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Peter D. Karp
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2020 – today
- 2022
- [j79]Valérie de Crécy-Lagard
, Rocio Amorin de Hegedus
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j78]Peter D. Karp
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation. Database J. Biol. Databases Curation 2022(2022) (2022) - [j77]Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips
Pathway Tools Management of Pathway/Genome Data for Microbial Communities. Frontiers Bioinform. 2 (2022) - 2021
- [j76]Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol A. Fulcher, Ingrid M. Keseler, Suzanne M. Paley:
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. Briefings Bioinform. 22(1): 109-126 (2021) - [j75]Suzanne M. Paley
The BioCyc Metabolic Network Explorer. BMC Bioinform. 22(1): 208 (2021) - 2020
- [j74]Wai Kit Ong
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models. Bioinform. 36(6): 1823-1830 (2020) - [j73]Ron Caspi
The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res. 48(Database-Issue): D445-D453 (2020)
2010 – 2019
- 2019
- [j72]Peter D. Karp, Richard Billington, Ron Caspi
The BioCyc collection of microbial genomes and metabolic pathways. Briefings Bioinform. 20(4): 1085-1093 (2019) - [j71]Suzanne M. Paley
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database. BMC Bioinform. 20(1): 399:1-399:13 (2019) - 2018
- [j70]Bohdan B. Khomtchouk, Edmund Weitz
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications. Briefings Bioinform. 19(3): 537-543 (2018) - [j69]Mario Latendresse
Evaluation of reaction gap-filling accuracy by randomization. BMC Bioinform. 19(1): 53:1-53:13 (2018) - [j68]Peter D. Karp
How accurate is automated gap filling of metabolic models? BMC Syst. Biol. 12(1): 73:1-73:11 (2018) - [j67]Ron Caspi
The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res. 46(Database-Issue): D633-D639 (2018) - 2017
- [j66]Bohdan B. Khomtchouk, Edmund Weitz, Peter D. Karp, Claes Wahlestedt:
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications. Briefings Bioinform. 18(5): 905 (2017) - [j65]Suzanne M. Paley
Update notifications for the BioCyc collection of databases. Database J. Biol. Databases Curation 2017: bax086 (2017) - [j64]Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res. 45(Database-Issue): D543-D550 (2017) - 2016
- [j63]Peter D. Karp, Mario Latendresse, Suzanne M. Paley, Markus Krummenacker, Quang Ong, Richard Billington, Anamika Kothari, Daniel S. Weaver, Thomas J. Lee, Pallavi Subhraveti, Aaron Spaulding, Carol A. Fulcher, Ingrid M. Keseler, Ron Caspi
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Briefings Bioinform. 17(5): 877-890 (2016) - [j62]Peter D. Karp:
How much does curation cost? Database J. Biol. Databases Curation 2016 (2016) - [j61]Peter D. Karp:
Crowd-sourcing and author submission as alternatives to professional curation. Database J. Biol. Databases Curation 2016 (2016) - [j60]Peter D. Karp:
Crowd-sourcing and author submission as alternatives to professional curation. Database J. Biol. Databases Curation 2016: baw149 (2016) - [j59]Suzanne M. Paley, Markus Krummenacker, Peter D. Karp:
Representation and inference of cellular architecture for metabolic reconstruction and modeling. Bioinform. 32(7): 1074-1079 (2016) - [j58]Suzanne M. Paley, Paul E. O'Maille, Daniel S. Weaver, Peter D. Karp
Pathway collages: personalized multi-pathway diagrams. BMC Bioinform. 17: 529:1-529:10 (2016) - [j57]Ron Caspi
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44(Database-Issue): 471-480 (2016) - 2015
- [j56]Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinform. 31(4): 616-617 (2015) - [j55]Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. PLoS Comput. Biol. 11(1) (2015) - 2014
- [j54]Ingrid M. Keseler, Marek S. Skrzypek, Deepika Weerasinghe, Albert Y. Chen, Carol A. Fulcher, Gene-Wei Li, Kimberly C. Lemmer, Katherine M. Mladinich, Edmond D. Chow, Gavin Sherlock
Curation accuracy of model organism databases. Database J. Biol. Databases Curation 2014 (2014) - [j53]Mario Latendresse, Markus Krummenacker, Peter D. Karp
Optimal metabolic route search based on atom mappings. Bioinform. 30(14): 2043-2050 (2014) - [j52]Daniel S. Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst. Biol. 8: 79 (2014) - [j51]Ron Caspi
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 42(Database-Issue): 459-471 (2014) - [j50]James C. Hu
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 42(Database-Issue): 677-684 (2014) - 2013
- [j49]Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp
