 76 (2004)
44		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)
43		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)
	2003
42		Peter D. Karp: Pathway Bioinformatics. CSB 2003: 27
41		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
40		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)
39		Peter D. Karp: What Database Management System(s) Should Be Employed in Bioinformatics Applications? OMICS 7(1): 35-36 (2003)
	2002
38		Peter D. Karp, Suzanne M. Paley, Pedro Romero: The Pathway Tools software. ISMB 2002: 225-232
37		Peter D. Karp, Pedro Romero, Eric P. Neumann: Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2002: 398-399
36		Suzanne M. Paley, Peter D. Karp: Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics 18(5): 715-724 (2002)
35		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)
34		Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole: The MetaCyc Database. Nucleic Acids Research 30(1): 59-61 (2002)
	2001
33		Peter D. Karp, Eric P. Neumann, Pedro Romero: Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2001: 420-421
32		Pedro Romero, Peter D. Karp: Nutrition-Related Analysis of Pathway/Genome Databases. Pacific Symposium on Biocomputing 2001: 470-482
31		Peter D. Karp, Suzanne M. Paley, Jingchun Zhu: Database verification studies of SWISS-PROT and GenBank. Bioinformatics 17(6): 526-532 (2001)
	2000
30		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
29		Peter D. Karp: An ontology for biological function based on molecular interactions. Bioinformatics 16(3): 269-285 (2000)
28		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)
	1999
27		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)
26		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)
	1998
25		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
24		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)
	1997
23		Terry Gaasterland, Peter D. Karp, Kevin Karplus, Christos A. Ouzounis, Chris Sander, Alfonso Valencia: Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997 AAAI 1997
22		Suzanne M. Paley, John D. Lowrance, Peter D. Karp: A Generic Knowledge-Base Browser and Editor. AAAI/IAAI 1997: 1045-1051
21		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
20		Vinay K. Chaudhri, Peter D. Karp: Querying Schema Information. KRDB 1997: 4.1-4.6
19		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)
18		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)
	1996
17		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
16		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
15		Peter D. Karp, Suzanne M. Paley: Integrated Access to Metabolic and Genomic Data. Journal of Computational Biology 3(1): 191- (1996)
14		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)
	1995
13		Peter D. Karp, Suzanne M. Paley: Knowledge Representation in the Large. IJCAI (1) 1995: 751-758
12		Peter D. Karp, Karen L. Myers, Thomas R. Gruber: The Generic Frame Protocol. IJCAI (1) 1995: 768-774
11		Peter D. Karp: A Strategy for Database Interoperation. Journal of Computational Biology 2(4): 573-586 (1995)
	1994
10		Russ B. Altman, Douglas L. Brutlag, Peter D. Karp, Richard H. Lathrop, David B. Searls: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USA AAAI 1994
9		Peter D. Karp, Suzanne M. Paley, Ira Greenberg: A Storage System for Scalable Knowledge Representation. CIKM 1994: 97-104
8		Peter D. Karp, Suzanne M. Paley: Representations of Metabolic Knowledge: Pathways. ISMB 1994: 203-211
7		Peter D. Karp, Michael L. Mavrovouniotis: Representing, Analyzing, and Synthesizing Biochemical Pathways. IEEE Expert 9(2): 11-21 (1994)
6		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)
	1993
5		Peter D. Karp, Monica Riley: Representations of Metabolic Knowledge. ISMB 1993: 207-215
4		Peter D. Karp: Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology. Machine Learning 12: 89-116 (1993)
	1992
3		Peter D. Karp: A knowledge base of the chemical compounds of intermediary metabolism. Computer Applications in the Biosciences 8(4): 347-357 (1992)
	1991
2		Peter D. Karp: Artificial intelligence methods for theory representation and hypothesis formation. Computer Applications in the Biosciences 7(3): 301-308 (1991)
	1990
1		Peter D. Karp: Hypothesis Formation and Qualitative Reasoning in Molecular Biology. AI Magazine 11(4): 9-10 (1990)

