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ORCIDBibTeX records: Peter D. Karp
@article{DBLP:journals/biodb/Crecy-LagardHAB22,
author = {Val{\'{e}}rie de Cr{\'{e}}cy{-}Lagard and
Rocio Amorin de Hegedus and
Cecilia N. Arighi and
Jill Babor and
Alex Bateman and
Ian Blaby and
Crysten Blaby{-}Haas and
Alan J. Bridge and
Stephen K. Burley and
Stacey Cleveland and
Lucy J. Colwell and
Ana Conesa and
Christian Dallago and
Antoine Danchin and
Anita de Waard and
Adam Deutschbauer and
Raquel Dias and
Yousong Ding and
Gang Fang and
Iddo Friedberg and
John Gerlt and
Joshua Goldford and
Mark Gorelik and
Benjamin M. Gyori and
Christopher S. Henry and
Geoffrey Hutinet and
Marshall Jaroch and
Peter D. Karp and
Liudmyla Kondratova and
Zhiyong Lu and
Aron Marchler{-}Bauer and
Maria Jesus Martin and
Claire D. McWhite and
Gaurav D. Moghe and
Paul Monaghan and
Anne Morgat and
Christopher J. Mungall and
Darren A. Natale and
William C. Nelson and
Se{\'{a}}n I. O'Donoghue and
Christine A. Orengo and
Katherine H. O'Toole and
Predrag Radivojac and
Colbie Reed and
Richard J. Roberts and
Dmitri Rodionov and
Irina A. Rodionova and
Jeffrey DePons and
Lana Saleh and
Gloria M. Sheynkman and
Fran{\c{c}}oise Thibaud{-}Nissen and
Paul D. Thomas and
Peter Uetz and
David Vallenet and
Erica Watson Carter and
Peter Weigele and
Valerie Wood and
Elisha M. Wood{-}Charlson and
Jin Xu},
title = {A roadmap for the functional annotation of protein families: a community
perspective},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac062},
doi = {10.1093/DATABASE/BAAC062},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/Crecy-LagardHAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Karp22,
author = {Peter D. Karp},
title = {Reviewing knowledgebase and database grant proposals in the life sciences:
the role of innovation},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac106},
doi = {10.1093/DATABASE/BAAC106},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/Karp22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/KarpPKKWP22,
author = {Peter D. Karp and
Suzanne M. Paley and
Markus Krummenacker and
Anamika Kothari and
Michael J. Wannemuehler and
Gregory J. Phillips},
title = {Pathway Tools Management of Pathway/Genome Data for Microbial Communities},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.869150},
doi = {10.3389/FBINF.2022.869150},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/KarpPKKWP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarpMBKKLOSCFKP21,
author = {Peter D. Karp and
Peter E. Midford and
Richard Billington and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Wai Kit Ong and
Pallavi Subhraveti and
Ron Caspi and
Carol A. Fulcher and
Ingrid M. Keseler and
Suzanne M. Paley},
title = {Pathway Tools version 23.0 update: software for pathway/genome informatics
and systems biology},
journal = {Briefings Bioinform.},
volume = {22},
number = {1},
pages = {109--126},
year = {2021},
url = {https://doi.org/10.1093/bib/bbz104},
doi = {10.1093/BIB/BBZ104},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarpMBKKLOSCFKP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaleyK21,
author = {Suzanne M. Paley and
Peter D. Karp},
title = {The BioCyc Metabolic Network Explorer},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {208},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04132-5},
doi = {10.1186/S12859-021-04132-5},
timestamp = {Thu, 29 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PaleyK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OngMK20,
author = {Wai Kit Ong and
Peter E. Midford and
Peter D. Karp},
title = {Taxonomic weighting improves the accuracy of a gap-filling algorithm
for metabolic models},
journal = {Bioinform.},
volume = {36},
number = {6},
pages = {1823--1830},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz813},
doi = {10.1093/BIOINFORMATICS/BTZ813},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OngMK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiBKKKMOPSK20,
author = {Ron Caspi and
Richard Billington and
Ingrid M. Keseler and
Anamika Kothari and
Markus Krummenacker and
Peter E. Midford and
Wai Kit Ong and
Suzanne M. Paley and
Pallavi Subhraveti and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes - a 2019 update},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D445--D453},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz862},
doi = {10.1093/NAR/GKZ862},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/CaspiBKKKMOPSK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarpBCFLKKKMOOP19,
author = {Peter D. Karp and
Richard Billington and
Ron Caspi and
Carol A. Fulcher and
Mario Latendresse and
Anamika Kothari and
Ingrid M. Keseler and
Markus Krummenacker and
Peter E. Midford and
Quang Ong and
Wai Kit Ong and
Suzanne M. Paley and
Pallavi Subhraveti},
title = {The BioCyc collection of microbial genomes and metabolic pathways},
journal = {Briefings Bioinform.},
volume = {20},
number = {4},
pages = {1085--1093},
year = {2019},
url = {https://doi.org/10.1093/bib/bbx085},
doi = {10.1093/BIB/BBX085},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarpBCFLKKKMOOP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaleyK19,
author = {Suzanne M. Paley and
Peter D. Karp},
title = {The MultiOmics Explainer: explaining omics results in the context
of a pathway/genome database},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {399:1--399:13},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2971-6},
doi = {10.1186/S12859-019-2971-6},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PaleyK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhomtchoukWKW18,
author = {Bohdan B. Khomtchouk and
Edmund Weitz and
Peter D. Karp and
Claes Wahlestedt},
title = {How the strengths of Lisp-family languages facilitate building complex
and flexible bioinformatics applications},
journal = {Briefings Bioinform.},
volume = {19},
number = {3},
pages = {537--543},
year = {2018},
url = {https://doi.org/10.1093/bib/bbw130},
doi = {10.1093/BIB/BBW130},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhomtchoukWKW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LatendresseK18,
author = {Mario Latendresse and
Peter D. Karp},
title = {Evaluation of reaction gap-filling accuracy by randomization},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {53:1--53:13},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2050-4},
doi = {10.1186/S12859-018-2050-4},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LatendresseK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/KarpWL18,
author = {Peter D. Karp and
Daniel S. Weaver and
Mario Latendresse},
title = {How accurate is automated gap filling of metabolic models?},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {1},
pages = {73:1--73:11},
year = {2018},
url = {https://doi.org/10.1186/s12918-018-0593-7},
doi = {10.1186/S12918-018-0593-7},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/KarpWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiBFKKKLMOOP18,
author = {Ron Caspi and
Richard Billington and
Carol A. Fulcher and
Ingrid M. Keseler and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Peter E. Midford and
Quang Ong and