Groups: knowledge spreadsheets for symbolic biocomputing. Database J. Biol. Databases Curation 2013 (2013) - [j48]Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi
A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinform. 14: 112 (2013) - [j47]Steven Eker, Markus Krummenacker, Alexander Glennon Shearer, Ashish Tiwari
Computing minimal nutrient sets from metabolic networks via linear constraint solving. BMC Bioinform. 14: 114 (2013) - [j46]Ingrid M. Keseler, Amanda Mackie, Martín Peralta-Gil
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41(Database-Issue): 605-612 (2013) - 2012
- [j45]Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp
Construction and completion of flux balance models from pathway databases. Bioinform. 28(3): 388-396 (2012) - [j44]Suzanne M. Paley, Mario Latendresse, Peter D. Karp
Regulatory network operations in the Pathway Tools software. BMC Bioinform. 13: 243 (2012) - [j43]Mario Latendresse, Jeremiah P. Malerich, Mike Travers, Peter D. Karp
Accurate Atom-Mapping Computation for Biochemical Reactions. J. Chem. Inf. Model. 52(11): 2970-2982 (2012) - [j42]Ron Caspi, Tomer Altman, Kate Dreher
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40(Database-Issue): 742-753 (2012) - 2011
- [j41]Luciana Ferrer, Alexander Glennon Shearer, Peter D. Karp
Discovering novel subsystems using comparative genomics. Bioinform. 27(18): 2478-2485 (2011) - [j40]Mario Latendresse, Peter D. Karp
Web-Based Metabolic Network Visualization with a Zooming User Interface. BMC Bioinform. 12: 176 (2011) - [j39]Ingrid M. Keseler, Julio Collado-Vides
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 39(Database-Issue): 583-590 (2011) - [c26]Peter D. Karp, Mario Latendresse, Suzanne M. Paley:
Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges. Human Vision and Electronic Imaging 2011: 78650G - 2010
- [j38]Peter D. Karp
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings Bioinform. 11(1): 40-79 (2010) - [j37]Mario Latendresse, Peter D. Karp
An advanced web query interface for biological databases. Database J. Biol. Databases Curation 2010 (2010) - [j36]Joseph M. Dale, Liviu Popescu, Peter D. Karp
Machine learning methods for metabolic pathway prediction. BMC Bioinform. 11: 15 (2010) - [j35]Luciana Ferrer, Joseph M. Dale, Peter D. Karp
A systematic study of genome context methods: calibration, normalization and combination. BMC Bioinform. 11: 493 (2010) - [j34]Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 38(Database-Issue): 473-479 (2010) - [c25]Peter D. Karp:
Databases and Algorithms for Pathway Bioinformatics. BIOSTEC 2010: 5 - [c24]Peter D. Karp:
Development of Large Scientific Knowledge Bases. ICAART (1) 2010: 23
2000 – 2009
- 2009
- [j33]Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides
EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37(Database-Issue): 464-470 (2009) - 2008
- [j32]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 Res. 36(Database-Issue): 623-631 (2008) - [c23]Peter D. Karp, Thomas J. Lee, Valerie Wagner:
BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. DILS 2008: 5-7 - [c22]Thomas J. Lee, Ian T. Paulsen
Annotation-based inference of transporter function. ISMB 2008: 259-267 - 2007
- [j31]Yannick Pouliot
A survey of orphan enzyme activities. BMC Bioinform. 8 (2007) - [c21]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 - 2006
- [j30]Heladia Salgado, Alberto Santos-Zavaleta
The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinform. 7: 5 (2006) - [j29]Thomas J. Lee, Yannick Pouliot
BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinform. 7: 170 (2006) - [j28]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 Res. 34(Database-Issue): 511-516 (2006) - 2005
- [j27]Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp
Querying and computing with BioCyc databases. Bioinform. 21(16): 3454-3455 (2005) - [j26]Ingrid M. Keseler, Julio Collado-Vides
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33(Database-Issue): 334-337 (2005) - 2004
- [j25]Pedro Romero, Peter D. Karp
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinform. 20(5): 709-717 (2004) - [j24]Michelle L. Green, Peter D. Karp
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinform. 5: 76 (2004) - [j23]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 Res. 32(Database-Issue): 438-442 (2004) - [c20]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 - 2003
- [j22]Iwei Yeh, Peter D. Karp
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinform. 19(2): 241-248 (2003) - [j21]Peter D. Karp
What Database Management System(s) Should Be Employed in Bioinformatics Applications? OMICS 7(1): 35-36 (2003) - [c19]Peter D. Karp:
