Peter D. Karp

According to our database1, Peter D. Karp authored at least 102 papers between 1989 and 2022.

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Bibliography

2022
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation.
Database J. Biol. Databases Curation, 2022

A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation, 2022

2021
The BioCyc Metabolic Network Explorer.
BMC Bioinform., 2021

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.
Briefings Bioinform., 2021

2020
The MetaCyc database of metabolic pathways and enzymes - a 2019 update.
Nucleic Acids Res., 2020

Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models.
Bioinform., 2020

2019
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database.
BMC Bioinform., 2019

The BioCyc collection of microbial genomes and metabolic pathways.
Briefings Bioinform., 2019

2018
The MetaCyc database of metabolic pathways and enzymes.
Nucleic Acids Res., 2018

How accurate is automated gap filling of metabolic models?
BMC Syst. Biol., 2018

Evaluation of reaction gap-filling accuracy by randomization.
BMC Bioinform., 2018

2017
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Nucleic Acids Res., 2017

Update notifications for the BioCyc collection of databases.
Database J. Biol. Databases Curation, 2017

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.
Briefings Bioinform., 2017

2016
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res., 2016

Pathway collages: personalized multi-pathway diagrams.
BMC Bioinform., 2016

Representation and inference of cellular architecture for metabolic reconstruction and modeling.
Bioinform., 2016

Crowd-sourcing and author submission as alternatives to professional curation.
Database J. Biol. Databases Curation, 2016

How much does curation cost?
Database J. Biol. Databases Curation, 2016

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Briefings Bioinform., 2016

2015
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
PLoS Comput. Biol., 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.
Bioinform., 2015

2014
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.
Nucleic Acids Res., 2014

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic Acids Res., 2014

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database.
BMC Syst. Biol., 2014

Optimal metabolic route search based on atom mappings.
Bioinform., 2014

Curation accuracy of model organism databases.
Database J. Biol. Databases Curation, 2014

2013
EcoCyc: fusing model organism databases with systems biology.
Nucleic Acids Res., 2013

Computing minimal nutrient sets from metabolic networks via linear constraint solving.
BMC Bioinform., 2013

A systematic comparison of the MetaCyc and KEGG pathway databases.
BMC Bioinform., 2013

Groups: knowledge spreadsheets for symbolic biocomputing.
Database J. Biol. Databases Curation, 2013

2012
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res., 2012

Accurate Atom-Mapping Computation for Biochemical Reactions.
J. Chem. Inf. Model., 2012

Regulatory network operations in the Pathway Tools software.
BMC Bioinform., 2012

Construction and completion of flux balance models from pathway databases.
Bioinform., 2012

2011
EcoCyc: a comprehensive database of <i>Escherichia coli</i> biology.
Nucleic Acids Res., 2011

Web-Based Metabolic Network Visualization with a Zooming User Interface.
BMC Bioinform., 2011

Discovering novel subsystems using comparative genomics.
Bioinform., 2011

Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges.
Proceedings of the Human Vision and Electronic Imaging XVI, 2011

2010
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res., 2010

A systematic study of genome context methods: calibration, normalization and combination.
BMC Bioinform., 2010

Machine learning methods for metabolic pathway prediction.
BMC Bioinform., 2010

An advanced web query interface for biological databases.
Database J. Biol. Databases Curation, 2010

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Briefings Bioinform., 2010

Development of Large Scientific Knowledge Bases.
Proceedings of the ICAART 2010 - Proceedings of the International Conference on Agents and Artificial Intelligence, Volume 1, 2010

Databases and Algorithms for Pathway Bioinformatics.
Proceedings of the HEALTHINF 2010, 2010

2009
EcoCyc: A comprehensive view of <i>Escherichia coli</i> biology.
Nucleic Acids Res., 2009

2008
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic Acids Res., 2008

Annotation-based inference of transporter function.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

2007
A survey of orphan enzyme activities.
BMC Bioinform., 2007

Using genome-context data to identify specific types of functional associations in pathway/genome databases.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic Acids Res., 2006

