Found: 21

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  • A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

    Published in:
    BMC Biology, 2018, v. 16, n. 1, p. 1, doi. 10.1186/s12915-018-0555-y
    By:
    • Santos-Zavaleta, Alberto;
    • Sánchez-Pérez, Mishael;
    • Salgado, Heladia;
    • Velázquez-Ramírez, David A.;
    • Gama-Castro, Socorro;
    • Tierrafría, Víctor H.;
    • Busby, Stephen J. W.;
    • Aquino, Patricia;
    • Fang, Xin;
    • Palsson, Bernhard O.;
    • Galagan, James E.;
    • Collado-Vides, Julio
    Publication type:
    Article

  • RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D212, doi. 10.1093/nar/gky1077
    By:
    • Santos-Zavaleta, Alberto;
    • Salgado, Heladia;
    • Gama-Castro, Socorro;
    • Sánchez-Pérez, Mishael;
    • Gómez-Romero, Laura;
    • Ledezma-Tejeida, Daniela;
    • García-Sotelo, Jair Santiago;
    • Alquicira-Hernández, Kevin;
    • Muñiz-Rascado, Luis José;
    • Peña-Loredo, Pablo;
    • Ishida-Gutiérrez, Cecilia;
    • Velázquez-Ramírez, David A;
    • Del Moral-Chávez, Víctor;
    • Bonavides-Martínez, César;
    • Méndez-Cruz, Carlos-Francisco;
    • Galagan, James;
    • Collado-Vides, Julio
    Publication type:
    Article

  • The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D543, doi. 10.1093/nar/gkw1003
    By:
    • Keseler, Ingrid M.;
    • Mackie, Amanda;
    • Santos-Zavaleta, Alberto;
    • Billington, Richard;
    • Bonavides-Martínez, César;
    • Caspi, Ron;
    • Fulcher, Carol;
    • Gama-Castro, Socorro;
    • Kothari, Anamika;
    • Krummenacker, Markus;
    • Latendresse, Mario;
    • Muñiz-Rascado, Luis;
    • Quang Ong;
    • Paley, Suzanne;
    • Peralta-Gil, Martin;
    • Subhraveti, Pallavi;
    • Velázquez-Ramírez, David A.;
    • Weaver, Daniel;
    • Collado-Vides, Julio;
    • Paulsen, Ian
    Publication type:
    Article

  • RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

    Published in:
    Nucleic Acids Research, 2016, v. 44, p. D133, doi. 10.1093/nar/gkv1156
    By:
    • Gama-Castro, Socorro;
    • Salgado, Heladia;
    • Santos-Zavaleta, Alberto;
    • Ledezma-Tejeida, Daniela;
    • Muñiz-Rascado, Luis;
    • García-Sotelo, Jair Santiago;
    • Alquicira-Hernández, Kevin;
    • Martínez-Flores, Irma;
    • Pannier, Lucia;
    • Castro-Mondragón, Jaime Abraham;
    • Medina-Rivera, Alejandra;
    • Solano-Lira, Hilda;
    • Bonavides-Martiníz, César;
    • Pérez-Rueda, Ernesto;
    • Alquicira-Hernández, Shirley;
    • Porrón-Sotelo, Liliana;
    • López-Fuentes, Alejandra;
    • Hernández-Koutoucheva, Anastasia;
    • Del Moral-Chávez, Víctor;
    • Rinaldi, Fabio
    Publication type:
    Article

  • RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

    Published in:
    Nucleic Acids Research, 2013, v. 41, p. D203, doi. 10.1093/nar/gks1201
    By:
    • Salgado, Heladia;
    • Peralta-Gil, Martin;
    • Gama-Castr, Socorro;
    • Santos-Zavaleta, Alberto;
    • Muñiz-Rascado, Luis;
    • García-Sotelo, Jair S.;
    • Weiss, Verena;
    • Solano-Lira, Hilda;
    • Martínez-Flores, Irma;
    • Medina-Rivera, Alejandra;
    • Salgado-Osorio, Gerardo;
    • Alquicira-Hernández, Shirley;
    • López-Fuentes, Alejandra;
    • Porrón-Sotelo, Liliana;
    • Huerta, Araceli M.;
    • Bonavides-Martínez, César;
    • Balderas-Martínez, Yalbi I.;
    • Pannier, Lucia;
    • Olvera, Maricela;
    • Labastida, Aurora
    Publication type:
    Article

  • EcoCyc: fusing model organism databases with systems biology.

