Suzanne M. Paley

47 papers A* 1A 4Misc 1Journal 39Unranked 2
YearRankTypeTitle / Venue / Authors
2024 J jnl
Visual analysis of multi-omics data.
Frontiers Bioinform.
Austin Swart, Ron Caspi, Suzanne M. Paley, Peter D. Karp
2022 J jnl
Pathway Tools Management of Pathway/Genome Data for Microbial Communities.
Frontiers Bioinform.
Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips
2021 J jnl
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.
Briefings Bioinform.
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
2021 J jnl
The BioCyc Metabolic Network Explorer.
BMC Bioinform.
Suzanne M. Paley, Peter D. Karp
2020 J jnl
The MetaCyc database of metabolic pathways and enzymes - a 2019 update.
Nucleic Acids Res.
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
2019 J jnl
The BioCyc collection of microbial genomes and metabolic pathways.
Briefings Bioinform.
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
2019 J jnl
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database.
BMC Bioinform.
Suzanne M. Paley, Peter D. Karp
2018 J jnl
The MetaCyc database of metabolic pathways and enzymes.
Nucleic Acids Res.
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
2017 J jnl
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Nucleic Acids Res.
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
2017 J jnl
Update notifications for the BioCyc collection of databases.
Database J. Biol. Databases Curation
Suzanne M. Paley, Peter D. Karp
2016 J jnl
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Briefings Bioinform.
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
2016 J jnl
Pathway collages: personalized multi-pathway diagrams.
BMC Bioinform.
Suzanne M. Paley, Paul E. O'Maille, Daniel S. Weaver, Peter D. Karp
2016 J jnl
Representation and inference of cellular architecture for metabolic reconstruction and modeling.
Bioinform.
Suzanne M. Paley, Markus Krummenacker, Peter D. Karp
2016 J jnl
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res.
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
2014 J jnl
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic Acids Res.
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
2013 J jnl
EcoCyc: fusing model organism databases with systems biology.
Nucleic Acids Res.
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
2013 J jnl
Groups: knowledge spreadsheets for symbolic biocomputing.
Database J. Biol. Databases Curation
Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp
2012 J jnl
Regulatory network operations in the Pathway Tools software.
BMC Bioinform.
Suzanne M. Paley, Mario Latendresse, Peter D. Karp
2012 J jnl
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res.
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
2011 J jnl
EcoCyc: a comprehensive database of
Nucleic Acids Res.
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
2011 — conf
Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges.
Human Vision and Electronic Imaging
Peter D. Karp, Mario Latendresse, Suzanne M. Paley
2010 J jnl
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Briefings Bioinform.
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
2010 J jnl
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Nucleic Acids Res.
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
2009 J jnl
EcoCyc: A comprehensive view of
Nucleic Acids Res.
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
2008 J jnl
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Nucleic Acids Res.
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
2006 J jnl
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic Acids Res.
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
2005 J jnl
EcoCyc: a comprehensive database resource for
Nucleic Acids Res.
Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp
2005 J jnl
Querying and computing with BioCyc databases.
Bioinform.
Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp
2004 Misc conf
An Evidence Ontology for Use in Pathway/Genome Databases.
Pacific Symposium on Biocomputing
Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang
2004 J jnl
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Nucleic Acids Res.
Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne M. Paley, Martha Arnaud, John Pick, Seung Yon Rhee, Peter D. Karp
2002 J jnl
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
Bioinform.
Suzanne M. Paley, Peter D. Karp
2002 J jnl
The EcoCyc Database.
Nucleic Acids Res.
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
2002 J jnl
The MetaCyc Database.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole
2002 A conf
The Pathway Tools software.
ISMB
Peter D. Karp, Suzanne M. Paley, Pedro Romero
2001 J jnl
Database verification studies of SWISS-PROT and GenBank.
Bioinform.
Peter D. Karp, Suzanne M. Paley, Jingchun Zhu
2000 J jnl
The EcoCyc and MetaCyc databases.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-Toole
1999 J jnl
A Collaborative Environment for Authoring Large Knowledge Bases.
J. Intell. Inf. Syst.
Peter D. Karp, Vinay K. Chaudhri, Suzanne M. Paley
1999 J jnl
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
1998 J jnl
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
1997 — conf
A Generic Knowledge-Base Browser and Editor.
AAAI/IAAI
Suzanne M. Paley, John D. Lowrance, Peter D. Karp
1997 J jnl
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
1996 J jnl
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.
Nucleic Acids Res.
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole
1996 A conf
HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae.
ISMB
Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley
1996 J jnl
Integrated Access to Metabolic and Genomic Data.
J. Comput. Biol.
Peter D. Karp, Suzanne M. Paley
1995 A* conf
Knowledge Representation in the Large.
IJCAI (1)
Peter D. Karp, Suzanne M. Paley
1994 A conf
A Storage System for Scalable Knowledge Representation.
CIKM
Peter D. Karp, Suzanne M. Paley, Ira B. Greenberg
1994 A conf
Representations of Metabolic Knowledge: Pathways.
ISMB
Peter D. Karp, Suzanne M. Paley