Wai Kit Ong and
Suzanne M. Paley and
Pallavi Subhraveti and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D633--D639},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx935},
doi = {10.1093/NAR/GKX935},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiBFKKKLMOOP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhomtchoukWKW17,
author = {Bohdan B. Khomtchouk and
Edmund Weitz and
Peter D. Karp and
Claes Wahlestedt},
title = {How the strengths of Lisp-family languages facilitate building complex
and flexible bioinformatics applications},
journal = {Briefings Bioinform.},
volume = {18},
number = {5},
pages = {905},
year = {2017},
url = {https://doi.org/10.1093/bib/bbx016},
doi = {10.1093/BIB/BBX016},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhomtchoukWKW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/PaleyK17,
author = {Suzanne M. Paley and
Peter D. Karp},
title = {Update notifications for the BioCyc collection of databases},
journal = {Database J. Biol. Databases Curation},
volume = {2017},
pages = {bax086},
year = {2017},
url = {https://doi.org/10.1093/database/bax086},
doi = {10.1093/DATABASE/BAX086},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/PaleyK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeselerMSBBCFGK17,
author = {Ingrid M. Keseler and
Amanda Mackie and
Alberto Santos{-}Zavaleta and
Richard Billington and
C{\'{e}}sar Bonavides{-}Mart{\'{\i}}nez and
Ron Caspi and
Carol A. Fulcher and
Socorro Gama{-}Castro and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Luis Mu{\~{n}}iz{-}Rascado and
Quang Ong and
Suzanne M. Paley and
Mart{\'{\i}}n Peralta{-}Gil and
Pallavi Subhraveti and
David A. Vel{\'{a}}zquez{-}Ram{\'{\i}}rez and
Daniel S. Weaver and
Julio Collado{-}Vides and
Ian T. Paulsen and
Peter D. Karp},
title = {The EcoCyc database: reflecting new knowledge about Escherichia coli
{K-12}},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D543--D550},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1003},
doi = {10.1093/NAR/GKW1003},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeselerMSBBCFGK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarpLPKOBKWLSSF16,
author = {Peter D. Karp and
Mario Latendresse and
Suzanne M. Paley and
Markus Krummenacker and
Quang Ong and
Richard Billington and
Anamika Kothari and
Daniel S. Weaver and
Thomas J. Lee and
Pallavi Subhraveti and
Aaron Spaulding and
Carol A. Fulcher and
Ingrid M. Keseler and
Ron Caspi},
title = {Pathway Tools version 19.0 update: software for pathway/genome informatics
and systems biology},
journal = {Briefings Bioinform.},
volume = {17},
number = {5},
pages = {877--890},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv079},
doi = {10.1093/BIB/BBV079},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarpLPKOBKWLSSF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Karp16,
author = {Peter D. Karp},
title = {How much does curation cost?},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw110},
doi = {10.1093/DATABASE/BAW110},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/Karp16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Karp16a,
author = {Peter D. Karp},
title = {Crowd-sourcing and author submission as alternatives to professional
curation},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw150},
doi = {10.1093/DATABASE/BAW150},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/Karp16a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Karp16b,
author = {Peter D. Karp},
title = {Crowd-sourcing and author submission as alternatives to professional
curation},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
pages = {baw149},
year = {2016},
url = {https://doi.org/10.1093/database/baw149},
doi = {10.1093/DATABASE/BAW149},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/Karp16b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaleyKK16,
author = {Suzanne M. Paley and
Markus Krummenacker and
Peter D. Karp},
title = {Representation and inference of cellular architecture for metabolic
reconstruction and modeling},
journal = {Bioinform.},
volume = {32},
number = {7},
pages = {1074--1079},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv702},
doi = {10.1093/BIOINFORMATICS/BTV702},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaleyKK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaleyOWK16,
author = {Suzanne M. Paley and
Paul E. O'Maille and
Daniel S. Weaver and
Peter D. Karp},
title = {Pathway collages: personalized multi-pathway diagrams},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {529:1--529:10},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1382-1},
doi = {10.1186/S12859-016-1382-1},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PaleyOWK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiBFFFKKKLMO16,
author = {Ron Caspi and
Richard Billington and
Luciana Ferrer and
Hartmut Foerster and
Carol A. Fulcher and
Ingrid M. Keseler and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Lukas A. Mueller and
Quang Ong and
Suzanne M. Paley and
Pallavi Subhraveti and
Daniel S. Weaver and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes and the BioCyc
collection of pathway/genome databases},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {471--480},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1164},
doi = {10.1093/NAR/GKV1164},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiBFFFKKKLMO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarpBKLLSHR15,
author = {Peter D. Karp and
Bonnie Berger and
Diane E. Kovats and
Thomas Lengauer and
Michal Linial and
Pardis Sabeti and
Winston Hide and
Burkhard Rost},
title = {Message from the {ISCB:} {ISCB} Ebola award for important future research
on the computational biology of Ebola virus},
journal = {Bioinform.},
volume = {31},
number = {4},
pages = {616--617},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv019},
doi = {10.1093/BIOINFORMATICS/BTV019},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarpBKLLSHR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KarpBKLLSHR15,
author = {Peter D. Karp and
Bonnie Berger and
Diane E. Kovats and
Thomas Lengauer and
Michal Linial and
Pardis Sabeti and
Winston Hide and
Burkhard Rost},
title = {{ISCB} Ebola Award for Important Future Research on the Computational
Biology of Ebola Virus},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {1},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004087},
doi = {10.1371/JOURNAL.PCBI.1004087},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/KarpBKLLSHR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/KeselerSWCFLLMCSK14,
author = {Ingrid M. Keseler and
Marek S. Skrzypek and
Deepika Weerasinghe and
Albert Y. Chen and
Carol A. Fulcher and
Gene{-}Wei Li and
Kimberly C. Lemmer and
Katherine M. Mladinich and
Edmond D. Chow and
Gavin Sherlock and
Peter D. Karp},
title = {Curation accuracy of model organism databases},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau058},
doi = {10.1093/DATABASE/BAU058},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/KeselerSWCFLLMCSK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LatendresseKK14,
author = {Mario Latendresse and
Markus Krummenacker and
Peter D. Karp},