The comprehensive updated regulatory network of <i>Escherichia coli </i>K-12.
BMC Bioinform., 2006

BioWarehouse: a bioinformatics database warehouse toolkit.
BMC Bioinform., 2006

2005
EcoCyc: a comprehensive database resource for <i>Escherichia coli</i>.
Nucleic Acids Res., 2005

Querying and computing with BioCyc databases.
Bioinform., 2005

2004
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic Acids Res., 2004

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
BMC Bioinform., 2004

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.
Bioinform., 2004

An Evidence Ontology for Use in Pathway/Genome Databases.
Proceedings of the Biocomputing 2004, 2004

2003
What Database Management System(s) Should Be Employed in Bioinformatics Applications?
OMICS, 2003

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
Bioinform., 2003

Genome, Pathway, and Interaction Bioinformatics - Session Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Pathway Bioinformatics.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
The EcoCyc Database.
Nucleic Acids Res., 2002

The MetaCyc Database.
Nucleic Acids Res., 2002

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
Bioinform., 2002

The Pathway Tools software.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001
Database verification studies of SWISS-PROT and GenBank.
Bioinform., 2001

Nutrition-Related Analysis of Pathway/Genome Databases.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Genome, Pathway and Interaction Bioinformatics - Session Introduction.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

2000
The EcoCyc and MetaCyc databases.
Nucleic Acids Res., 2000

An ontology for biological function based on molecular interactions.
Bioinform., 2000

An Evaluation of Ontology Exchange Languages for Bioinformatics.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res., 1999

A Collaborative Environment for Authoring Large Knowledge Bases.
J. Intell. Inf. Syst., 1999

1998
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res., 1998

OKBC: A Programmatic Foundation for Knowledge Base Interoperability.
Proceedings of the Fifteenth National Conference on Artificial Intelligence and Tenth Innovative Applications of Artificial Intelligence Conference, 1998

1997
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.
Nucleic Acids Res., 1997

Estimation of equilibrium constants using automated group contribution methods.
Comput. Appl. Biosci., 1997

Querying Schema Information.
Proceedings of the Intelligent Access to Heterogeneous Information, 1997

Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

A Generic Knowledge-Base Browser and Editor.
Proceedings of the Fourteenth National Conference on Artificial Intelligence and Ninth Innovative Applications of Artificial Intelligence Conference, 1997

1996
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res., 1996

Integrated Access to Metabolic and Genomic Data.
J. Comput. Biol., 1996

HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

Three Models of Gene Regulation in E.coli.
Proceedings of the German Conference on Bioinformatics, 1996

1995
A Strategy for Database Interoperation.
J. Comput. Biol., 1995

Knowledge Representation in the Large.
Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, 1995

The Generic Frame Protocol.
Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, 1995

1994
The Grasper-CL Graph Management System.
LISP Symb. Comput., 1994

Representing, Analyzing, and Synthesizing Biochemical Pathways.
IEEE Expert, 1994

Representations of Metabolic Knowledge: Pathways.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

A Storage System for Scalable Knowledge Representation.
Proceedings of the Third International Conference on Information and Knowledge Management (CIKM'94), Gaithersburg, Maryland, USA, November 29, 1994

1993
Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology.
Mach. Learn., 1993

Detection and elimination of inference channels in multilevel relational database systems.
Proceedings of the 1993 IEEE Computer Society Symposium on Research in Security and Privacy, 1993

Representations of Metabolic Knowledge.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

1992
A knowledge base of the chemical compounds of intermediary metabolism.
Comput. Appl. Biosci., 1992

1991
Artificial intelligence methods for theory representation and hypothesis formation.
Comput. Appl. Biosci., 1991

1990
Hypothesis Formation and Qualitative Reasoning in Molecular Biology.
AI Mag., 1990

1989
Hypothesis formation and qualitative reasoning in molecular biology.
PhD thesis, 1989


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