Julio Collado-Vides
Julio Collado-Vides
Professor of Computational Genomics, CCG, UNAM
Dirección de correo verificada de ccg.unam.mx - Página principal
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, ...
Nucleic acids research 25 (17), 3389-3402, 1997
768851997
The complete genome sequence of Escherichia coli K-12
FR Blattner, G Plunkett, CA Bloch, NT Perna, V Burland, M Riley, ...
science 277 (5331), 1453-1462, 1997
86031997
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
J van Helden, B André, J Collado-Vides
Journal of molecular biology 281 (5), 827-842, 1998
9611998
EcoCyc: a comprehensive database resource for Escherichia coli
IM Keseler, J Collado-Vides, S Gama-Castro, J Ingraham, S Paley, ...
Nucleic acids research 33 (suppl_1), D334-D337, 2005
8892005
EcoCyc: fusing model organism databases with systems biology
IM Keseler, A Mackie, M Peralta-Gil, A Santos-Zavaleta, S Gama-Castro, ...
Nucleic acids research 41 (D1), D605-D612, 2013
6372013
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
6312010
Minimum information requested in the annotation of biochemical models (MIRIAM)
N Le Novère, A Finney, M Hucka, US Bhalla, F Campagne, ...
Nature biotechnology 23 (12), 1509-1515, 2005
6042005
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli
D Thieffry, AM Huerta, E Pérez‐Rueda, J Collado‐Vides
Bioessays 20 (5), 433-440, 1998
6031998
The ecocyc database
PD Karp, M Riley, M Saier, IT Paulsen, J Collado-Vides, SM Paley, ...
Nucleic acids research 30 (1), 56-58, 2002
5952002
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
S Gama-Castro, V Jiménez-Jacinto, M Peralta-Gil, A Santos-Zavaleta, ...
Nucleic acids research 36 (suppl_1), D120-D124, 2008
5942008
Control site location and transcriptional regulation in Escherichia coli.
J Collado-Vides, B Magasanik, JD Gralla
Microbiology and Molecular Biology Reviews 55 (3), 371-394, 1991
5931991
Identifying global regulators in transcriptional regulatory networks in bacteria
A Martınez-Antonio, J Collado-Vides
Current opinion in microbiology 6 (5), 482-489, 2003
5402003
EcoCyc: a comprehensive database of Escherichia coli biology
IM Keseler, J Collado-Vides, A Santos-Zavaleta, M Peralta-Gil, ...
Nucleic acids research 39 (suppl_1), D583-D590, 2010
5242010
RegulonDB v8. 0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
H Salgado, M Peralta-Gil, S Gama-Castro, A Santos-Zavaleta, ...
Nucleic acids research 41 (D1), D203-D213, 2013
4652013
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
H Salgado, S Gama-Castro, M Peralta-Gil, E Díaz-Peredo, ...
Nucleic acids research 34 (suppl_1), D394-D397, 2006
4572006
Operons in Escherichia coli: genomic analyses and predictions
H Salgado, G Moreno-Hagelsieb, TF Smith, J Collado-Vides
Proceedings of the National Academy of Sciences 97 (12), 6652-6657, 2000
4412000
EcoCyc: A comprehensive view of Escherichia coli biology
IM Keseler, C Bonavides-Martínez, J Collado-Vides, S Gama-Castro, ...
Nucleic acids research 37 (suppl_1), D464-D470, 2009
4402009
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
S Gama-Castro, H Salgado, M Peralta-Gil, A Santos-Zavaleta, ...
Nucleic acids research 39 (suppl_1), D98-D105, 2010
4382010
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
J Helden, AF Rios, J Collado-Vides
Nucleic acids research 28 (8), 1808-1818, 2000
4232000
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
S Gama-Castro, H Salgado, A Santos-Zavaleta, D Ledezma-Tejeida, ...
Nucleic acids research 44 (D1), D133-D143, 2016
3882016
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