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Journal Articles
- 2017
[j15]Liam D. H. Elbourne
, Sasha G. Tetu, Karl A. Hassan, Ian T. Paulsen:
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res. 45(Database-Issue): D320-D324 (2017)- [j14]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) - 2014
- [j13]Daniel S. Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen, Peter D. Karp:
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst. Biol. 8: 79 (2014) - 2013
- [j12]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) - 2011
- [j11]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) - 2010
- [j10]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) - 2009
- [j9]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) - 2007
- [j8]Qinghu Ren, Kaixi Chen, Ian T. Paulsen:
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res. 35(Database-Issue): 274-279 (2007) - 2005
- [j7]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) - [j6]Qinghu Ren, Ian T. Paulsen:
Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. PLoS Comput. Biol. 1(3) (2005) - 2004
- [j5]Qinghu Ren, Katherine H. Kang, Ian T. Paulsen:
TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res. 32(Database-Issue): 284-288 (2004) - 2003
- [j4]Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, David S. Roos:
ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Res. 31(1): 234-236 (2003) - 2002
- [j3]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) - 2001
- [j2]Daniel H. Haft, Brendan J. Loftus, Delwood L. Richardson, Fan Yang, Jonathan A. Eisen, Ian T. Paulsen, Owen White:
TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29(1): 41-43 (2001) - 2000
- [j1]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)
Conference and Workshop Papers
- 2008
- [c1]Thomas J. Lee, Ian T. Paulsen, Peter D. Karp:
Annotation-based inference of transporter function. ISMB 2008: 259-267
Coauthor Index
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