Peter D Karp
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Explore the profile of Peter D Karp including associated specialties, affiliations and a list of published articles.
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117
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9351
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Recent Articles
11.
Karp P, Paley S, Caspi R, Kothari A, Krummenacker M, Midford P, et al.
EcoSal Plus
. 2023 May;
11(1):eesp00022023.
PMID: 37220074
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the...
12.
Proctor A, Parvinroo S, Richie T, Jia X, Lee S, Karp P, et al.
mSystems
. 2023 Feb;
8(2):e0120522.
PMID: 36749080
No abstract available.
13.
Karp P
Database (Oxford)
. 2022 Dec;
2022.
PMID: 36520791
This article offers thoughts on reviewing grant proposals for biological knowledgebases and databases (KDs) in the hope of aiding grant reviewers and applicants in addressing the issue of innovation. Assessing...
14.
Karp P, Paley S, Krummenacker M, Kothari A, Wannemuehler M, Phillips G
Front Bioinform
. 2022 Oct;
2:869150.
PMID: 36304298
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A...
15.
Proctor A, Parvinroo S, Richie T, Jia X, Lee S, Karp P, et al.
mSystems
. 2022 Aug;
7(5):e0029322.
PMID: 35968975
Animals colonized with a defined microbiota represent useful experimental systems to investigate microbiome function. The altered Schaedler flora (ASF) represents a consortium of eight murine bacterial species that have been...
16.
de Crecy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, et al.
Database (Oxford)
. 2022 Aug;
2022.
PMID: 35961013
Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of...
17.
Latendresse M, Ong W, Karp P
Methods Mol Biol
. 2021 Oct;
2349:259-289.
PMID: 34718999
The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA). MetaFlux offers four modes of operation: (1) solving mode executes an FBA model...
18.
Keseler I, Gama-Castro S, Mackie A, Billington R, Bonavides-Martinez C, Caspi R, et al.
Front Microbiol
. 2021 Aug;
12:711077.
PMID: 34394059
The EcoCyc model-organism database collects and summarizes experimental data for K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways,...
19.
Paley S, Karp P
BMC Bioinformatics
. 2021 Apr;
22(1):208.
PMID: 33882841
Background: The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network...
20.
Paley S, Keseler I, Krummenacker M, Karp P
Front Microbiol
. 2021 Mar;
12:614355.
PMID: 33763039
Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced...