A Storage System for Scalable Knowledge Representation. - Peter D. Karp; Suzanne M. Paley; Ira B. Greenberg (CIKM, 1994)

Representations of Metabolic Knowledge: Pathways. - Peter D. Karp; Suzanne M. Paley (ISMB, 1994)

Knowledge Representation in the Large. - Peter D. Karp; Suzanne M. Paley (IJCAI (1), 1995)

HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. - Peter D. Karp; Christos A. Ouzounis; Suzanne M. Paley (ISMB, 1996)

Integrated Access to Metabolic and Genomic Data. - Peter D. Karp; Suzanne M. Paley (J. Comput. Biol., 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)

A Generic Knowledge-Base Browser and Editor. - Suzanne M. Paley; John D. Lowrance; Peter D. Karp (AAAI/IAAI, 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)

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)

A Collaborative Environment for Authoring Large Knowledge Bases. - Peter D. Karp; Vinay K. Chaudhri; Suzanne M. Paley (J. Intell. Inf. Syst., 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)

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)

Database verification studies of SWISS-PROT and GenBank. - Peter D. Karp; Suzanne M. Paley; Jingchun Zhu (Bioinform., 2001)

The Pathway Tools software. - Peter D. Karp; Suzanne M. Paley; Pedro Romero (ISMB, 2002)

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. - Suzanne M. Paley; Peter D. Karp (Bioinform., 2002)

The MetaCyc Database. - Peter D. Karp; Monica Riley; Suzanne M. Paley; Alida Pellegrini-Toole (Nucleic Acids Res., 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)

An Evidence Ontology for Use in Pathway/Genome Databases. - Peter D. Karp; Suzanne M. Paley; Cynthia J. Krieger; Peifen Zhang (Pacific Symposium on Biocomputing, 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)

Querying and computing with BioCyc databases. - Markus Krummenacker; Suzanne M. Paley; Lukas A. Mueller; Thomas Yan; Peter D. Karp (Bioinform., 2005)

EcoCyc: a comprehensive database resource for Escherichia coli. - 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)

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; et al. (Nucleic Acids Res., 2006)

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; et al. (Nucleic Acids Res., 2008)

EcoCyc: A comprehensive view of Escherichia coli 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; et al. (Nucleic Acids Res., 2009)

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; et al. (Briefings Bioinform., 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; et al. (Nucleic Acids Res., 2010)

Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges. - Peter D. Karp; Mario Latendresse; Suzanne M. Paley (Human Vision and Electronic Imaging, 2011)

EcoCyc: a comprehensive database of Escherichia coli 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; et al. (Nucleic Acids Res., 2011)

Regulatory network operations in the Pathway Tools software. - Suzanne M. Paley; Mario Latendresse; Peter D. Karp (BMC Bioinform., 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; et al. (Nucleic Acids Res., 2012)

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)

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; et al. (Nucleic Acids Res., 2013)

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; et al. (Nucleic Acids Res., 2014)

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; et al. (Briefings Bioinform., 2016)

Representation and inference of cellular architecture for metabolic reconstruction and modeling. - Suzanne M. Paley; Markus Krummenacker; Peter D. Karp (Bioinform., 2016)

Pathway collages: personalized multi-pathway diagrams. - Suzanne M. Paley; Paul E. O'Maille; Daniel S. Weaver; Peter D. Karp (BMC Bioinform., 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; et al. (Nucleic Acids Res., 2016)

Update notifications for the BioCyc collection of databases. - Suzanne M. Paley; Peter D. Karp (Database J. Biol. Databases Curation, 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; et al. (Nucleic Acids Res., 2017)

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; et al. (Nucleic Acids Res., 2018)

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; et al. (Briefings Bioinform., 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 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)

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)

The BioCyc Metabolic Network Explorer. - Suzanne M. Paley; Peter D. Karp (BMC Bioinform., 2021)

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)

Visual analysis of multi-omics data. - Austin Swart; Ron Caspi; Suzanne M. Paley; Peter D. Karp (Frontiers Bioinform., 2024)