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Peter Karp
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Research Profile (preview)
Concepts & Ideas
Activities & Behaviors
Occupations
Genes & Molecular Sequences
Chemicals & Drugs
Living Beings
Physiology
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Network (preview)
24
Paley, Suzanne
12
Krummenacker, Markus
7
Riley, Monica
6
Pellegrini-Toole, Alida
5
Green, Michelle
4
Gama-Castro, Socorro
4
Collado-Vides, Julio
4
Paulsen, Ian
4
Rhee, Soo-Yon
3
Ouzounis, Christos
3
Zhang, Peifen
3
Peralta-Gil, Martín
2
Santos-Zavaleta, Alberto
2
Romero, Pedro
2
Saier, Milton
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Geonetwork of Peter Karp (preview)
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All Publications
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2009: Hu James C; Karp Peter D; Keseler Ingrid M; Krummenacker Markus; Siegele Deborah A
What we can learn about Escherichia coli through application of Gene Ontology.
Trends in microbiology 2009;17(7):269-78.
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2008: Lee Thomas J; Paulsen Ian; Karp Peter
Annotation-based inference of transporter function.
Bioinformatics (Oxford, England) 2008;24(13):i259-67.
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2008: Caspi Ron; Foerster Hartmut; Fulcher Carol A; Kaipa Pallavi; Krummenacker Markus; Latendresse Mario; Paley Suzanne; Rhee Seung Y; Shearer Alexander G; Tissier Christophe; Walk Thomas C; Zhang Peifen; Karp Peter D
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic acids research 2008;36(Database issue):D623-31.
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2007: Green Michelle L; Karp Peter D
Using genome-context data to identify specific types of functional associations in pathway/genome databases.
Bioinformatics (Oxford, England) 2007;23(13):i205-11.
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2007: Karp Peter D; Keseler Ingrid M; Shearer Alexander; Latendresse Mario; Krummenacker Markus; Paley Suzanne M; Paulsen Ian; Collado-Vides Julio; Gama-Castro Socorro; Peralta-Gil Martin; Santos-Zavaleta Alberto; Peñaloza-Spínola Mónica I; Bonavides-Martinez César; Ingraham John
Multidimensional annotation of the Escherichia coli K-12 genome.
Nucleic acids research 2007;35(22):7577-90.
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2007: Pouliot Yannick; Karp Peter D
A survey of orphan enzyme activities.
BMC bioinformatics 2007;8():244.
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2007: Feist Adam M; Henry Christopher S; Reed Jennifer L; Krummenacker Markus; Joyce Andrew R; Karp Peter D; Broadbelt Linda J; Hatzimanikatis Vassily; Palsson Bernhard Ø
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Molecular systems biology 2007;3():121.
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2006: Caspi Ron; Foerster Hartmut; Fulcher Carol A; Hopkinson Rebecca; Ingraham John; Kaipa Pallavi; Krummenacker Markus; Paley Suzanne; Pick John; Rhee Seung Y; Tissier Christophe; Zhang Peifen; Karp Peter D
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2006;34(Database issue):D511-6.
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2006: Paley Suzanne M; Karp Peter D
The Pathway Tools cellular overview diagram and Omics Viewer.
Nucleic acids research 2006;34(13):3771-8.
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2006: Green M L; Karp P D
The outcomes of pathway database computations depend on pathway ontology.
Nucleic acids research 2006;34(13):3687-97.
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2006: Shi Jing; Romero Pedro R; Schoolnik Gary K; Spormann Alfred M; Karp Peter D
Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests.
Nucleic acids research 2006;34(8):2438-44.
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2006: Lee Thomas J; Pouliot Yannick; Wagner Valerie; Gupta Priyanka; Stringer-Calvert David W J; Tenenbaum Jessica D; Karp Peter D
BioWarehouse: a bioinformatics database warehouse toolkit.
BMC bioinformatics 2006;7():170.
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2006: Salgado Heladia; Santos-Zavaleta Alberto; Gama-Castro Socorro; Peralta-Gil Martín; Peñaloza-Spínola Mónica I; Martínez-Antonio Agustino; Karp Peter D; Collado-Vides Julio
The comprehensive updated regulatory network of Escherichia coli K-12.
BMC bioinformatics 2006;7():5.
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2005: Krummenacker Markus; Paley Suzanne; Mueller Lukas; Yan Thomas; Karp Peter D
Querying and computing with BioCyc databases.
Bioinformatics (Oxford, England) 2005;21(16):3454-5.
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2005: Zhang Peifen; Foerster Hartmut; Tissier Christophe P; Mueller Lukas; Paley Suzanne; Karp Peter D; Rhee Seung Y
MetaCyc and AraCyc. Metabolic pathway databases for plant research.
Plant physiology 2005;138(1):27-37.
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2005: Keseler Ingrid M; Collado-Vides Julio; Gama-Castro Socorro; Ingraham John; Paley Suzanne; Paulsen Ian T; Peralta-Gil Martín; Karp Peter D
EcoCyc: a comprehensive database resource for Escherichia coli.
