Suzanne M. Paley

According to our database, Suzanne M. Paley authored at least 46 papers between 1994 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2022

Pathway Tools Management of Pathway/Genome Data for Microbial Communities.

Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips

Frontiers Bioinform., 2022

2021

The BioCyc Metabolic Network Explorer.

Suzanne M. Paley, Peter D. Karp

BMC Bioinform., 2021

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

Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol A. Fulcher, Ingrid M. Keseler, Suzanne M. Paley

Briefings Bioinform., 2021

2020

The MetaCyc database of metabolic pathways and enzymes - a 2019 update.

Ron Caspi, Richard Billington, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp

Nucleic Acids Res., 2020

2019

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

Suzanne M. Paley, Peter D. Karp

BMC Bioinform., 2019

The BioCyc collection of microbial genomes and metabolic pathways.

Peter D. Karp, Richard Billington, Ron Caspi, Carol A. Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M. Keseler, Markus Krummenacker, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti

Briefings Bioinform., 2019

2018

The MetaCyc database of metabolic pathways and enzymes.

Ron Caspi, Richard Billington, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp

Nucleic Acids Res., 2018

2017

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol A. Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Martín Peralta-Gil, Pallavi Subhraveti, David A. Velázquez-Ramírez, Daniel S. Weaver, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp

Nucleic Acids Res., 2017

Update notifications for the BioCyc collection of databases.

Suzanne M. Paley, Peter D. Karp

Database J. Biol. Databases Curation, 2017

2016

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, Peter D. Karp

Nucleic Acids Res., 2016

Pathway collages: personalized multi-pathway diagrams.

Suzanne M. Paley, Paul E. O'Maille, Daniel S. Weaver, Peter D. Karp

BMC Bioinform., 2016

Representation and inference of cellular architecture for metabolic reconstruction and modeling.

Suzanne M. Paley, Markus Krummenacker, Peter D. Karp

Bioinform., 2016

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

Peter D. Karp, Mario Latendresse, Suzanne M. Paley, Markus Krummenacker, Quang Ong, Richard Billington, Anamika Kothari, Daniel S. Weaver, Thomas J. Lee, Pallavi Subhraveti, Aaron Spaulding, Carol A. Fulcher, Ingrid M. Keseler, Ron Caspi

Briefings Bioinform., 2016

2014

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp

Nucleic Acids Res., 2014

2013

EcoCyc: fusing model organism databases with systems biology.

Ingrid M. Keseler, Amanda Mackie, Martín Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol A. Fulcher, Araceli M. Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Imke Schröder, Alexander Glennon Shearer, Pallavi Subhraveti, Michael Travers, Deepika Weerasinghe, Verena Weiss, Julio Collado-Vides, Robert P. Gunsalus, Ian T. Paulsen, Peter D. Karp

Nucleic Acids Res., 2013

Groups: knowledge spreadsheets for symbolic biocomputing.

Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp

Database J. Biol. Databases Curation, 2013

2012

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Ron Caspi, Tomer Altman, Kate Dreher, Carol A. Fulcher, Pallavi Subhraveti, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Anuradha Pujar, Alexander Glennon Shearer, Michael Travers, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp

Nucleic Acids Res., 2012

Regulatory network operations in the Pathway Tools software.

Suzanne M. Paley, Mario Latendresse, Peter D. Karp

BMC Bioinform., 2012

2011

EcoCyc: a comprehensive database of <i>Escherichia coli</i> biology.

Ingrid M. Keseler, Julio Collado-Vides, Alberto Santos-Zavaleta, Martín Peralta-Gil, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martínez, Suzanne M. Paley, Markus Krummenacker, Tomer Altman, Pallavi Kaipa, Aaron Spaulding, John Pacheco, Mario Latendresse, Carol A. Fulcher, Malabika Sarker, Alexander Glennon Shearer, Amanda Mackie, Ian T. Paulsen, Robert P. Gunsalus, Peter D. Karp

Nucleic Acids Res., 2011

Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges.

Peter D. Karp, Mario Latendresse, Suzanne M. Paley

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.

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne M. Paley, Liviu Popescu, Anuradha Pujar, Alexander Glennon Shearer, Peifen Zhang, Peter D. Karp

Nucleic Acids Res., 2010

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

Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Mario Latendresse, Joseph M. Dale, Thomas J. Lee, Pallavi Kaipa, Fred Gilham, Aaron Spaulding, Liviu Popescu, Tomer Altman, Ian T. Paulsen, Ingrid M. Keseler, Ron Caspi

Briefings Bioinform., 2010

2009

EcoCyc: A comprehensive view of <i>Escherichia coli</i> biology.

Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides, Socorro Gama-Castro, Robert P. Gunsalus, D. Aaron Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Alberto D. Santos-Zavaleta, Alexander Glennon Shearer, Peter D. Karp

Nucleic Acids Res., 2009

2008

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Yon Rhee, Alexander Glennon Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, Peter D. Karp

Nucleic Acids Res., 2008

2006

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne M. Paley, John Pick, Seung Yon Rhee, Christophe Tissier, Peifen Zhang, Peter D. Karp

Nucleic Acids Res., 2006

2005

EcoCyc: a comprehensive database resource for <i>Escherichia coli</i>.

Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp

Nucleic Acids Res., 2005

Querying and computing with BioCyc databases.

Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp

Bioinform., 2005

2004

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne M. Paley, Martha Arnaud, John Pick, Seung Yon Rhee, Peter D. Karp

Nucleic Acids Res., 2004

An Evidence Ontology for Use in Pathway/Genome Databases.

Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang

Proceedings of the Biocomputing 2004, 2004

2002

The EcoCyc Database.

Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, Alida Pellegrini-Toole, César Bonavides-Martínez, Socorro Gama-Castro

Nucleic Acids Res., 2002

The MetaCyc Database.

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole

Nucleic Acids Res., 2002

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

Suzanne M. Paley, Peter D. Karp

Bioinform., 2002

The Pathway Tools software.

Peter D. Karp, Suzanne M. Paley, Pedro Romero

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001

Database verification studies of SWISS-PROT and GenBank.

Peter D. Karp, Suzanne M. Paley, Jingchun Zhu

Bioinform., 2001

2000

The EcoCyc and MetaCyc databases.

Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-Toole

Nucleic Acids Res., 2000

1999

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker

Nucleic Acids Res., 1999

A Collaborative Environment for Authoring Large Knowledge Bases.

Peter D. Karp, Vinay K. Chaudhri, Suzanne M. Paley

J. Intell. Inf. Syst., 1999

1998

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker

Nucleic Acids Res., 1998

1997

EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker

Nucleic Acids Res., 1997

A Generic Knowledge-Base Browser and Editor.

Suzanne M. Paley, John D. Lowrance, Peter D. Karp

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.

Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole

Nucleic Acids Res., 1996

Integrated Access to Metabolic and Genomic Data.

Peter D. Karp, Suzanne M. Paley

J. Comput. Biol., 1996

HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae.

Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1995

Knowledge Representation in the Large.

Peter D. Karp, Suzanne M. Paley

Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, 1995

1994

Representations of Metabolic Knowledge: Pathways.

Peter D. Karp, Suzanne M. Paley

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

A Storage System for Scalable Knowledge Representation.

Peter D. Karp, Suzanne M. Paley, Ira B. Greenberg

Proceedings of the Third International Conference on Information and Knowledge Management (CIKM'94), Gaithersburg, Maryland, USA, November 29, 1994