title = {Optimal metabolic route search based on atom mappings},
journal = {Bioinform.},
volume = {30},
number = {14},
pages = {2043--2050},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu150},
doi = {10.1093/BIOINFORMATICS/BTU150},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LatendresseKK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WeaverKMPK14,
author = {Daniel S. Weaver and
Ingrid M. Keseler and
Amanda Mackie and
Ian T. Paulsen and
Peter D. Karp},
title = {A genome-scale metabolic flux model of Escherichia coli {K-12} derived
from the EcoCyc database},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {79},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-79},
doi = {10.1186/1752-0509-8-79},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/WeaverKMPK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiABDFFHKKKKLMOPSWWZK14,
author = {Ron Caspi and
Tomer Altman and
Richard Billington and
Kate Dreher and
Hartmut Foerster and
Carol A. Fulcher and
Timothy A. Holland and
Ingrid M. Keseler and
Anamika Kothari and
Aya Kubo and
Markus Krummenacker and
Mario Latendresse and
Lukas A. Mueller and
Quang Ong and
Suzanne M. Paley and
Pallavi Subhraveti and
Daniel S. Weaver and
Deepika Weerasinghe and
Peifen Zhang and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes and the BioCyc
collection of Pathway/Genome Databases},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {459--471},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1103},
doi = {10.1093/NAR/GKT1103},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiABDFFHKKKKLMOPSWWZK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HuSSABDGHKLLMMMWT14,
author = {James C. Hu and
Gavin Sherlock and
Deborah A. Siegele and
Suzanne A. Aleksander and
Catherine A. Ball and
Janos Demeter and
Sushanth Gouni and
Timothy A. Holland and
Peter D. Karp and
John E. Lewis and
Nathan M. Liles and
Brenley K. McIntosh and
Huaiyu Mi and
Anushya Muruganujan and
Farrell Wymore and
Paul D. Thomas},
title = {PortEco: a resource for exploring bacterial biology through high-throughput
data and analysis tools},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {677--684},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1203},
doi = {10.1093/NAR/GKT1203},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HuSSABDGHKLLMMMWT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/TraversPSHK13,
author = {Michael Travers and
Suzanne M. Paley and
Jeff Shrager and
Timothy A. Holland and
Peter D. Karp},
title = {Groups: knowledge spreadsheets for symbolic biocomputing},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat061},
doi = {10.1093/DATABASE/BAT061},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/TraversPSHK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AltmanTKCK13,
author = {Tomer Altman and
Michael Travers and
Anamika Kothari and
Ron Caspi and
Peter D. Karp},
title = {A systematic comparison of the MetaCyc and {KEGG} pathway databases},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {112},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-112},
doi = {10.1186/1471-2105-14-112},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AltmanTKCK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EkerKSTKTK13,
author = {Steven Eker and
Markus Krummenacker and
Alexander Glennon Shearer and
Ashish Tiwari and
Ingrid M. Keseler and
Carolyn L. Talcott and
Peter D. Karp},
title = {Computing minimal nutrient sets from metabolic networks via linear
constraint solving},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {114},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-114},
doi = {10.1186/1471-2105-14-114},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/EkerKSTKTK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeselerMPSGBFHKKLMOPSSSTWWCGPK13,
author = {Ingrid M. Keseler and
Amanda Mackie and
Mart{\'{\i}}n Peralta{-}Gil and
Alberto Santos{-}Zavaleta and
Socorro Gama{-}Castro and
C{\'{e}}sar Bonavides{-}Mart{\'{\i}}nez and
Carol A. Fulcher and
Araceli M. Huerta and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Luis Mu{\~{n}}iz{-}Rascado and
Quang Ong and
Suzanne M. Paley and
Imke Schr{\"{o}}der and
Alexander Glennon Shearer and
Pallavi Subhraveti and
Michael Travers and
Deepika Weerasinghe and
Verena Weiss and
Julio Collado{-}Vides and
Robert P. Gunsalus and
Ian T. Paulsen and
Peter D. Karp},
title = {EcoCyc: fusing model organism databases with systems biology},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {605--612},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1027},
doi = {10.1093/NAR/GKS1027},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeselerMPSGBFHKKLMOPSSSTWWCGPK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LatendresseKTK12,
author = {Mario Latendresse and
Markus Krummenacker and
Miles Trupp and
Peter D. Karp},
title = {Construction and completion of flux balance models from pathway databases},
journal = {Bioinform.},
volume = {28},
number = {3},
pages = {388--396},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr681},
doi = {10.1093/BIOINFORMATICS/BTR681},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LatendresseKTK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaleyLK12,
author = {Suzanne M. Paley and
Mario Latendresse and
Peter D. Karp},
title = {Regulatory network operations in the Pathway Tools software},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {243},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-243},
doi = {10.1186/1471-2105-13-243},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PaleyLK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LatendresseMTK12,
author = {Mario Latendresse and
Jeremiah P. Malerich and
Mike Travers and
Peter D. Karp},
title = {Accurate Atom-Mapping Computation for Biochemical Reactions},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {11},
pages = {2970--2982},
year = {2012},
url = {https://doi.org/10.1021/ci3002217},
doi = {10.1021/CI3002217},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LatendresseMTK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiADFSKKKLMOPPSTWZK12,
author = {Ron Caspi and
Tomer Altman and
Kate Dreher and
Carol A. Fulcher and
Pallavi Subhraveti and
Ingrid M. Keseler and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Lukas A. Mueller and
Quang Ong and
Suzanne M. Paley and
Anuradha Pujar and
Alexander Glennon Shearer and
Michael Travers and
Deepika Weerasinghe and
Peifen Zhang and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes and the BioCyc
collection of pathway/genome databases},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {742--753},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1014},
doi = {10.1093/NAR/GKR1014},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiADFSKKKLMOPPSTWZK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FerrerSK11,
author = {Luciana Ferrer and
Alexander Glennon Shearer and
Peter D. Karp},
title = {Discovering novel subsystems using comparative genomics},
journal = {Bioinform.},
volume = {27},
number = {18},
pages = {2478--2485},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr428},