Pathway Bioinformatics. CSB 2003: 27 - [c18]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 - 2002
- [j20]Suzanne M. Paley, Peter D. Karp
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinform. 18(5): 715-724 (2002) - [j19]Peter D. Karp
The EcoCyc Database. Nucleic Acids Res. 30(1): 56-58 (2002) - [j18]Peter D. Karp
The MetaCyc Database. Nucleic Acids Res. 30(1): 59-61 (2002) - [c17]Peter D. Karp, Suzanne M. Paley, Pedro Romero:
The Pathway Tools software. ISMB 2002: 225-232 - [c16]Peter D. Karp, Pedro Romero, Eric P. Neumann:
Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2002: 398-399 - 2001
- [j17]Peter D. Karp
Database verification studies of SWISS-PROT and GenBank. Bioinform. 17(6): 526-532 (2001) - [c15]Peter D. Karp, Eric P. Neumann, Pedro Romero:
Genome, Pathway and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2001: 420-421 - [c14]Pedro Romero, Peter D. Karp:
Nutrition-Related Analysis of Pathway/Genome Databases. Pacific Symposium on Biocomputing 2001: 470-482 - 2000
- [j16]Peter D. Karp
An ontology for biological function based on molecular interactions. Bioinform. 16(3): 269-285 (2000) - [j15]Peter D. Karp
The EcoCyc and MetaCyc databases. Nucleic Acids Res. 28(1): 56-59 (2000) - [c13]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
1990 – 1999
- 1999
- [j14]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) - [j13]Peter D. Karp
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 27(1): 55-58 (1999) - 1998
- [j12]Peter D. Karp
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 26(1): 50-53 (1998) - [c12]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 - 1997
- [j11]Ronald G. Forsythe Jr., Peter D. Karp, Michael L. Mavrovouniotis:
Estimation of equilibrium constants using automated group contribution methods. Comput. Appl. Biosci. 13(5): 537-543 (1997) - [j10]Peter D. Karp
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism. Nucleic Acids Res. 25(1): 43-51 (1997) - [c11]Suzanne M. Paley, John D. Lowrance, Peter D. Karp:
A Generic Knowledge-Base Browser and Editor. AAAI/IAAI 1997: 1045-1051 - [c10]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 - [c9]Vinay K. Chaudhri, Peter D. Karp:
Querying Schema Information. KRDB 1997: 4.1-4.6 - [e2]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, ISBN 1-57735-022-7 [contents] - 1996
- [j9]Peter D. Karp
Integrated Access to Metabolic and Genomic Data. J. Comput. Biol. 3(1): 191-212 (1996) - [j8]Peter D. Karp
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 24(1): 32-39 (1996) - [c8]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 - [c7]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 - 1995
- [j7]Peter D. Karp
A Strategy for Database Interoperation. J. Comput. Biol. 2(4): 573-586 (1995) - [c6]Peter D. Karp, Suzanne M. Paley:
Knowledge Representation in the Large. IJCAI (1) 1995: 751-758 - [c5]Peter D. Karp, Karen L. Myers, Thomas R. Gruber:
The Generic Frame Protocol. IJCAI (1) 1995: 768-774 - 1994
- [j6]Peter D. Karp, Michael L. Mavrovouniotis:
Representing, Analyzing, and Synthesizing Biochemical Pathways. IEEE Expert 9(2): 11-21 (1994) - [j5]Peter D. Karp, John D. Lowrance, Thomas M. Strat, David E. Wilkins:
The Grasper-CL Graph Management System. LISP Symb. Comput. 7(4): 251-290 (1994) - [c4]Peter D. Karp, Suzanne M. Paley, Ira B. Greenberg:
A Storage System for Scalable Knowledge Representation. CIKM 1994: 97-104 - [c3]Peter D. Karp, Suzanne M. Paley:
Representations of Metabolic Knowledge: Pathways. ISMB 1994: 203-211 - [e1]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, ISBN 0-929280-68-7 [contents] - 1993
- [j4]Peter D. Karp:
Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology. Mach. Learn. 12: 89-116 (1993) - [c2]Peter D. Karp, Monica Riley:
Representations of Metabolic Knowledge. ISMB 1993: 207-215 - [c1]Xiaolei Qian, Mark E. Stickel, Peter D. Karp, Teresa F. Lunt, Thomas D. Garvey:
Detection and elimination of inference channels in multilevel relational database systems. S&P 1993: 196-205 - 1992
- [j3]Peter D. Karp:
A knowledge base of the chemical compounds of intermediary metabolism. Comput. Appl. Biosci. 8(4): 347-357 (1992) - 1991
- [j2]Peter D. Karp:
Artificial intelligence methods for theory representation and hypothesis formation. Comput. Appl. Biosci. 7(3): 301-308 (1991) - 1990
- [j1]Peter D. Karp:
Hypothesis Formation and Qualitative Reasoning in Molecular Biology. AI Mag. 11(4): 9-10 (1990)
1980 – 1989
- 1989
- [b1]Peter D. Karp:
Hypothesis formation and qualitative reasoning in molecular biology. Stanford University, USA, 1989
Coauthor Index
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