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Peter Karp

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Genes & Molecular Sequences

Bacterial Genomes

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TOP 3
Steven Eker; Ingrid Keseler; Markus Krummenacker; Alexander G Shearer; Carolyn Talcott; Ashish Tiwari; Peter D Karp
Computing minimal nutrient sets from metabolic networks via linear constraint solving.
Peter D Karp; Suzanne Paley; Tomer Altman
Data mining in the MetaCyc family of pathway databases.
Ingrid Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Amanda Mackie; Luis Muñiz-Rascado; Quang Ong; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Alberto Santos-Zavaleta; Imke Schröder; Alexander G Shearer; Pallavi Subhraveti; Mike Travers; Deepika Weerasinghe; Verena Weiss; César Bonavides-Martínez; Julio Collado-Vides; Carol Fulcher; Socorro Gama-Castro; Robert P Gunsalus; Araceli M Huerta; Peter D Karp
EcoCyc: fusing model organism databases with systems biology.

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All Publications

2013: Steven Eker; Ingrid Keseler; Markus Krummenacker; Alexander G Shearer; Carolyn Talcott; Ashish Tiwari; Peter D Karp
Computing minimal nutrient sets from metabolic networks via linear constraint solving.
BMC bioinformatics 2013;14():114.
2013: Peter D Karp; Suzanne Paley; Tomer Altman
Data mining in the MetaCyc family of pathway databases.
Methods in molecular biology (Clifton, N.J.) 2013;939():183-200.
2013: Ingrid Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Amanda Mackie; Luis Muñiz-Rascado; Quang Ong; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Alberto Santos-Zavaleta; Imke Schröder; Alexander G Shearer; Pallavi Subhraveti; Mike Travers; Deepika Weerasinghe; Verena Weiss; César Bonavides-Martínez; Julio Collado-Vides; Carol Fulcher; Socorro Gama-Castro; Robert P Gunsalus; Araceli M Huerta; Peter D Karp
EcoCyc: fusing model organism databases with systems biology.
Nucleic acids research 2013;41(Database issue):D605-12.
2012: Mario Latendresse; Jeremiah P Malerich; Mike Travers; Peter D Karp
Accurate atom-mapping computation for biochemical reactions.
Journal of chemical information and modeling 2012;52(11):2970-82.
2012: Mario Latendresse; Miles Trupp; Markus Krummenacker; Peter D Karp
Construction and completion of flux balance models from pathway databases.
Bioinformatics (Oxford, England) 2012;28(3):388-96.
2012: Suzanne Paley; Mario Latendresse; Peter D Karp
Regulatory network operations in the Pathway Tools software.
BMC bioinformatics 2012;13():243.
2012: Miles Trupp; William R Wikoff; Zhao-Bang Zeng; Hongjie Zhu; Rebecca A Baillie; Oliver Fiehn; Peter D Karp; Ronald M Krauss; Rima Kaddurah-Daouk
Metabolomics reveals amino acids contribute to variation in response to simvastatin treatment.
PloS one 2012;7(7):e38386.
2012: Mario Latendresse; Suzanne Paley; Peter D Karp
Browsing metabolic and regulatory networks with BioCyc.
Methods in molecular biology (Clifton, N.J.) 2012;804():197-216.
2011: Peter D Karp; Mario Latendresse; Ron Caspi
The pathway tools pathway prediction algorithm.
Standards in genomic sciences 2011;5(3):424-9.
2011: Luciana Ferrer; Alexander G Shearer; Peter D Karp
Discovering novel subsystems using comparative genomics.
Bioinformatics (Oxford, England) 2011;27(18):2478-85.
2011: Peter D Karp; Ron Caspi
A survey of metabolic databases emphasizing the MetaCyc family.
Archives of toxicology 2011;85(9):1015-33.
2011: Mario Latendresse; Peter D Karp
Web-based metabolic network visualization with a zooming user interface.
BMC bioinformatics 2011;12():176.
2010: Luciana Ferrer; Joseph M Dale; Peter D Karp
A systematic study of genome context methods: calibration, normalization and combination.
BMC bioinformatics 2010;11():493.
2010: Mario Latendresse; Peter D Karp
An advanced web query interface for biological databases.
Database : the journal of biological databases and curation 2010;2010():baq006.
2010: Joseph M Dale; Liviu Popescu; Peter D Karp
Machine learning methods for metabolic pathway prediction.
BMC bioinformatics 2010;11():15.
2009: James C Hu; Peter D Karp; Ingrid Keseler; Markus Krummenacker; Deborah Siegele