doi = {10.1093/BIOINFORMATICS/BTR428},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FerrerSK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LatendresseK11,
author = {Mario Latendresse and
Peter D. Karp},
title = {Web-Based Metabolic Network Visualization with a Zooming User Interface},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {176},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-176},
doi = {10.1186/1471-2105-12-176},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LatendresseK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeselerCSPGMBPKAKSPLFSSMPGK11,
author = {Ingrid M. Keseler and
Julio Collado{-}Vides and
Alberto Santos{-}Zavaleta and
Mart{\'{\i}}n Peralta{-}Gil and
Socorro Gama{-}Castro and
Luis Mu{\~{n}}iz{-}Rascado and
C{\'{e}}sar Bonavides{-}Mart{\'{\i}}nez and
Suzanne M. Paley and
Markus Krummenacker and
Tomer Altman and
Pallavi Kaipa and
Aaron Spaulding and
John Pacheco and
Mario Latendresse and
Carol A. Fulcher and
Malabika Sarker and
Alexander Glennon Shearer and
Amanda Mackie and
Ian T. Paulsen and
Robert P. Gunsalus and
Peter D. Karp},
title = {EcoCyc: a comprehensive database of \emph{Escherichia coli} biology},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {583--590},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1143},
doi = {10.1093/NAR/GKQ1143},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeselerCSPGMBPKAKSPLFSSMPGK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hvei/KarpLP11,
author = {Peter D. Karp and
Mario Latendresse and
Suzanne M. Paley},
editor = {Bernice E. Rogowitz and
Thrasyvoulos N. Pappas},
title = {Using cellular network diagrams to interpret large-scale datasets:
past progress and future challenges},
booktitle = {Human Vision and Electronic Imaging XVI, part of the IS{\&}T-SPIE
Electronic Imaging Symposium, San Francisco Airport, California, USA,
January 24-27, 2011, Proceedings},
series = {{SPIE} Proceedings},
volume = {7865},
pages = {78650G},
publisher = {SPIE/IS{\&}T},
year = {2011},
url = {https://doi.org/10.1117/12.881997},
doi = {10.1117/12.881997},
timestamp = {Sun, 21 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hvei/KarpLP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarpPKLDLKGSPAPKC10,
author = {Peter D. Karp and
Suzanne M. Paley and
Markus Krummenacker and
Mario Latendresse and
Joseph M. Dale and
Thomas J. Lee and
Pallavi Kaipa and
Fred Gilham and
Aaron Spaulding and
Liviu Popescu and
Tomer Altman and
Ian T. Paulsen and
Ingrid M. Keseler and
Ron Caspi},
title = {Pathway Tools version 13.0: integrated software for pathway/genome
informatics and systems biology},
journal = {Briefings Bioinform.},
volume = {11},
number = {1},
pages = {40--79},
year = {2010},
url = {https://doi.org/10.1093/bib/bbp043},
doi = {10.1093/BIB/BBP043},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarpPKLDLKGSPAPKC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LatendresseK10,
author = {Mario Latendresse and
Peter D. Karp},
title = {An advanced web query interface for biological databases},
journal = {Database J. Biol. Databases Curation},
volume = {2010},
year = {2010},
url = {https://doi.org/10.1093/database/baq006},
doi = {10.1093/DATABASE/BAQ006},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/LatendresseK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DalePK10,
author = {Joseph M. Dale and
Liviu Popescu and
Peter D. Karp},
title = {Machine learning methods for metabolic pathway prediction},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {15},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-15},
doi = {10.1186/1471-2105-11-15},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DalePK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FerrerDK10,
author = {Luciana Ferrer and
Joseph M. Dale and
Peter D. Karp},
title = {A systematic study of genome context methods: calibration, normalization
and combination},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {493},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-493},
doi = {10.1186/1471-2105-11-493},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FerrerDK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiADDFGKKKKLMPPPSZK10,
author = {Ron Caspi and
Tomer Altman and
Joseph M. Dale and
Kate Dreher and
Carol A. Fulcher and
Fred Gilham and
Pallavi Kaipa and
Athikkattuvalasu S. Karthikeyan and
Anamika Kothari and
Markus Krummenacker and
Mario Latendresse and
Lukas A. Mueller and
Suzanne M. Paley and
Liviu Popescu and
Anuradha Pujar and
Alexander Glennon Shearer and
Peifen Zhang and
Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes and the BioCyc
collection of pathway/genome databases},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {473--479},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp875},
doi = {10.1093/NAR/GKP875},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiADDFGKKKKLMPPPSZK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/Karp10,
author = {Peter D. Karp},
editor = {Ana L. N. Fred and
Joaquim Filipe and
Hugo Gamboa},
title = {Databases and Algorithms for Pathway Bioinformatics},
booktitle = {{HEALTHINF} 2010 - Proceedings of the Third International Conference
on Health Informatics, Valencia, Spain, January 20-23, 2010},
pages = {5},
publisher = {{INSTICC} Press},
year = {2010},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/biostec/Karp10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icaart/Karp10,
author = {Peter D. Karp},
editor = {Joaquim Filipe and
Ana L. N. Fred and
Bernadette Sharp},
title = {Development of Large Scientific Knowledge Bases},
booktitle = {{ICAART} 2010 - Proceedings of the International Conference on Agents
and Artificial Intelligence, Volume 1 - Artificial Intelligence, Valencia,
Spain, January 22-24, 2010},
pages = {23},
publisher = {{INSTICC} Press},
year = {2010},
timestamp = {Wed, 03 Mar 2010 08:01:07 +0100},
biburl = {https://dblp.org/rec/conf/icaart/Karp10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeselerBCGGJKNPPPSSK09,
author = {Ingrid M. Keseler and
C{\'{e}}sar Bonavides{-}Mart{\'{\i}}nez and
Julio Collado{-}Vides and
Socorro Gama{-}Castro and
Robert P. Gunsalus and
D. Aaron Johnson and
Markus Krummenacker and
Laura M. Nolan and
Suzanne M. Paley and
Ian T. Paulsen and
Mart{\'{\i}}n Peralta{-}Gil and
Alberto D. Santos{-}Zavaleta and
Alexander Glennon Shearer and
Peter D. Karp},
title = {EcoCyc: {A} comprehensive view of \emph{Escherichia coli} biology},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {464--470},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn751},
doi = {10.1093/NAR/GKN751},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeselerBCGGJKNPPPSSK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiFFKKLPRSTWZK08,
author = {Ron Caspi and
Hartmut Foerster and
Carol A. Fulcher and
Pallavi Kaipa and
Markus Krummenacker and
Mario Latendresse and
Suzanne M. Paley and
Seung Yon Rhee and
Alexander Glennon Shearer and
Christophe Tissier and
Thomas C. Walk and
Peifen Zhang and
Peter D. Karp},
title = {The MetaCyc Database of metabolic pathways and enzymes and the BioCyc
collection of Pathway/Genome Databases},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {623--631},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm900},
