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Julio Collado-Vides: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides
    NLP-Based Curation of Bacterial Regulatory Networks. [Citation Graph (0, 0)][DBLP]
    CICLing, 2007, pp:575-586 [Conf]
  2. Julio Collado-Vides, Gabriel Moreno-Hagelsieb, Ernesto Pérez-Rueda, Heladia Salgado, Araceli M. Huerta, Rosa María Gutiérrez, David A. Rosenblueth, Andrés Christen, Esperanza Benítez-Bellón, Arturo Medrano-Soto, Socorro Gama-Castro, Alberto Santos-Zavaleta, César Bonavides-Martínez, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Dulce María Millá
    Genomics of Gene Regulation: The View from Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Gene Regulations and Metabolism, 2002, pp:103-128 [Conf]
  3. Julio Collado-Vides, Araceli M. Huerta, Kathleen Klose
    Three Models of Gene Regulation in E. coli. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics - Selected Papers, 1996, pp:72-78 [Conf]
  4. Araceli M. Huerta, Julio Collado-Vides, Peter D. Karp, Kathleen Klose
    Three Models of Gene Regulation in E.coli. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1996, pp:64-67 [Conf]
  5. Bruno Contreras-Moreira, Julio Collado-Vides
    Comparative footprinting of DNA-binding proteins. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2006, pp:74-80 [Conf]
  6. Gabriel Moreno-Hagelsieb, Julio Collado-Vides
    A powerful non-homology method for the prediction of operons in prokaryotes. [Citation Graph (0, 0)][DBLP]
    ISMB, 2002, pp:329-336 [Conf]
  7. Julio Collado-Vides
    The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1991, v:7, n:3, pp:321-326 [Journal]
  8. David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides
    Syntactic recognition of regulatory regions in Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1996, v:12, n:5, pp:415-422 [Journal]
  9. Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides
    Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:5, pp:391-400 [Journal]
  10. Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides
    The comprehensive updated regulatory network of Escherichia coli K-12. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:5- [Journal]
  11. Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia
    Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. [Citation Graph (0, 0)][DBLP]
    Computational Biology and Chemistry, 2004, v:28, n:5-6, pp:341-350 [Journal]
  12. Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides
    Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. [Citation Graph (0, 0)][DBLP]
    In Silico Biology, 2004, v:5, n:, pp:- [Journal]
  13. Gabriel Moreno-Hagelsieb, Julio Collado-Vides
    Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context. [Citation Graph (0, 0)][DBLP]
    In Silico Biology, 2002, v:2, n:, pp:8- [Journal]
  14. Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
    RegulonDB: a database on transcriptional regulation in Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 1998, v:26, n:1, pp:55-59 [Journal]
  15. Peter D. Karp, Monica Riley, Milton H. Saier Jr., Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, Alida Pellegrini-Toole, César Bonavides, Socorro Gama-Castro
    The EcoCyc Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2002, v:30, n:1, pp:56-58 [Journal]
  16. Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, Julio Collado-Vides
    RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2004, v:32, n:Database-Issue, pp:303-306 [Journal]
  17. Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz, Julio Collado-Vides
    RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 1999, v:27, n:1, pp:59-60 [Journal]
  18. Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, Julio Collado-Vides
    RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2000, v:28, n:1, pp:65-67 [Journal]
  19. Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda, César Bonavides-Martínez, Julio Collado-Vides
    RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2001, v:29, n:1, pp:72-74 [Journal]
  20. 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. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:334-337 [Journal]
  21. Abel D. González, Vladimir Espinosa, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides
    TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:98-102 [Journal]
  22. Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, Julio Collado-Vides
    RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Database-Issue, pp:394-397 [Journal]
  23. Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides
    Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2007, v:35, n:Database-Issue, pp:132-136 [Journal]

  24. TFmodeller: comparative modelling of protein-DNA complexes. [Citation Graph (, )][DBLP]


  25. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. [Citation Graph (, )][DBLP]


  26. Prediction of TF target sites based on atomistic models of protein-DNA complexes. [Citation Graph (, )][DBLP]


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