Author details

Full Name

Peter D Karp

Affiliation

Pangea Systems Inc., USA and Marine Biological Laboratory

ORCID

Career Start Year

1981

Papers

146

H Index

Expertise

CM4AI Collaborator

Gloria M Sheynkman (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36749080	Erratum for Proctor et al., "Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function".	mSystems	2023
37220074	The EcoCyc Database (2023).	EcoSal Plus	2023
34718999	Metabolic Modeling with MetaFlux.	Methods Mol Biol	2022
36520791	Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation.	Database (Oxford)	2022
35968975	Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function.	mSystems	2022
36304298	Pathway Tools Management of Pathway/Genome Data for Microbial Communities.	Front Bioinform	2022
35961013	A roadmap for the functional annotation of protein families: a community perspective.	Database (Oxford)	2022
31813964	Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.	Brief Bioinform	2021
33882841	The BioCyc Metabolic Network Explorer.	BMC Bioinformatics	2021
33763039	Leveraging Curation Among <i>Escherichia coli</i> Pathway/Genome Databases Using Ortholog-Based Annotation Propagation.	Front Microbiol	2021
33726670	Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics.	BMC Genomics	2021
33499002	Pathway Tools Visualization of Organism-Scale Metabolic Networks.	Metabolites	2021
34403192	Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.	J Integr Plant Biol	2021
34394059	The EcoCyc Database in 2021.	Front Microbiol	2021
31586394	The MetaCyc database of metabolic pathways and enzymes - a 2019 update.	Nucleic Acids Res	2020
31688932	Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models.	Bioinformatics	2020
33203762	Erratum for Tong et al., "Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments".	mBio	2020
32994326	Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments.	mBio	2020
32703847	Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.	Science	2020
29447345	The BioCyc collection of microbial genomes and metabolic pathways.	Brief Bioinform	2019
31319812	The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database.	BMC Bioinformatics	2019
31174602	Metabolic route computation in organism communities.	Microbiome	2019
30853946	A Comparison of Microbial Genome Web Portals.	Front Microbiol	2019
31052521	Using Pathway Covering to Explore Connections among Metabolites.	Metabolites	2019
28040748	How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.	Brief Bioinform	2018
29914471	How accurate is automated gap filling of metabolic models?	BMC Syst Biol	2018
30406744	The EcoCyc Database.	EcoSal Plus	2018
29444634	Evaluation of reaction gap-filling accuracy by randomization.	BMC Bioinformatics	2018
29059334	The MetaCyc database of metabolic pathways and enzymes.	Nucleic Acids Res	2018
27899573	The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.	Nucleic Acids Res	2017
28334156	How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.	Brief Bioinform	2017
29220477	Update notifications for the BioCyc collection of databases.	Database (Oxford)	2017
29040755	The Omics Dashboard for interactive exploration of gene-expression data.	Nucleic Acids Res	2017
26891337	The Time Is Right to Focus on Model Organism Metabolomes.	Metabolites	2016
26628588	Representation and inference of cellular architecture for metabolic reconstruction and modeling.	Bioinformatics	2016
26454094	Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.	Brief Bioinform	2016
26527732	The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.	Nucleic Acids Res	2016
28025341	Can we replace curation with information extraction software?	Database (Oxford)	2016
28025340	Crowd-sourcing and author submission as alternatives to professional curation.	Database (Oxford)	2016
27964719	Pathway collages: personalized multi-pathway diagrams.	BMC Bioinformatics	2016
27504008	How much does curation cost?	Database (Oxford)	2016
25644272	Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.	Bioinformatics	2015
26097686	ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.	F1000Res	2015
26011592	Computational Metabolomics Operations at BioCyc.org.	Metabolites	2015
24225315	The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.	Nucleic Acids Res	2014
26442933	The EcoCyc Database.	EcoSal Plus	2014
24974895	A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database.	BMC Syst Biol	2014
25048541	Metabolic pathways for the whole community.	BMC Genomics	2014
24894379	A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs.	Biol Direct	2014
24923819	Curation accuracy of model organism databases.	Database (Oxford)	2014

