Publications by authors named "Peter D Karp"

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The EcoCyc database (2025).
Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker

EcoSal Plus· December 2025

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Revisiting the y-ome of Escherichia coli.
Lisa R Moore, Ron Caspi, Dana Boyd, Mehmet Berkmen, Amanda Mackie, Peter D Karp

Nucleic Acids Res· November 2024

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Visual analysis of multi-omics data.
Austin Swart, Ron Caspi, Suzanne Paley, Peter D Karp

Front Bioinform· September 2024

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The Genome Explorer genome browser.
James Herson, Markus Krummenacker, Aaron Spaulding, Paul O'Maille, Peter D Karp

mSystems· July 2024

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The Comparative Genome Dashboard.
Suzanne Paley, Ron Caspi, Paul O'Maille, Peter D Karp

Front Microbiol· July 2024

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The Comparative Genome Dashboard.
Suzanne Paley, Ron Caspi, Paul O'Maille, Peter D Karp

bioRxiv· June 2024

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Improved BioCyc Operon Prediction: Revisiting the Operon Prediction Problem.
Peter E Midford, John Cadigan, Peter D Karp

bioRxiv· June 2024

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An evaluation of ChatGPT and Bard (Gemini) in the context of biological knowledge retrieval.
Ron Caspi, Peter D Karp

Access Microbiol· June 2024

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Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.
Gwanggyu Sun, Mialy M DeFelice, Taryn E Gillies, Travis A Ahn-Horst, Cecelia J Andrews, Peter D Karp

Cell Syst· March 2024

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The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data.
Suzanne Paley, Peter D Karp

Metabolites· January 2024

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CyanoCyc cyanobacterial web portal.
Lisa R Moore, Ron Caspi, Douglas A Campbell, John R Casey, Sophie Crevecoeur, Peter D Karp

Front Microbiol· January 2024

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The EcoCyc Database (2023).
Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker

EcoSal Plus· December 2023

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Erratum for Proctor et al., "Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function".
Alexandra Proctor, Shadi Parvinroo, Tanner Richie, Xinglin Jia, Sonny T M Lee, Peter D Karp

mSystems· April 2023

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Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation.
Peter D Karp

Database (Oxford)· December 2022

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Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function.
Alexandra Proctor, Shadi Parvinroo, Tanner Richie, Xinglin Jia, Sonny T M Lee, Peter D Karp

mSystems· October 2022

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A roadmap for the functional annotation of protein families: a community perspective.
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia Arighi, Jill Babor, Alex Bateman, Peter D Karp

Database (Oxford)· August 2022

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Pathway Tools Management of Pathway/Genome Data for Microbial Communities.
Peter D Karp, Suzanne Paley, Markus Krummenacker, Anamika Kothari, Michael J Wannemuehler

Front Bioinform· April 2022

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Metabolic Modeling with MetaFlux.
Mario Latendresse, Wai Kit Ong, Peter D Karp

Methods Mol Biol· January 2022

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The EcoCyc Database in 2021.
Ingrid M Keseler, Socorro Gama-Castro, Amanda Mackie, Richard Billington, César Bonavides-Martínez, Peter D Karp

Front Microbiol· July 2021

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The BioCyc Metabolic Network Explorer.
Suzanne Paley, Peter D Karp

BMC Bioinformatics· April 2021

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Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics.
Peter D Karp, Peter E Midford, Ron Caspi, Arkady Khodursky

BMC Genomics· March 2021

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Leveraging Curation Among Pathway/Genome Databases Using Ortholog-Based Annotation Propagation.
Suzanne Paley, Ingrid M Keseler, Markus Krummenacker, Peter D Karp

Front Microbiol· March 2021

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Pathway Tools Visualization of Organism-Scale Metabolic Networks.
Suzanne Paley, Richard Billington, James Herson, Markus Krummenacker, Peter D Karp

Metabolites· January 2021

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Erratum for Tong et al., "Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments".
Madeline Tong, Shawn French, Sara S El Zahed, Wai Kit Ong, Peter D Karp

mBio· November 2020

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Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments.
Madeline Tong, Shawn French, Sara S El Zahed, Wai Kit Ong, Peter D Karp

mBio· September 2020

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