doi = {10.1093/NAR/GKM900},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiFFKKLPRSTWZK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dils/KarpLW08,
author = {Peter D. Karp and
Thomas J. Lee and
Valerie Wagner},
editor = {Amos Bairoch and
Sarah Cohen Boulakia and
Christine Froidevaux},
title = {BioWarehouse: Relational Integration of Eleven Bioinformatics Databases
and Formats},
booktitle = {Data Integration in the Life Sciences, 5th International Workshop,
{DILS} 2008, Evry, France, June 25-27, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5109},
pages = {5--7},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-69828-9\_2},
doi = {10.1007/978-3-540-69828-9\_2},
timestamp = {Mon, 16 Sep 2019 15:28:31 +0200},
biburl = {https://dblp.org/rec/conf/dils/KarpLW08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/LeePK08,
author = {Thomas J. Lee and
Ian T. Paulsen and
Peter D. Karp},
title = {Annotation-based inference of transporter function},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {259--267},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn180},
doi = {10.1093/BIOINFORMATICS/BTN180},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/LeePK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PouliotK07,
author = {Yannick Pouliot and
Peter D. Karp},
title = {A survey of orphan enzyme activities},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-244},
doi = {10.1186/1471-2105-8-244},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PouliotK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/GreenK07,
author = {Michelle L. Green and
Peter D. Karp},
title = {Using genome-context data to identify specific types of functional
associations in pathway/genome databases},
booktitle = {Proceedings 15th International Conference on Intelligent Systems for
Molecular Biology {(ISMB)} {\&} 6th European Conference on Computational
Biology (ECCB), Vienna, Austria, July 21-25, 2007},
pages = {205--211},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm213},
doi = {10.1093/BIOINFORMATICS/BTM213},
timestamp = {Sat, 07 Sep 2019 11:59:25 +0200},
biburl = {https://dblp.org/rec/conf/ismb/GreenK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SalgadoSGPPMKC06,
author = {Heladia Salgado and
Alberto Santos{-}Zavaleta and
Socorro Gama{-}Castro and
Mart{\'{\i}}n Peralta{-}Gil and
M{\'{o}}nica I. Pe{\~{n}}aloza{-}Sp{\'{\i}}nola and
Agustino Mart{\'{\i}}nez{-}Antonio and
Peter D. Karp and
Julio Collado{-}Vides},
title = {The comprehensive updated regulatory network of \emph{Escherichia
coli }K-12},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {5},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-5},
doi = {10.1186/1471-2105-7-5},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SalgadoSGPPMKC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LeePWGSTK06,
author = {Thomas J. Lee and
Yannick Pouliot and
Valerie Wagner and
Priyanka Gupta and
David W. J. Stringer{-}Calvert and
Jessica D. Tenenbaum and
Peter D. Karp},
title = {BioWarehouse: a bioinformatics database warehouse toolkit},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {170},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-170},
doi = {10.1186/1471-2105-7-170},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LeePWGSTK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CaspiFFHIKKPPRTZK06,
author = {Ron Caspi and
Hartmut Foerster and
Carol A. Fulcher and
Rebecca Hopkinson and
John Ingraham and
Pallavi Kaipa and
Markus Krummenacker and
Suzanne M. Paley and
John Pick and
Seung Yon Rhee and
Christophe Tissier and
Peifen Zhang and
Peter D. Karp},
title = {MetaCyc: a multiorganism database of metabolic pathways and enzymes},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {511--516},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj128},
doi = {10.1093/NAR/GKJ128},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CaspiFFHIKKPPRTZK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KrummenackerPMYK05,
author = {Markus Krummenacker and
Suzanne M. Paley and
Lukas A. Mueller and
Thomas Yan and
Peter D. Karp},
title = {Querying and computing with BioCyc databases},
journal = {Bioinform.},
volume = {21},
number = {16},
pages = {3454--3455},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti546},
doi = {10.1093/BIOINFORMATICS/BTI546},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KrummenackerPMYK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeselerCGIPPPK05,
author = {Ingrid M. Keseler and
Julio Collado{-}Vides and
Socorro Gama{-}Castro and
John Ingraham and
Suzanne M. Paley and
Ian T. Paulsen and
Mart{\'{\i}}n Peralta{-}Gil and
Peter D. Karp},
title = {EcoCyc: a comprehensive database resource for \emph{Escherichia coli}},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {334--337},
year = {2005},
url = {https://doi.org/10.1093/nar/gki108},
doi = {10.1093/NAR/GKI108},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeselerCGIPPPK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RomeroK04,
author = {Pedro Romero and
Peter D. Karp},
title = {Using functional and organizational information to improve genome-wide
computational prediction of transcription units on pathway-genome
databases},
journal = {Bioinform.},
volume = {20},
number = {5},
pages = {709--717},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg471},
doi = {10.1093/BIOINFORMATICS/BTG471},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RomeroK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GreenK04,
author = {Michelle L. Green and
Peter D. Karp},
title = {A Bayesian method for identifying missing enzymes in predicted metabolic
pathway databases},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {76},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-76},
doi = {10.1186/1471-2105-5-76},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GreenK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KriegerZMWPAPRK04,
author = {Cynthia J. Krieger and
Peifen Zhang and
Lukas A. Mueller and
Alfred Wang and
Suzanne M. Paley and
Martha Arnaud and
John Pick and
Seung Yon Rhee and
Peter D. Karp},
title = {MetaCyc: a multiorganism database of metabolic pathways and enzymes},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {438--442},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh100},
doi = {10.1093/NAR/GKH100},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KriegerZMWPAPRK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarpPKZ04,
author = {Peter D. Karp and
Suzanne M. Paley and
Cynthia J. Krieger and
Peifen Zhang},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany A. Jung and
Teri E. Klein},
title = {An Evidence Ontology for Use in Pathway/Genome Databases},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
6-10 January 2004},
pages = {190--201},
publisher = {World Scientific},
year = {2004},
url = {http://psb.stanford.edu/psb-online/proceedings/psb04/karp.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarpPKZ04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YehKNA03,
author = {Iwei Yeh and
Peter D. Karp and
Natalya Fridman Noy and
Russ B. Altman},
title = {Knowledge acquisition, consistency checking and concurrency control
for Gene Ontology {(GO)}},