What we can learn about Escherichia coli through application of Gene Ontology.
Trends in microbiology 2009;17(7):269-78.
2008: Thomas J Lee; Ian Paulsen; Peter D Karp
Annotation-based inference of transporter function.
Bioinformatics (Oxford, England) 2008;24(13):i259-67.
2008: Ron Caspi; Hartmut Foerster; Carol A Fulcher; Pallavi Kaipa; Markus Krummenacker; Mario Latendresse; Suzanne Paley; Seung-Yon Rhee; Alexander G Shearer; Christophe Tissier; Thomas C Walk; Peifen Zhang; Peter D Karp
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic acids research 2008;36(Database issue):D623-31.
2007: Michelle L Green; Peter D Karp
Using genome-context data to identify specific types of functional associations in pathway/genome databases.
Bioinformatics (Oxford, England) 2007;23(13):i205-11.
2007: Peter D Karp; Ingrid Keseler; Alexander Shearer; Mario Latendresse; Markus Krummenacker; Suzanne Paley; Ian Paulsen; Julio Collado-Vides; Socorro Gama-Castro; Martín Peralta-Gil; Alberto Santos-Zavaleta; Mónica I Peñaloza-Spínola; César Bonavides-Martinez; John Ingraham
Multidimensional annotation of the Escherichia coli K-12 genome.
Nucleic acids research 2007;35(22):7577-90.
2007: Yannick Pouliot; Peter D Karp
A survey of orphan enzyme activities.
BMC bioinformatics 2007;8():244.
2007: Adam M Feist; Christopher S Henry; Jennifer L Reed; Markus Krummenacker; Andrew R Joyce; Peter D Karp; Linda J Broadbelt; Vassily Hatzimanikatis; Bernhard Ø Palsson
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.
2006: Suzanne Paley; Peter D Karp
The Pathway Tools cellular overview diagram and Omics Viewer.
Nucleic acids research 2006;34(13):3771-8.
2006: Michelle L Green; Peter D Karp
The outcomes of pathway database computations depend on pathway ontology.
Nucleic acids research 2006;34(13):3687-97.
2006: Jing Shi; Pedro R Romero; Gary K Schoolnik; Alfred M Spormann; Peter D Karp
Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests.
Nucleic acids research 2006;34(8):2438-44.
2006: Thomas J Lee; Yannick Pouliot; Valerie Wagner; Priyanka Gupta; David W J Stringer-Calvert; Jessica Tenenbaum; Peter D Karp
BioWarehouse: a bioinformatics database warehouse toolkit.
BMC bioinformatics 2006;7():170.
2006: Heladia Salgado; Alberto Santos-Zavaleta; Socorro Gama-Castro; Martín Peralta-Gil; Mónica I Peñaloza-Spínola; Agustino Martínez-Antonio; Peter D Karp; Julio Collado-Vides
The comprehensive updated regulatory network of Escherichia coli K-12.
BMC bioinformatics 2006;7():5.
2006: Ron Caspi; Hartmut Foerster; Carol A Fulcher; Rebecca Hopkinson; John Ingraham; Pallavi Kaipa; Markus Krummenacker; Suzanne Paley; John Pick; Seung-Yon Rhee; Christophe Tissier; Peifen Zhang; Peter D Karp
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2006;34(Database issue):D511-6.
2005: Markus Krummenacker; Suzanne Paley; Lukas Mueller; Thomas Yan; Peter D Karp
Querying and computing with BioCyc databases.
Bioinformatics (Oxford, England) 2005;21(16):3454-5.
2005: Peifen Zhang; Hartmut Foerster; Christophe P Tissier; Lukas Mueller; Suzanne Paley; Peter D Karp; Seung-Yon Rhee
MetaCyc and AraCyc. Metabolic pathway databases for plant research.
Plant physiology 2005;138(1):27-37.
2005: Peter D Karp; Christos Ouzounis; Caroline Moore-Kochlacs; Leon Goldovsky; Pallavi Kaipa; Dag Ahrén; Sophia Tsoka; Nikos Darzentas; Victor Kunin; Núria López-Bigas
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
Nucleic acids research 2005;33(19):6083-9.
2005: Michelle L Green; Peter D Karp
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.
Nucleic acids research 2005;33(13):4035-9.
2005: Pedro Romero; Jonathan K Wagg; Michelle L Green; Armin Dale Kaiser; Markus Krummenacker; Peter D Karp
Computational prediction of human metabolic pathways from the complete human genome.
Genome biology 2005;6(1):R2.
2005: Ingrid Keseler; Julio Collado-Vides; Socorro Gama-Castro; John Ingraham; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Peter D Karp
EcoCyc: a comprehensive database resource for Escherichia coli.
Nucleic acids research 2005;33(Database issue):D334-7.
2004: Michelle L Green; Peter D Karp
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
