Markus Krummenacker

Publication Activity (10 Years)

Years Active: 1997-2023
Publications (10 Years): 10

Top Topics

High Throughput

Metabolic Pathways

Biological Systems

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Mario Latendresse, Jeremiah P. Malerich, James Herson, Markus Krummenacker, Judy Szeto, Vi-Anh Vu, Nathan Collins, Peter B. Madrid
SynRoute: A Retrosynthetic Planning Software. J. Chem. Inf. Model. 63 (17) (2023)
Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips
Pathway Tools Management of Pathway/Genome Data for Microbial Communities. Frontiers Bioinform. 2 (2022)
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
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. Briefings Bioinform. 22 (1) (2021)
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
The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
The BioCyc collection of microbial genomes and metabolic pathways. Briefings Bioinform. 20 (4) (2019)
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
The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res. 46 (Database-Issue) (2018)
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
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res. 45 (Database-Issue) (2017)
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
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44 (Database-Issue) (2016)
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
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Briefings Bioinform. 17 (5) (2016)
Suzanne M. Paley, Markus Krummenacker, Peter D. Karp
Representation and inference of cellular architecture for metabolic reconstruction and modeling. Bioinform. 32 (7) (2016)
Mario Latendresse, Markus Krummenacker, Peter D. Karp
Optimal metabolic route search based on atom mappings. Bioinform. 30 (14) (2014)
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
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 42 (Database-Issue) (2014)
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
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41 (Database-Issue) (2013)
Steven Eker, Markus Krummenacker, Alexander Glennon Shearer, Ashish Tiwari, Ingrid M. Keseler, Carolyn L. Talcott, Peter D. Karp
Computing minimal nutrient sets from metabolic networks via linear constraint solving. BMC Bioinform. 14 (2013)
Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp
Construction and completion of flux balance models from pathway databases. Bioinform. 28 (3) (2012)
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
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40 (Database-Issue) (2012)
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
biology. Nucleic Acids Res. 39 (Database-Issue) (2011)
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
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 38 (Database-Issue) (2010)
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
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings Bioinform. 11 (1) (2010)
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
biology. Nucleic Acids Res. 37 (Database-Issue) (2009)
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
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 36 (Database-Issue) (2008)
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
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34 (Database-Issue) (2006)
Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp
Querying and computing with BioCyc databases. Bioinform. 21 (16) (2005)
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 27 (1) (1999)
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 26 (1) (1998)
Marie desJardins, Peter D. Karp, Markus Krummenacker, Thomas J. Lee, Christos A. Ouzounis
Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. ISMB (1997)
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism. Nucleic Acids Res. 25 (1) (1997)