Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. - Marie desJardins; Peter D. Karp; Markus Krummenacker; Thomas J. Lee; Christos A. Ouzounis (ISMB, 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)

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)

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

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)

Construction and completion of flux balance models from pathway databases. - Mario Latendresse; Markus Krummenacker; Miles Trupp; Peter D. Karp (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)

Computing minimal nutrient sets from metabolic networks via linear constraint solving. - Steven Eker; Markus Krummenacker; Alexander Glennon Shearer; Ashish Tiwari 001; Ingrid M. Keseler; Carolyn L. Talcott; Peter D. Karp (BMC Bioinform., 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)

Optimal metabolic route search based on atom mappings. - Mario Latendresse; Markus Krummenacker; Peter D. Karp (Bioinform., 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; 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)

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)

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 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)

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)

SynRoute: A Retrosynthetic Planning Software. - Mario Latendresse; Jeremiah P. Malerich; James Herson; Markus Krummenacker; Judy Szeto; Vi-Anh Vu; Nathan Collins; Peter B. Madrid (J. Chem. Inf. Model., 2023)