Coauthor Index

1	Neil F. Abernethy	[30]
2	Russ B. Altman	[10] [40]
3	Martha Arnaud	[43]
4	David Benton	[30]
5	César Bonavides-Martínez	[35] [57]
6	Douglas L. Brutlag	[10]
7	Ron Caspi	[49] [54]
8	Vinay K. Chaudhri	[20] [25] [27]
9	Julio Collado-Vides	[17] [35] [47] [50] [57]
10	Matt DeJongh	[30]
11	Adam Farquhar	[25]
12	Richard Fikes	[25]
13	Hartmut Foerster	[49] [54]
14	Ronald G. Forsythe Jr.	[19]
15	Carol A. Fulcher	[49] [54]
16	Terry Gaasterland	[23]
17	Socorro Gama-Castro	[35] [47] [50] [57]
18	Michelle L. Green	[45] [53]
19	Ira Greenberg	[9]
20	Thomas R. Gruber (Tom Gruber)	[12]
21	Robert P. Gunsalus	[57]
22	Priyanka Gupta	[51]
23	Alexander J. Hartemink	[41]
24	Gregg Helt	[30]
25	Dan Hodnett	[30]
26	Rebecca Hopkinson	[49]
27	Araceli M. Huerta	[17]
28	John Ingraham	[47] [49]
29	D. Aaron Johnson	[57]
30	Pallavi Kaipa	[49] [54]
31	Kevin Karplus	[23]
32	Robert Kent	[30]
33	Ingrid M. Keseler	[47] [57]
34	Kathleen Klose	[17]
35	Anthony Kosky	[30]
36	Cynthia J. Krieger	[43] [46]
37	Markus Krummenacker	[18] [21] [24] [26] [48] [49] [54] [57]
38	Mario Latendresse	[54]
39	Richard H. Lathrop	[10]
40	Thomas J. Lee	[21] [51] [55] [56]
41	Suzanna Lewis	[30]
42	John D. Lowrance	[6] [22]
43	Agustino Martínez-Antonio	[50]
44	Michael L. Mavrovouniotis	[7] [19]
45	Robin McEntire	[30]
46	Lukas A. Mueller	[43] [48]
47	Karen L. Myers	[12]
48	Eric P. Neumann	[30] [33] [37] [41]
49	Laura M. Nolan	[57]
50	Natalya Fridman Noy (Natasha Fridman Noy, Natasha F. Noy)	[40]
51	Frank Olken	[30]
52	Christos A. Ouzounis	[16] [21] [23]
53	Suzanne M. Paley	[8] [9] [13] [14] [15] [16] [18] [22] [24] [26] [27] [28] [31] [34] [35] [36] [38] [43] [46] [47] [48] [49] [54] [57]
54	Dhiraj K. Pathak	[30]
55	Ian T. Paulsen	[28] [35] [47] [55] [57]
56	Alida Pellegrini-Toole	[14] [18] [24] [26] [28] [34] [35]
57	Mónica I. Peñaloza-Spínola	[50]
58	Martín Peralta-Gil	[47] [50] [57]
59	John Pick	[43] [49]
60	Yannick Pouliot	[51] [52]
61	Seung Yon Rhee	[43] [49] [54]
62	James Rice	[25]
63	Monica Riley	[5] [14] [18] [24] [26] [28] [34] [35]
64	Pedro Romero	[32] [33] [37] [38] [41] [44]
65	Milton H. Saier Jr.	[28] [35]
66	Heladia Salgado	[50]
67	Chris Sander	[23]
68	Alberto Santos-Zavaleta	[50]
69	Alberto D. Santos-Zavaleta	[57]
70	David B. Searls	[10]
71	Alexander Glennon Shearer	[54] [57]
72	Thomas M. Strat	[6]
73	David W. J. Stringer-Calvert	[51]
74	Peter Tarczy-Hornoch	[30]
75	Jessica D. Tenenbaum	[51]
76	Christophe Tissier	[49] [54]
77	Luca Toldo	[30]
78	Thodoros Topaloglou	[30]
79	Alfonso Valencia	[23]
80	Valerie Wagner	[51] [56]
81	Thomas C. Walk	[54]
82	Alfred Wang	[43]
83	David E. Wilkins	[6]
84	Thomas Yan	[48]
85	Iwei Yeh	[40]
86	Peifen Zhang	[43] [46] [49] [54]
87	Jingchun Zhu	[31]
88	Marie desJardins	[21]

Colors in the list of coauthors