Nucleic acids research 2005;33(Database issue):D334-7.
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2005: Karp Peter D; Ouzounis Christos A; Moore-Kochlacs Caroline; Goldovsky Leon; Kaipa Pallavi; Ahrén Dag; Tsoka Sophia; Darzentas Nikos; Kunin Victor; López-Bigas Núria
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
Nucleic acids research 2005;33(19):6083-9.
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2005: Green M L; Karp P D
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.
Nucleic acids research 2005;33(13):4035-9.
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2005: Romero Pedro; Wagg Jonathan; Green Michelle L; Kaiser Dale; Krummenacker Markus; Karp Peter D
Computational prediction of human metabolic pathways from the complete human genome.
Genome biology 2005;6(1):R2.
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2004: Green Michelle L; Karp Peter D
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
BMC bioinformatics 2004;5():76.
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2004: Yeh Iwei; Hanekamp Theodor; Tsoka Sophia; Karp Peter D; Altman Russ B
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery.
Genome research 2004;14(5):917-24.
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2004: Romero P R; Karp P D
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.
Bioinformatics (Oxford, England) 2004;20(5):709-17.
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2004: Krieger Cynthia J; Zhang Peifen; Mueller Lukas A; Wang Alfred; Paley Suzanne; Arnaud Martha; Pick John; Rhee Seung Y; Karp Peter D
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2004;32(Database issue):D438-42.
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2004: Karp P D; Paley S; Krieger C J; Zhang P
An evidence ontology for use in pathway/genome databases.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():190-201.
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2003: Yeh Iwei; Karp Peter D; Noy Natalya F; Altman Russ B
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
Bioinformatics (Oxford, England) 2003;19(2):241-8.
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2002: Paley Suzanne M; Karp Peter D
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
Bioinformatics (Oxford, England) 2002;18(5):715-24.
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2002: Karp Peter D; Riley Monica; Paley Suzanne M; Pellegrini-Toole Alida
The MetaCyc Database.
Nucleic acids research 2002;30(1):59-61.
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2002: Karp Peter D; Riley Monica; Saier Milton; Paulsen Ian T; Collado-Vides Julio; Paley Suzanne M; Pellegrini-Toole Alida; Bonavides César; Gama-Castro Socorro
The EcoCyc Database.
Nucleic acids research 2002;30(1):56-8.
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2002: Karp Peter D; Paley Suzanne; Romero Pedro
The Pathway Tools software.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S225-32.
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2001: Karp P D; Paley S; Zhu J
Database verification studies of SWISS-PROT and GenBank.
Bioinformatics (Oxford, England) 2001;17(6):526-32; discussion 533-4.
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2001: Romero P R; Karp P
Nutrient-related analysis of pathway/genome databases.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():471-82.
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2000: Karp P D
An ontology for biological function based on molecular interactions.
Bioinformatics (Oxford, England) 2000;16(3):269-85.
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2000: Karp P D; Riley M; Saier M; Paulsen I T; Paley S M; Pellegrini-Toole A
The EcoCyc and MetaCyc databases.
Nucleic acids research 2000;28(1):56-9.
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1999: Karp P D; Krummenacker M; Paley S; Wagg J
Integrated pathway-genome databases and their role in drug discovery.
Trends in biotechnology 1999;17(7):275-81.
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1999: Karp P D; Riley M; Paley S M; Pellegrini-Toole A; Krummenacker M
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1999;27(1):55-8.
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1998: Karp P D; Riley M; Paley S M; Pellegrini-Toole A; Krummenacker M
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1998;26(1):50-3.
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1997: Karp P D; Riley M; Paley S M; Pellegrini-Toole A; Krummenacker M
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.
Nucleic acids research 1997;25(1):43-51.
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1997: des Jardins M; Karp P D; Krummenacker M; Lee T J; Ouzounis C A
Prediction of enzyme classification from protein sequence without the use of sequence similarity.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():92-9.
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1996: Karp P D
Database links are a foundation for interoperability.
Trends in biotechnology 1996;14(8):273-9.
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1996: Paley S M; Karp P D
Adapting EcoCyc for use on the World Wide Web.
Gene 1996;172(1):GC43-50.
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1996: Karp P D; Riley M; Paley S M; Pelligrini-Toole A
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1996;24(1):32-9.
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1996: Karp P D
A protocol for maintaining multidatabase referential integrity.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():438-45.
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1996: Karp P D; Ouzounis C; Paley S
HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():116-24.
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1996: Karp P D; Paley S
Integrated access to metabolic and genomic data.
Journal of computational biology : a journal of computational molecular cell biology 1996;3(1):191-212.
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1995: Karp P D
A strategy for database interoperation.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(4):573-86.
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1994: Karp P D; Paley S M
Representations of metabolic knowledge: pathways.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():203-11.
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1992: Karp P D
A knowledge base of the chemical compounds of intermediary metabolism.
Computer applications in the biosciences : CABIOS 1992;8(4):347-57.
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