    Published in:
    Nucleic Acids Research, 2013, v. 41, p. D605, doi. 10.1093/nar/gks1027
    By:
    • Keseler, Ingrid M.;
    • Mackie, Amanda;
    • Peralta-Gil, Martin;
    • Santos-Zavaleta, Alberto;
    • Gama-Castro, Socorro;
    • Bonavides-Martínez, César;
    • Fulcher, Carol;
    • Huerta, Araceli M.;
    • Kothari, Anamika;
    • Krummenacker, Markus;
    • Latendresse, Mario;
    • Muñiz-Rascado, Luis;
    • Quang Ong;
    • Paley, Suzanne;
    • Schröder, Imke;
    • Shearer, Alexander G.;
    • Subhraveti, Pallavi;
    • Travers, Mike;
    • Weerasinghe, Deepika;
    • Weiss, Verena
    Publication type:
    Article

  • RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

    Published in:
    Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D98, doi. 10.1093/nar/gkq1110
    By:
    • Gama-Castro, Socorro;
    • Salgado, Heladia;
    • Peralta-Gil, Martin;
    • Santos-Zavaleta, Alberto;
    • Muñiz-Rascado, Luis;
    • Solano-Lira, Hilda;
    • Jimenez-Jacinto, Verónica;
    • Weiss, Verena;
    • García-Sotelo, Jair S.;
    • López-Fuentes, Alejandra;
    • Porrón-Sotelo, Liliana;
    • Alquicira-Hernández, Shirley;
    • Medina-Rivera, Alejandra;
    • Martínez-Flores, Irma;
    • Alquicira-Hernández, Kevin;
    • Martínez-Adame, Ruth;
    • Bonavides-Martínez, César;
    • Miranda-Ríos, Juan;
    • Huerta, Araceli M.;
    • Mendoza-Vargas, Alfredo
    Publication type:
    Article

  • EcoCyc: a comprehensive database of Escherichia coli biology.

    Published in:
    Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D583, doi. 10.1093/nar/gkq1143
    By:
    • Keseler, Ingrid M.;
    • Collado-Vides, Julio;
    • Santos-Zavaleta, Alberto;
    • Peralta-Gil, Martin;
    • Gama-Castro, Socorro;
    • Muñiz-Rascado, Luis;
    • Bonavides-Martinez, César;
    • Paley, Suzanne;
    • Krummenacker, Markus;
    • Altman, Tomer;
    • Kaipa, Pallavi;
    • Spaulding, Aaron;
    • Pacheco, John;
    • Latendresse, Mario;
    • Fulcher, Carol;
    • Sarker, Malabika;
    • Shearer, Alexander G.;
    • Mackie, Amanda;
    • Paulsen, Ian;
    • Gunsalus, Robert P.
    Publication type:
    Article

  • EcoCyc: A comprehensive view of Escherichia coli biology.

    Published in:
    Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D464, doi. 10.1093/nar/gkn751
    By:
    • Keseler, Ingrid M.;
    • Bonavides-Martínez, César;
    • Collado-Vides, Julio;
    • Gama-Castro, Socorro;
    • Gunsalus, Robert P.;
    • Johnson, D. Aaron;
    • Krummenacker, Markus;
    • Nolan, Laura M.;
    • Paley, Suzanne;
    • Paulsen, Ian T.;
    • Peralta-Gil, Martin;
    • Santos-Zavaleta, Alberto;
    • Shearer, Alexander Glennon;
    • Karp, Peter D.
    Publication type:
    Article

  • RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

    Published in:
    Nucleic Acids Research, 2008, v. 36, p. D120
    By:
    • Gama-Castro, Socorro;
    • Jiménez-Jacinto, Verónica;
    • Peralta-Gil, Martín;
    • Santos-Zavaleta, Alberto;
    • Peñaloza-Spinola, Mónica I.;
    • Contreras-Moreira, Bruno;
    • Segura-Salazar, Juan;
    • Muñiz-Rascado, Luis;
    • Martínez-Flores, Irma;
    • Salgado, Heladia;
    • Bonavides-Martínez, César;
    • Abreu-Goodger, Cei;
    • Rodríguez-Penagos, Carlos;
    • Miranda-Ríos, Juan;
    • Morett, Enrique;
    • Merino, Enrique;
    • Huerta, Araceli M.;
    • Treviño-Quintanilla, Luis;
    • Collado-Vides, Julio
    Publication type:
    Article

  • Multidimensional annotation of the Escherichia coli K-12 genome.

    Published in:
    Nucleic Acids Research, 2007, v. 35, n. 22, p. 7577, doi. 10.1093/nar/gkm740
    By:
    • Karp, Peter D.;
    • Keseler, Ingrid M.;
    • Shearer, Alexander;
    • Latendresse, Mario;
    • Krummenacker, Markus;
    • Paley, Suzanne M.;
    • Paulsen, Ian;
    • Collado-Vides, Julio;
    • Gama-Castro, Socorro;
    • Peralta-Gil, Martin;
    • Santos-Zavaleta, Alberto;
    • Peñaloza-Spínola, Mónica I.;
    • Bonavides-Martinez, César;
    • Ingraham, John
    Publication type:
    Article

  • Similarity corpus on microbial transcriptional regulation.