journal = {Bioinform.},
volume = {19},
number = {2},
pages = {241--248},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/19.2.241},
doi = {10.1093/BIOINFORMATICS/19.2.241},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YehKNA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/omics/Karp03,
author = {Peter D. Karp},
title = {What Database Management System(s) Should Be Employed in Bioinformatics
Applications?},
journal = {{OMICS}},
volume = {7},
number = {1},
pages = {35--36},
year = {2003},
url = {https://doi.org/10.1089/153623103322006571},
doi = {10.1089/153623103322006571},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/omics/Karp03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/Karp03a,
author = {Peter D. Karp},
title = {Pathway Bioinformatics},
booktitle = {2nd {IEEE} Computer Society Bioinformatics Conference, {CSB} 2003,
Stanford, CA, USA, August 11-14, 2003},
pages = {27},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CSB.2003.1227294},
doi = {10.1109/CSB.2003.1227294},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/Karp03a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarpNHR03,
author = {Peter D. Karp and
Eric P. Neumann and
Alexander J. Hartemink and
Pedro Romero},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Genome, Pathway, and Interaction Bioinformatics - Session Introduction},
booktitle = {Proceedings of the 8th Pacific Symposium on Biocomputing, {PSB} 2003,
Lihue, Hawaii, USA, January 3-7, 2003},
pages = {101--103},
year = {2003},
url = {http://psb.stanford.edu/psb-online/proceedings/psb03/intro-path.doc},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarpNHR03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaleyK02,
author = {Suzanne M. Paley and
Peter D. Karp},
title = {Evaluation of computational metabolic-pathway predictions for Helicobacter
pylori},
journal = {Bioinform.},
volume = {18},
number = {5},
pages = {715--724},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.5.715},
doi = {10.1093/BIOINFORMATICS/18.5.715},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaleyK02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRSPCPPBG03,
author = {Peter D. Karp and
Monica Riley and
Milton H. Saier Jr. and
Ian T. Paulsen and
Julio Collado{-}Vides and
Suzanne M. Paley and
Alida Pellegrini{-}Toole and
C{\'{e}}sar Bonavides{-}Mart{\'{\i}}nez and
Socorro Gama{-}Castro},
title = {The EcoCyc Database},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {56--58},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.56},
doi = {10.1093/NAR/30.1.56},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRSPCPPBG03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRPP03,
author = {Peter D. Karp and
Monica Riley and
Suzanne M. Paley and
Alida Pellegrini{-}Toole},
title = {The MetaCyc Database},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {59--61},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.59},
doi = {10.1093/NAR/30.1.59},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRPP03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarpPR02,
author = {Peter D. Karp and
Suzanne M. Paley and
Pedro Romero},
title = {The Pathway Tools software},
booktitle = {Proceedings of the Tenth International Conference on Intelligent Systems
for Molecular Biology, August 3-7, 2002, Edmonton, Alberta, Canada},
pages = {225--232},
year = {2002},
timestamp = {Wed, 29 Jun 2011 14:55:41 +0200},
biburl = {https://dblp.org/rec/conf/ismb/KarpPR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarpRN02,
author = {Peter D. Karp and
Pedro Romero and
Eric P. Neumann},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Genome, Pathway and Interaction Bioinformatics - Session Introduction},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {398--399},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/genomepathwayIntro.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarpRN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarpPZ01,
author = {Peter D. Karp and
Suzanne M. Paley and
Jingchun Zhu},
title = {Database verification studies of {SWISS-PROT} and GenBank},
journal = {Bioinform.},
volume = {17},
number = {6},
pages = {526--532},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.6.526},
doi = {10.1093/BIOINFORMATICS/17.6.526},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarpPZ01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarpNR01,
author = {Peter D. Karp and
Eric P. Neumann and
Pedro Romero},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Genome, Pathway and Interaction Bioinformatics - Session Introduction},
booktitle = {Proceedings of the 6th Pacific Symposium on Biocomputing, {PSB} 2001,
Hawaii, USA, January 3-7, 2001},
pages = {420--421},
year = {2001},
url = {http://psb.stanford.edu/psb-online/proceedings/psb01/PATH.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarpNR01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/RomeroK01,
author = {Pedro Romero and
Peter D. Karp},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Nutrition-Related Analysis of Pathway/Genome Databases},
booktitle = {Proceedings of the 6th Pacific Symposium on Biocomputing, {PSB} 2001,
Hawaii, USA, January 3-7, 2001},
pages = {470--482},
year = {2001},
url = {http://psb.stanford.edu/psb-online/proceedings/psb01/romero.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/RomeroK01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Karp00,
author = {Peter D. Karp},
title = {An ontology for biological function based on molecular interactions},
journal = {Bioinform.},
volume = {16},
number = {3},
pages = {269--285},
year = {2000},
url = {https://doi.org/10.1093/bioinformatics/16.3.269},
doi = {10.1093/BIOINFORMATICS/16.3.269},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Karp00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRSPPP00,
author = {Peter D. Karp and
Monica Riley and
Milton H. Saier Jr. and
Ian T. Paulsen and
Suzanne M. Paley and
Alida Pellegrini{-}Toole},
title = {The EcoCyc and MetaCyc databases},
journal = {Nucleic Acids Res.},
volume = {28},
number = {1},
pages = {56--59},
year = {2000},
url = {https://doi.org/10.1093/nar/28.1.56},
doi = {10.1093/NAR/28.1.56},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRSPPP00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/McEntireKABHDKKLHNOPTTT00,
author = {Robin McEntire and
Peter D. Karp and
Neil F. Abernethy and
David Benton and
Gregg Helt and
Matt DeJongh and
Robert Kent and
Anthony Kosky and
Suzanna Lewis and
Dan Hodnett and
Eric P. Neumann and
Frank Olken and
Dhiraj K. Pathak and
Peter Tarczy{-}Hornoch and
Luca Toldo and
Thodoros Topaloglou},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {An Evaluation of Ontology Exchange Languages for Bioinformatics},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {239--250},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-025.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/McEntireKABHDKKLHNOPTTT00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jiis/KarpCP99,
author = {Peter D. Karp and
Vinay K. Chaudhri and
Suzanne M. Paley},
title = {A Collaborative Environment for Authoring Large Knowledge Bases},
journal = {J. Intell. Inf. Syst.},
