Julio Collado-Vides

	2009
29		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 Research 37(Database-Issue): 464-470 (2009)
	2008
28		Vladimir Espinosa Angarica, Abel González Pérez, Ana Tereza R. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira: Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics 9: (2008)
27		Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, Julio Collado-Vides: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research 36(Database-Issue): 120-124 (2008)
	2007
26		Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides: NLP-Based Curation of Bacterial Regulatory Networks. CICLing 2007: 575-586
25		Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides: Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 8: (2007)
24		Bruno Contreras-Moreira, Pierre-Alain Branger, Julio Collado-Vides: TFmodeller: comparative modelling of protein-DNA complexes. Bioinformatics 23(13): 1694-1696 (2007)
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. Nucleic Acids Research 35(Database-Issue): 132-136 (2007)
	2006
22		Bruno Contreras-Moreira, Julio Collado-Vides: Comparative footprinting of DNA-binding proteins. ISMB (Supplement of Bioinformatics) 2006: 74-80
21		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. BMC Bioinformatics 7: 5 (2006)
20		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. Nucleic Acids Research 34(Database-Issue): 394-397 (2006)
	2005
19		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 Research 33(Database-Issue): 334-337 (2005)
18		Abel D. González, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides: TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Research 33(Database-Issue): 98-102 (2005)
	2004
17		Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia: Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Computational Biology and Chemistry 28(5-6): 341-350 (2004)
16		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. In Silico Biology 5: (2004)
15		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. Nucleic Acids Research 32(Database-Issue): 303-306 (2004)
	2002
14		Julio Collado-Vides, Ralf Hofestädt: Gene Regulations and Metabolism - Postgenomic Computational Approaches MIT Press 2002
13		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. Gene Regulations and Metabolism 2002: 103-128
12		Gabriel Moreno-Hagelsieb, Julio Collado-Vides: A powerful non-homology method for the prediction of operons in prokaryotes. ISMB 2002: 329-336
11		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. In Silico Biology 2: 8 (2002)
10		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 Research 30(1): 56-58 (2002)
	2001
9		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. Nucleic Acids Research 29(1): 72-74 (2001)
	2000
8		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. Nucleic Acids Research 28(1): 65-67 (2000)
	1999
7		Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides: RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Research 27(1): 59-60 (1999)
	1998
6		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. Bioinformatics 14(5): 391-400 (1998)
5		Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides: RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Research 26(1): 55-59 (1998)
	1996
4		Araceli M. Huerta, Julio Collado-Vides, Peter D. Karp, Kathleen Klose: Three Models of Gene Regulation in E.coli. German Conference on Bioinformatics 1996: 64-67
3		Julio Collado-Vides, Araceli M. Huerta, Kathleen Klose: Three Models of Gene Regulation in E. coli. German Conference on Bioinformatics - Selected Papers 1996: 72-78
2		David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides: Syntactic recognition of regulatory regions in Escherichia coli. Computer Applications in the Biosciences 12(5): 415-422 (1996)
	1991
1		Julio Collado-Vides: The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. Computer Applications in the Biosciences 7(3): 321-326 (1991)

Coauthor Index

1	Cei Abreu-Goodger	[27]
2	Vladimir Espinosa Angarica	[16] [18] [23] [28]
3	Esperanza Benítez-Bellón	[13]
4	Frederick R. Blattner	[8]
5	César Bonavides-Martínez	[9] [10] [13] [15] [20] [27] [29]
6	Pierre-Alain Branger	[24]
7	Andrés Christen	[13]
8	Bruno Contreras-Moreira	[22] [24] [27] [28]
9	Edgar Díaz-Peredo	[7] [9] [13] [15] [20]
10	Socorro Gama-Castro	[8] [9] [10] [13] [15] [19] [20] [21] [27] [29]
11	Delfino Garcia-Alonso	[15]
12	Ulises Garza-Ramos	[7]
13	Abel D. González	[18]
14	Marylens Hernández Guía	[16]
15	Robert P. Gunsalus	[29]
16	Rosa María Gutiérrez	[13]
17	Jacques van Helden	[7]
18	Ralf Hofestädt	[14]
19	Araceli M. Huerta	[2] [3] [4] [5] [6] [13] [27]
20	John Ingraham	[19]
21	Verónica Jiménez-Jacinto	[15] [20] [27]
22	D. Aaron Johnson	[29]
23	Peter D. Karp	[4] [10] [19] [21] [29]
24	Ingrid M. Keseler	[19] [29]
25	Kathleen Klose	[3] [4]
26	Markus Krummenacker	[29]
27	Agustino Martínez-Antonio	[15] [20] [21]
28	Irma Martínez-Flores	[20] [25] [26] [27]
29	Arturo Medrano-Soto	[13]
30	Enrique Merino	[27]
31	Dulce María Millá	[13]
32	Dulce Millán-Zárate	[8] [9]
33	Juan Miranda-Ríos	[27]
34	Gabriel Moreno-Hagelsieb	[11] [12] [13]
35	Enrique Morett	[27]
36	Luis Muñiz-Rascado	[27]
37	Laura M. Nolan	[29]
38	Suzanne M. Paley	[10] [19] [29]
39	Ian T. Paulsen	[10] [19] [29]
40	Alida Pellegrini-Toole	[10]
41	Carlos Rodríguez Penagos	[25] [26] [27]
42	Mónica I. Peñaloza-Spínola	[21] [27]
43	Martín Peralta-Gil	[15] [19] [20] [21] [27] [29]
44	Abel González Pérez	[16] [23] [28]
45	Ernesto Pérez-Rueda	[9] [13] [17] [18]
46	Monica Riley	[10]
47	David A. Rosenblueth	[2] [13]
48	Milton H. Saier Jr.	[10]
49	Heladia Salgado	[2] [5] [6] [7] [8] [9] [13] [15] [20] [21] [25] [26] [27]
50	Fabiola Sánchez-Solano	[9] [13] [15] [20]
51	Alberto Santos-Zavaleta	[7] [8] [9] [13] [15] [20] [21] [27]
52	Alberto D. Santos-Zavaleta	[29]
53	Lorenzo Segovia	[17]
54	Juan Segura-Salazar	[20] [27]
55	Alexander Glennon Shearer	[29]
56	Denis Thieffry	[2] [5] [6]
57	Luis Treviño-Quintanilla	[27]
58	Ana Tereza R. Vasconcelos	[16] [18] [23] [28]

Colors in the list of coauthors