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Peter D. Karp
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2020 – today
- 2022
- [j79]Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
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, Peter D. Karp:
The BioCyc Metabolic Network Explorer. BMC Bioinform. 22(1): 208 (2021) - 2020
- [j74]Wai Kit Ong, Peter E. Midford, Peter D. Karp:
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models. Bioinform. 36(6): 1823-1830 (2020) - [j73]Ron Caspi, Richard Billington, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp:
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, Carol A. Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M. Keseler, Markus Krummenacker, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti:
The BioCyc collection of microbial genomes and metabolic pathways. Briefings Bioinform. 20(4): 1085-1093 (2019) - [j71]Suzanne M. Paley, Peter D. Karp:
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, Peter D. Karp, Claes Wahlestedt:
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications. Briefings Bioinform. 19(3): 537-543 (2018) - [j69]Mario Latendresse, Peter D. Karp:
Evaluation of reaction gap-filling accuracy by randomization. BMC Bioinform. 19(1): 53:1-53:13 (2018) - [j68]Peter D. Karp, Daniel S. Weaver, Mario Latendresse:
How accurate is automated gap filling of metabolic models? BMC Syst. Biol. 12(1): 73:1-73:11 (2018) - [j67]Ron Caspi, Richard Billington, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp:
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, Peter D. Karp:
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, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol A. Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Martín Peralta-Gil, Pallavi Subhraveti, David A. Velázquez-Ramírez, Daniel S. Weaver, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp:
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, 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 S. Weaver, Peter D. Karp:
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, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost:
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, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost:
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, Peter D. Karp:
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, Peter D. Karp:
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, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, 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 Res. 42(Database-Issue): 459-471 (2014) - [j50]James C. Hu, Gavin Sherlock, Deborah A. Siegele, Suzanne A. Aleksander, Catherine A. Ball, Janos Demeter, Sushanth Gouni, Timothy A. Holland, Peter D. Karp, John E. Lewis, Nathan M. Liles, Brenley K. McIntosh, Huaiyu Mi, Anushya Muruganujan, Farrell Wymore, Paul D. Thomas:
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, Peter D. Karp:
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, Ingrid M. Keseler, Carolyn L. Talcott, Peter D. Karp:
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, 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 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, 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 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, 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 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, 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 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, 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 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, 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 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, Peter D. Karp:
Annotation-based inference of transporter function. ISMB 2008: 259-267 - 2007
- [j31]Yannick Pouliot, Peter D. Karp:
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, 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 Bioinform. 7: 5 (2006) - [j29]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 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, 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 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, Natalya Fridman Noy, Russ B. Altman:
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, 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 Res. 30(1): 56-58 (2002) - [j18]Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole:
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, Suzanne M. Paley, Jingchun Zhu:
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, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-Toole:
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, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker:
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 27(1): 55-58 (1999) - 1998
- [j12]Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker:
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, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker:
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, Suzanne M. Paley:
Integrated Access to Metabolic and Genomic Data. J. Comput. Biol. 3(1): 191-212 (1996) - [j8]Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole:
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]