BMC bioinformatics 2004;5():76.
2004: Iwei Yeh; Theodor Hanekamp; Sophia Tsoka; Peter D Karp; Russ B Altman
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery.
Genome research 2004;14(5):917-24.
2004: P R Romero; Peter D Karp
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.
2004: Peter D Karp; Suzanne Paley; C J Krieger; P Zhang
An evidence ontology for use in pathway/genome databases.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():190-201.
2004: Cynthia J Krieger; Peifen Zhang; Lukas Mueller; Alfred Wang; Suzanne Paley; Martha Arnaud; John Pick; Seung-Yon Rhee; Peter D Karp
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic acids research 2004;32(Database issue):D438-42.
2003: Iwei Yeh; Peter D Karp; Natalya F Noy; Russ B Altman
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
Bioinformatics (Oxford, England) 2003;19(2):241-8.
2002: Suzanne Paley; Peter D Karp
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
Bioinformatics (Oxford, England) 2002;18(5):715-24.
2002: Peter D Karp; Suzanne Paley; Pedro Romero
The Pathway Tools software.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S225-32.
2002: Peter D Karp; Monica Riley; Suzanne Paley; Alida Pellegrini-Toole
The MetaCyc Database.
Nucleic acids research 2002;30(1):59-61.
2002: Peter D Karp; Monica Riley; Milton H Saier; Ian Paulsen; Julio Collado-Vides; Suzanne Paley; Alida Pellegrini-Toole; César Bonavides; Socorro Gama-Castro
The EcoCyc Database.
Nucleic acids research 2002;30(1):56-8.
2001: Peter D Karp; Suzanne Paley; J Zhu
Database verification studies of SWISS-PROT and GenBank.
Bioinformatics (Oxford, England) 2001;17(6):526-32; discussion 533-4.
2001: P R Romero; Peter D Karp
Nutrient-related analysis of pathway/genome databases.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():471-82.
2000: Peter D Karp
An ontology for biological function based on molecular interactions.
Bioinformatics (Oxford, England) 2000;16(3):269-85.
2000: Peter D Karp; Monica Riley; Milton H Saier; Ian Paulsen; Suzanne Paley; Alida Pellegrini-Toole
The EcoCyc and MetaCyc databases.
Nucleic acids research 2000;28(1):56-9.
1999: Peter D Karp; Markus Krummenacker; Suzanne Paley; Jonathan K Wagg
Integrated pathway-genome databases and their role in drug discovery.
Trends in biotechnology 1999;17(7):275-81.
1999: Peter D Karp; Monica Riley; Suzanne Paley; Alida Pellegrini-Toole; Markus Krummenacker
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1999;27(1):55-8.
1998: Peter D Karp; Monica Riley; Suzanne Paley; Alida Pellegrini-Toole; Markus Krummenacker
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1998;26(1):50-3.
1997: M des Jardins; Peter D Karp; Markus Krummenacker; T J Lee; Christos Ouzounis
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.
1997: Peter D Karp; Monica Riley; Suzanne Paley; Alida Pellegrini-Toole; Markus Krummenacker
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.
Nucleic acids research 1997;25(1):43-51.
1996: Peter D Karp
Database links are a foundation for interoperability.
Trends in biotechnology 1996;14(8):273-9.
1996: Suzanne Paley; Peter D Karp
Adapting EcoCyc for use on the World Wide Web.
Gene 1996;172(1):GC43-50.
1996: Peter D Karp
A protocol for maintaining multidatabase referential integrity.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():438-45.
1996: Peter D Karp; Christos Ouzounis; Suzanne Paley
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.
1996: Peter D Karp; Suzanne Paley
Integrated access to metabolic and genomic data.
Journal of computational biology : a journal of computational molecular cell biology 1996;3(1):191-212.
1996: Peter D Karp; Monica Riley; Suzanne Paley; A Pelligrini-Toole
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.
Nucleic acids research 1996;24(1):32-9.
1995: Peter D Karp
A strategy for database interoperation.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(4):573-86.
1994: Peter D Karp; Suzanne Paley
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.
1992: Peter D Karp
A knowledge base of the chemical compounds of intermediary metabolism.
Computer applications in the biosciences : CABIOS 1992;8(4):347-57.