    Published in:
    Journal of Biomedical Semantics, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13326-019-0200-x
    By:
    • Lithgow-Serrano, Oscar;
    • Gama-Castro, Socorro;
    • Ishida-Gutiérrez, Cecilia;
    • Mejía-Almonte, Citlalli;
    • Tierrafría, Víctor H.;
    • Martínez-Luna, Sara;
    • Santos-Zavaleta, Alberto;
    • Velázquez-Ramírez, David;
    • Collado-Vides, Julio
    Publication type:
    Article

  • Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2014, v. 2014, p. 1, doi. 10.1093/database/bau049
    By:
    • Gama-Castro, Socorro;
    • Rinaldi, Fabio;
    • López-Fuentes, Alejandra;
    • Itzel Balderas-Martínez, Yalbi;
    • Clematide, Simon;
    • Ellendorff, Tilia Renate;
    • Santos-Zavaleta, Alberto;
    • Marques-Madeira, Hernani;
    • Collado-Vides, Julio
    Publication type:
    Article

  • Evidence classification of high-throughput protocols and confidence integration in RegulonDB.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bas059
    By:
    • Weiss, Verena;
    • Medina-Rivera, Alejandra;
    • Huerta, Araceli M.;
    • Santos-Zavaleta, Alberto;
    • Salgado, Heladia;
    • Morett, Enrique;
    • Collado-Vides, Julio
    Publication type:
    Article

  • The comprehensive updated regulatory network of Escherichia coli K-12.

    Published in:
    BMC Bioinformatics, 2006, v. 7, p. 1, doi. 10.1186/1471-2105-7-5
    By:
    • Salgado, Heladia;
    • Santos-Zavaleta, Alberto;
    • Gama-Castro, Socorro;
    • Peralta-Gil, Martín;
    • Peñaloza-Spínola, Mónica I;
    • Martínez-Antonio, Agustino;
    • Karp, Peter D;
    • Collado-Vides, Julio
    Publication type:
    Article

  • RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.

    Published in:
    Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d394, doi. 10.1093/nar/gkj156
    By:
    • Salgado, Heladia;
    • Gama-Castro, Socorro;
    • Peralta-Gil, Martín;
    • Díaz-Peredo, Edgar;
    • Sánchez-Solano, Fabiola;
    • Santos-Zavaleta, Alberto;
    • Martínez-Flores, Irma;
    • Jiménez-Jacinto, Verónica;
    • Bonavides-Martínez, César;
    • Segura-Salazar, Juan;
    • Martínez-Antonio, Agustino;
    • Collado-Vides, Julio
    Publication type:
    Article

  • RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K‐12.

    Published in:
    Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d303
    By:
    • Salgado, Heladia;
    • Gama‐Castro, Socorro;
    • Martínez‐Antonio, Agustino;
    • Díaz‐Peredo, Edgar;
    • Sánchez‐Solano, Fabiola;
    • Peralta‐Gil, Martín;
    • Garcia‐Alonso, Delfino;
    • Jiménez‐Jacinto, Verónica;
    • Santos‐Zavaleta, Alberto;
    • Bonavides‐Martínez, César;
    • Collado‐Vides, Julio
    Publication type:
    Article

  • RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.

    Published in:
    Nucleic Acids Research, 2001, v. 29, n. 1, p. 72, doi. 10.1093/nar/29.1.72
    By:
    • Salgado, Heladia;
    • Santos-Zavaleta, Alberto;
    • Gama-Castro, Socorro;
    • Millán-Zárate, Dulce;
    • Díaz-Peredo, Edgar;
    • Sánchez-Solano, Fabiola;
    • Pérez-Rueda, Ernesto;
    • Bonavides-Martínez, César;
    • Collado-Vides, Julio
    Publication type:
    Article

  • PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites.

    Published in:
    Nucleic Acids Research, 2001, v. 29, n. 1, p. 277, doi. 10.1093/nar/29.1.277
    By:
    • Hershberg, Ruti;
    • Bejerano, Gill;
    • Santos-Zavaleta, Alberto;
    • Margalit, Hanah
    Publication type:
    Article

  • RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.

    Published in:
    Nucleic Acids Research, 2000, v. 28, n. 1, p. 65, doi. 10.1093/nar/28.1.65
    By:
    • Salgado, Heladia;
    • Santos-Zavaleta, Alberto;
    • Gama-Castro, Socorro;
    • Millán-Zárate, Dulce;
    • Blattner, Frederick R.;
    • Collado-Vides, Julio
    Publication type:
    Article

  • The EcoCyc Database in 2021.

    Published in:
    Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.711077
    By:
    • Keseler, Ingrid M.;
    • Gama-Castro, Socorro;
    • Mackie, Amanda;
    • Billington, Richard;
    • Bonavides-Martínez, César;
    • Caspi, Ron;
    • Kothari, Anamika;
    • Krummenacker, Markus;
    • Midford, Peter E.;
    • Muñiz-Rascado, Luis;
    • Ong, Wai Kit;
    • Paley, Suzanne;
    • Santos-Zavaleta, Alberto;
    • Subhraveti, Pallavi;
    • Tierrafría, Víctor H.;
    • Wolfe, Alan J.;
    • Collado-Vides, Julio;
    • Paulsen, Ian T.;
    • Karp, Peter D.
    Publication type:
    Article