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ORCIDSuzanne M. Paley
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2020 – today
- 2022
[j38]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)- 2021
- [j37]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): 109-126 (2021) - [j36]Suzanne M. Paley, Peter D. Karp:
The BioCyc Metabolic Network Explorer. BMC Bioinform. 22(1): 208 (2021) - 2020
- [j35]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): D445-D453 (2020)
2010 – 2019
- 2019
- [j34]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): 1085-1093 (2019) - [j33]Suzanne M. Paley, Peter D. Karp:
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database. BMC Bioinform. 20(1): 399:1-399:13 (2019) - 2018
- [j32]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): D633-D639 (2018) - 2017
- [j31]Suzanne M. Paley, Peter D. Karp:
Update notifications for the BioCyc collection of databases. Database J. Biol. Databases Curation 2017: bax086 (2017) - [j30]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): D543-D550 (2017) - 2016
- [j29]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): 877-890 (2016) - [j28]Suzanne M. Paley, Markus Krummenacker, Peter D. Karp:
Representation and inference of cellular architecture for metabolic reconstruction and modeling. Bioinform. 32(7): 1074-1079 (2016) - [j27]Suzanne M. Paley, Paul E. O'Maille, Daniel S. Weaver, Peter D. Karp:
Pathway collages: personalized multi-pathway diagrams. BMC Bioinform. 17: 529:1-529:10 (2016) - [j26]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): 471-480 (2016) - 2014
- [j25]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): 459-471 (2014) - 2013
- [j24]Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp:
Groups: knowledge spreadsheets for symbolic biocomputing. Database J. Biol. Databases Curation 2013 (2013) - [j23]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): 605-612 (2013) - 2012
- [j22]Suzanne M. Paley, Mario Latendresse, Peter D. Karp:
Regulatory network operations in the Pathway Tools software. BMC Bioinform. 13: 243 (2012) - [j21]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): 742-753 (2012) - 2011
- [j20]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:
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 39(Database-Issue): 583-590 (2011) - [c8]Peter D. Karp, Mario Latendresse, Suzanne M. Paley:
Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges. Human Vision and Electronic Imaging 2011: 78650G - 2010
- [j19]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): 40-79 (2010) - [j18]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): 473-479 (2010)
2000 – 2009
- 2009
- [j17]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:
EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37(Database-Issue): 464-470 (2009) - 2008
- [j16]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): 623-631 (2008) - 2006
- [j15]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): 511-516 (2006) - 2005
- [j14]Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp:
Querying and computing with BioCyc databases. Bioinform. 21(16): 3454-3455 (2005) - [j13]Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp:
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33(Database-Issue): 334-337 (2005) - 2004
- [j12]Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne M. Paley, Martha Arnaud, John Pick, Seung Yon Rhee, Peter D. Karp:
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32(Database-Issue): 438-442 (2004) - [c7]Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang:
An Evidence Ontology for Use in Pathway/Genome Databases. Pacific Symposium on Biocomputing 2004: 190-201 - 2002
- [j11]Suzanne M. Paley, Peter D. Karp:
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinform. 18(5): 715-724 (2002) - [j10]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:
The EcoCyc Database. Nucleic Acids Res. 30(1): 56-58 (2002) - [j9]Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole:
The MetaCyc Database. Nucleic Acids Res. 30(1): 59-61 (2002) - [c6]Peter D. Karp, Suzanne M. Paley, Pedro Romero:
The Pathway Tools software. ISMB 2002: 225-232 - 2001
- [j8]Peter D. Karp, Suzanne M. Paley, Jingchun Zhu:
Database verification studies of SWISS-PROT and GenBank. Bioinform. 17(6): 526-532 (2001) - 2000
- [j7]Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-Toole:
The EcoCyc and MetaCyc databases. Nucleic Acids Res. 28(1): 56-59 (2000)
1990 – 1999
- 1999
- [j6]Peter D. Karp, Vinay K. Chaudhri, Suzanne M. Paley:
A Collaborative Environment for Authoring Large Knowledge Bases. J. Intell. Inf. Syst. 13(3): 155-194 (1999) - [j5]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): 55-58 (1999) - 1998
- [j4]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): 50-53 (1998) - 1997
- [j3]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): 43-51 (1997) - [c5]Suzanne M. Paley, John D. Lowrance, Peter D. Karp:
A Generic Knowledge-Base Browser and Editor. AAAI/IAAI 1997: 1045-1051 - 1996
- [j2]Peter D. Karp, Suzanne M. Paley:
Integrated Access to Metabolic and Genomic Data. J. Comput. Biol. 3(1): 191-212 (1996) - [j1]Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole:
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 24(1): 32-39 (1996) - [c4]Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley:
HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. ISMB 1996: 116-124 - 1995
- [c3]Peter D. Karp, Suzanne M. Paley:
Knowledge Representation in the Large. IJCAI (1) 1995: 751-758 - 1994
- [c2]Peter D. Karp, Suzanne M. Paley, Ira B. Greenberg:
A Storage System for Scalable Knowledge Representation. CIKM 1994: 97-104 - [c1]Peter D. Karp, Suzanne M. Paley:
Representations of Metabolic Knowledge: Pathways. ISMB 1994: 203-211
Coauthor Index
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