volume = {13},
number = {3},
pages = {155--194},
year = {1999},
url = {https://doi.org/10.1023/A:1008763932600},
doi = {10.1023/A:1008763932600},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jiis/KarpCP99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRPPK99,
author = {Peter D. Karp and
Monica Riley and
Suzanne M. Paley and
Alida Pellegrini{-}Toole and
Markus Krummenacker},
title = {Eco Cyc: encyclopedia of Escherichia coli genes and metabolism},
journal = {Nucleic Acids Res.},
volume = {27},
number = {1},
pages = {55--58},
year = {1999},
url = {https://doi.org/10.1093/nar/27.1.55},
doi = {10.1093/NAR/27.1.55},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRPPK99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRPPK98,
author = {Peter D. Karp and
Monica Riley and
Suzanne M. Paley and
Alida Pellegrini{-}Toole and
Markus Krummenacker},
title = {EcoCyc: Encyclopedia of Escherichia coli genes and metabolism},
journal = {Nucleic Acids Res.},
volume = {26},
number = {1},
pages = {50--53},
year = {1998},
url = {https://doi.org/10.1093/nar/26.1.50},
doi = {10.1093/NAR/26.1.50},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRPPK98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/ChaudhriFFKR98,
author = {Vinay K. Chaudhri and
Adam Farquhar and
Richard Fikes and
Peter D. Karp and
James Rice},
editor = {Jack Mostow and
Chuck Rich},
title = {{OKBC:} {A} Programmatic Foundation for Knowledge Base Interoperability},
booktitle = {Proceedings of the Fifteenth National Conference on Artificial Intelligence
and Tenth Innovative Applications of Artificial Intelligence Conference,
{AAAI} 98, {IAAI} 98, July 26-30, 1998, Madison, Wisconsin, {USA}},
pages = {600--607},
publisher = {{AAAI} Press / The {MIT} Press},
year = {1998},
url = {http://www.aaai.org/Library/AAAI/1998/aaai98-085.php},
timestamp = {Tue, 05 Sep 2023 09:10:47 +0200},
biburl = {https://dblp.org/rec/conf/aaai/ChaudhriFFKR98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForsytheKM97,
author = {Ronald G. Forsythe Jr. and
Peter D. Karp and
Michael L. Mavrovouniotis},
title = {Estimation of equilibrium constants using automated group contribution
methods},
journal = {Comput. Appl. Biosci.},
volume = {13},
number = {5},
pages = {537--543},
year = {1997},
url = {https://doi.org/10.1093/bioinformatics/13.5.537},
doi = {10.1093/BIOINFORMATICS/13.5.537},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForsytheKM97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRPPK97,
author = {Peter D. Karp and
Monica Riley and
Suzanne M. Paley and
Alida Pellegrini{-}Toole and
Markus Krummenacker},
title = {EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism},
journal = {Nucleic Acids Res.},
volume = {25},
number = {1},
pages = {43--51},
year = {1997},
url = {https://doi.org/10.1093/nar/25.1.43},
doi = {10.1093/NAR/25.1.43},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRPPK97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/PaleyLK97,
author = {Suzanne M. Paley and
John D. Lowrance and
Peter D. Karp},
editor = {Benjamin Kuipers and
Bonnie L. Webber},
title = {A Generic Knowledge-Base Browser and Editor},
booktitle = {Proceedings of the Fourteenth National Conference on Artificial Intelligence
and Ninth Innovative Applications of Artificial Intelligence Conference,
{AAAI} 97, {IAAI} 97, July 27-31, 1997, Providence, Rhode Island,
{USA}},
pages = {1045--1051},
publisher = {{AAAI} Press / The {MIT} Press},
year = {1997},
url = {http://www.aaai.org/Library/IAAI/1997/iaai97-207.php},
timestamp = {Tue, 05 Sep 2023 08:53:09 +0200},
biburl = {https://dblp.org/rec/conf/aaai/PaleyLK97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/JardinsKKLO97,
author = {Marie desJardins and
Peter D. Karp and
Markus Krummenacker and
Thomas J. Lee and
Christos A. Ouzounis},
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Prediction of Enzyme Classification from Protein Sequence without
the Use of Sequence Similarity},
booktitle = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
pages = {92--99},
publisher = {{AAAI}},
year = {1997},
url = {http://www.aaai.org/Library/ISMB/1997/ismb97-014.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/JardinsKKLO97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/krdb/ChaudhriK97,
author = {Vinay K. Chaudhri and
Peter D. Karp},
editor = {Franz Baader and
Manfred A. Jeusfeld and
Werner Nutt},
title = {Querying Schema Information},
booktitle = {Intelligent Access to Heterogeneous Information, Proceedings of the
4th Workshop KRDB-97, Athens, Greece, August 30, 1997},
series = {{CEUR} Workshop Proceedings},
volume = {8},
pages = {4.1--4.6},
publisher = {CEUR-WS.org},
year = {1997},
url = {https://ceur-ws.org/Vol-8/paper-4.ps},
timestamp = {Fri, 10 Mar 2023 16:23:34 +0100},
biburl = {https://dblp.org/rec/conf/krdb/ChaudhriK97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/ismb/1997,
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
publisher = {{AAAI}},
year = {1997},
isbn = {1-57735-022-7},
timestamp = {Tue, 01 Jul 2003 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/1997.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KarpP96,
author = {Peter D. Karp and
Suzanne M. Paley},
title = {Integrated Access to Metabolic and Genomic Data},
journal = {J. Comput. Biol.},
volume = {3},
number = {1},
pages = {191--212},
year = {1996},
url = {https://doi.org/10.1089/cmb.1996.3.191},
doi = {10.1089/CMB.1996.3.191},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KarpP96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarpRPP96,
author = {Peter D. Karp and
Monica Riley and
Suzanne M. Paley and
Alida Pellegrini{-}Toole},
title = {EcoCyc: an encyclopedia of Escherichia coli genes and metabolism},
journal = {Nucleic Acids Res.},
volume = {24},
number = {1},
pages = {32--39},
year = {1996},
url = {https://doi.org/10.1093/nar/24.1.32},
doi = {10.1093/NAR/24.1.32},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarpRPP96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/HuertaCKK96,
author = {Araceli M. Huerta and
Julio Collado{-}Vides and
Peter D. Karp and
Kathleen Klose},
title = {Three Models of Gene Regulation in E.coli},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1996,
Leipzig, Germany, September 30 - October 2, 1996},
pages = {64--67},
year = {1996},
timestamp = {Sat, 07 Sep 2019 11:59:23 +0200},
biburl = {https://dblp.org/rec/conf/gcb/HuertaCKK96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarpOP96,
author = {Peter D. Karp and
Christos A. Ouzounis and
Suzanne M. Paley},
editor = {David J. States and
Pankaj Agarwal and
Terry Gaasterland and
Lawrence Hunter and
Randall Smith},
title = {HinCyc: {A} Knowledge Base of the Complete Genome and Metabolic Pathways
of H. influenzae},
booktitle = {Proceedings of the Fourth International Conference on Intelligent
Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996},
pages = {116--124},
publisher = {{AAAI}},
year = {1996},
url = {http://www.aaai.org/Library/ISMB/1996/ismb96-013.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KarpOP96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Karp95,
author = {Peter D. Karp},
title = {A Strategy for Database Interoperation},
journal = {J. Comput. Biol.},