1 - 50 of 146

Neal Conrad

University of Chicago

Career Start Year 2016

Number of shared co-authors 5

Jos?? P Faria

Argonne National Laboratory

Career Start Year 2014

Number of shared co-authors 6

Nawar Al-Obaidi

Cardiovascular Research Unit, Newark Beth Israel Medical Center

Career Start Year 2013

Number of shared co-authors 6

Sara Calhoun

US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory

Career Start Year 2011

Number of shared co-authors 4

Janaka N Edirisinghe

Computation Institute, University of Chicago

Career Start Year 2011

Number of shared co-authors 7

Natalie J Stanford

University of Manchester

Career Start Year 2010

Number of shared co-authors 2

Marnix H Medema

Wageningen University

Career Start Year 2008

Number of shared co-authors 1

Fangfang Xia

University of Chicago

Career Start Year 2007

Number of shared co-authors 6

Neil Swainston

Institute of Systems, University of Liverpool

Career Start Year 2006

Number of shared co-authors 5

Mustafa H Syed

Memorial Sloan Kettering Cancer Center

Career Start Year 2006

Number of shared co-authors 4

Tomer Shlomi

Technion-Israel Institute of Technology

Career Start Year 2005

Number of shared co-authors 1

Takuji Yamada

Tokyo Institute of Technology

Career Start Year 2004

Number of shared co-authors 1

Morgan N Price

Lawrence Berkeley National Laboratory

Career Start Year 2004

Number of shared co-authors 2

Jeremy Zucker

Pacific Northwest National Laboratory

Career Start Year 2003

Number of shared co-authors 6

Vera van Noort

Leiden University, Institute of Biology Leiden

Career Start Year 2003

Number of shared co-authors 0

Hector Garcia Martin

Lawrence Berkeley National Laboratory

Career Start Year 2002

Number of shared co-authors 3

Ying Xu

The China-Japan Union Hospital, Jilin University

Career Start Year 2002

Number of shared co-authors 1

Nathan D Price

Institute for Systems Biology

Career Start Year 2002

Number of shared co-authors 4

Jason A Papin

University of Virginia

Career Start Year 2002

Number of shared co-authors 3

Aaron A Best

Hope College

Career Start Year 2001

Number of shared co-authors 8

Yunchen Gong

University of Toronto

Career Start Year 2000

Number of shared co-authors 0

Patrik D'haeseleer

Lawrence Livermore National Laboratory

Career Start Year 1999

Number of shared co-authors 5

Matthew Pocock

Newcastle University

Career Start Year 1998

Number of shared co-authors 2

Marcin P Joachimiak

E O Lawrence Berkeley National Laboratory, UCSF Medical Center, University of California, Berkeley, University of Chicago

Career Start Year 1997

Number of shared co-authors 10

Michelle Giglio

University of Maryland School of Medicine, Institute for Genome Sciences

Career Start Year 1996

Number of shared co-authors 40

Heidi J Sofia

National Human Genome Research Institute

Career Start Year 1993

Number of shared co-authors 1

Lee Ann McCue

Pacific Northwest National Laboratory

Career Start Year 1991

Number of shared co-authors 4

Adam P Arkin

Lawrence Berkeley National Laboratory

Career Start Year 1990

Number of shared co-authors 12

Peer Bork

University of Wurzburg

Career Start Year 1989

Number of shared co-authors 37

Jens Nielsen

Chalmers University of Technology

Career Start Year 1989

Number of shared co-authors 4

row(s) 1 - 30 of 30

Ingrid M Keseler

Co-authored papers 26

Ian T Paulsen

Macquarie University

Co-authored papers 18

Socorro Gama-Castro

Co-authored papers 12

Peter E Midford

University of Kansas

Co-authored papers 10

Lukas A Mueller

Boyce Thompson Institute (BTI)

Co-authored papers 8

Seung Y Rhee

Carnegie Institution for Science

Co-authored papers 6

Maria J Martin

European Bioinformatics Institute (EMBL-EBI)

Co-authored papers 2

Granger G Sutton

J. Craig Venter Institute

Co-authored papers 2

Russ B Altman

Stanford University

Co-authored papers 2

Pardis C Sabeti

Harvard University

Co-authored papers 2

John A Gerlt

University of Illinois at Urbana-Champaign

Co-authored papers 2

Alex Bateman

European Bioinformatics Institute (EMBL-EBI)

Co-authored papers 2

Christopher S Henry

Argonne National Laboratory

Co-authored papers 2

Paul D Thomas

University of Southern California

Co-authored papers 2

James C Hu

Texas A&M University and Texas Agrilife Research, College Station

Co-authored papers 2

Bernhard O Palsson

University of California San Diego

Co-authored papers 2

Michal Linial

Institute of Life Sciences, The Hebrew University of Jerusalem

Co-authored papers 2

Val??rie de Cr??cy-Lagard

University of Florida

Co-authored papers 2

Irina A Rodionova

University of California at San Diego

Co-authored papers 2

Deborah A Siegele

Texas A&M University, College Station

Co-authored papers 2

Iddo Friedberg

Iowa State University

Co-authored papers 2

Milton H Saier

University of California at San Diego

Co-authored papers 2

Bonnie Berger

Massachusetts Institute of Technology

Co-authored papers 2

Burkhard Rost

Technical University of Munich (TUM)

Co-authored papers 2

Winston Hide

Harvard Medical School

Co-authored papers 2

Claes Wahlestedt

Co-authored papers 2

Mark Gorelik

University of Florida

Co-authored papers 1

Simon Kasif

Boston University

Co-authored papers 1

David Vallenet

Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay

Co-authored papers 1

Richard J Roberts

Co-authored papers 1

1 - 30

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