volume = {2},
number = {4},
pages = {573--586},
year = {1995},
url = {https://doi.org/10.1089/cmb.1995.2.573},
doi = {10.1089/CMB.1995.2.573},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Karp95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcai/KarpP95,
author = {Peter D. Karp and
Suzanne M. Paley},
title = {Knowledge Representation in the Large},
booktitle = {Proceedings of the Fourteenth International Joint Conference on Artificial
Intelligence, {IJCAI} 95, Montr{\'{e}}al Qu{\'{e}}bec, Canada,
August 20-25 1995, 2 Volumes},
pages = {751--758},
publisher = {Morgan Kaufmann},
year = {1995},
url = {http://ijcai.org/Proceedings/95-1/Papers/098.pdf},
timestamp = {Tue, 20 Aug 2019 16:17:30 +0200},
biburl = {https://dblp.org/rec/conf/ijcai/KarpP95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcai/KarpMG95,
author = {Peter D. Karp and
Karen L. Myers and
Thomas R. Gruber},
title = {The Generic Frame Protocol},
booktitle = {Proceedings of the Fourteenth International Joint Conference on Artificial
Intelligence, {IJCAI} 95, Montr{\'{e}}al Qu{\'{e}}bec, Canada,
August 20-25 1995, 2 Volumes},
pages = {768--774},
publisher = {Morgan Kaufmann},
year = {1995},
url = {http://ijcai.org/Proceedings/95-1/Papers/100.pdf},
timestamp = {Tue, 20 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ijcai/KarpMG95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/expert/KarpM94,
author = {Peter D. Karp and
Michael L. Mavrovouniotis},
title = {Representing, Analyzing, and Synthesizing Biochemical Pathways},
journal = {{IEEE} Expert},
volume = {9},
number = {2},
pages = {11--21},
year = {1994},
url = {https://doi.org/10.1109/64.294129},
doi = {10.1109/64.294129},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/expert/KarpM94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/lisp/KarpLSW94,
author = {Peter D. Karp and
John D. Lowrance and
Thomas M. Strat and
David E. Wilkins},
title = {The Grasper-CL Graph Management System},
journal = {{LISP} Symb. Comput.},
volume = {7},
number = {4},
pages = {251--290},
year = {1994},
timestamp = {Thu, 21 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/lisp/KarpLSW94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cikm/KarpPG94,
author = {Peter D. Karp and
Suzanne M. Paley and
Ira B. Greenberg},
title = {A Storage System for Scalable Knowledge Representation},
booktitle = {Proceedings of the Third International Conference on Information and
Knowledge Management (CIKM'94), Gaithersburg, Maryland, USA, November
29 - December 2, 1994},
pages = {97--104},
publisher = {{ACM}},
year = {1994},
url = {https://doi.org/10.1145/191246.191265},
doi = {10.1145/191246.191265},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cikm/KarpPG94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarpP94,
author = {Peter D. Karp and
Suzanne M. Paley},
editor = {Russ B. Altman and
Douglas L. Brutlag and
Peter D. Karp and
Richard H. Lathrop and
David B. Searls},
title = {Representations of Metabolic Knowledge: Pathways},
booktitle = {Proceedings of the Second International Conference on Intelligent
Systems for Molecular Biology, August 14-17, 1994, Stanford University,
Stanford, California, {USA}},
pages = {203--211},
publisher = {{AAAI}},
year = {1994},
url = {http://www.aaai.org/Library/ISMB/1994/ismb94-025.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KarpP94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/ismb/1994,
editor = {Russ B. Altman and
Douglas L. Brutlag and
Peter D. Karp and
Richard H. Lathrop and
David B. Searls},
title = {Proceedings of the Second International Conference on Intelligent
Systems for Molecular Biology, August 14-17, 1994, Stanford University,
Stanford, California, {USA}},
publisher = {{AAAI}},
year = {1994},
isbn = {0-929280-68-7},
timestamp = {Tue, 01 Jul 2003 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/1994.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ml/Karp93,
author = {Peter D. Karp},
title = {Design Methods for Scientific Hypothesis Formation and Their Application
to Molecular Biology},
journal = {Mach. Learn.},
volume = {12},
pages = {89--116},
year = {1993},
url = {https://doi.org/10.1007/BF00993062},
doi = {10.1007/BF00993062},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ml/Karp93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarpR93,
author = {Peter D. Karp and
Monica Riley},
editor = {Lawrence Hunter and
David B. Searls and
Jude W. Shavlik},
title = {Representations of Metabolic Knowledge},
booktitle = {Proceedings of the 1st International Conference on Intelligent Systems
for Molecular Biology, Bethesda, MD, USA, July 1993},
pages = {207--215},
publisher = {{AAAI}},
year = {1993},
url = {http://www.aaai.org/Library/ISMB/1993/ismb93-024.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KarpR93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sp/QianSKLG93,
author = {Xiaolei Qian and
Mark E. Stickel and
Peter D. Karp and
Teresa F. Lunt and
Thomas D. Garvey},
title = {Detection and elimination of inference channels in multilevel relational
database systems},
booktitle = {1993 {IEEE} Computer Society Symposium on Research in Security and
Privacy, Oakland, CA, USA, May 24-26, 1993},
pages = {196--205},
publisher = {{IEEE} Computer Society},
year = {1993},
url = {https://doi.org/10.1109/RISP.1993.287632},
doi = {10.1109/RISP.1993.287632},
timestamp = {Thu, 21 Sep 2023 15:57:35 +0200},
biburl = {https://dblp.org/rec/conf/sp/QianSKLG93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Karp92,
author = {Peter D. Karp},
title = {A knowledge base of the chemical compounds of intermediary metabolism},
journal = {Comput. Appl. Biosci.},
volume = {8},
number = {4},
pages = {347--357},
year = {1992},
url = {https://doi.org/10.1093/bioinformatics/8.4.347},
doi = {10.1093/BIOINFORMATICS/8.4.347},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Karp92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Karp91,
author = {Peter D. Karp},
title = {Artificial intelligence methods for theory representation and hypothesis
formation},
journal = {Comput. Appl. Biosci.},
volume = {7},
number = {3},
pages = {301--308},
year = {1991},
url = {https://doi.org/10.1093/bioinformatics/7.3.301},
doi = {10.1093/BIOINFORMATICS/7.3.301},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Karp91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/aim/Karp90,
author = {Peter D. Karp},
title = {Hypothesis Formation and Qualitative Reasoning in Molecular Biology},
journal = {{AI} Mag.},
volume = {11},
number = {4},
pages = {9--10},
year = {1990},
url = {https://doi.org/10.1609/aimag.v11i4.859},
doi = {10.1609/AIMAG.V11I4.859},
timestamp = {Tue, 25 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/aim/Karp90.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/us/Karp89,
author = {Peter D. Karp},
title = {Hypothesis formation and qualitative reasoning in molecular biology},
school = {Stanford University, {USA}},
year = {1989},
url = {https://searchworks.stanford.edu/view/1346368},
timestamp = {Tue, 23 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/us/Karp89.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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