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From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.
Thieffry D, Huerta AM, Pérez-Rueda E, Collado-Vides J. Thieffry D, et al. Among authors: huerta am. Bioessays. 1998 May;20(5):433-40. doi: 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2. Bioessays. 1998. PMID: 9670816
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J. Salgado H, et al. Among authors: huerta am. Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29. Nucleic Acids Res. 2013. PMID: 23203884 Free PMC article.
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes.
Huerta AM, Collado-Vides J, Francino MP; SMBE Tri-National Young Investigators. Huerta AM, et al. Mol Biol Evol. 2006 May;23(5):997-1010. doi: 10.1093/molbev/msk004. Epub 2006 Mar 17. Mol Biol Evol. 2006. PMID: 16547149
Evidence classification of high-throughput protocols and confidence integration in RegulonDB.
Weiss V, Medina-Rivera A, Huerta AM, Santos-Zavaleta A, Salgado H, Morett E, Collado-Vides J. Weiss V, et al. Among authors: huerta am. Database (Oxford). 2013 Jan 17;2013:bas059. doi: 10.1093/database/bas059. Print 2013. Database (Oxford). 2013. PMID: 23327937 Free PMC article.
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J. Gama-Castro S, et al. Among authors: huerta am. Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4. Nucleic Acids Res. 2011. PMID: 21051347 Free PMC article.
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.
Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E. Mendoza-Vargas A, et al. Among authors: huerta am. PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526. PLoS One. 2009. PMID: 19838305 Free PMC article.
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J. Gama-Castro S, et al. Among authors: huerta am. Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. doi: 10.1093/nar/gkm994. Epub 2007 Dec 23. Nucleic Acids Res. 2008. PMID: 18158297 Free PMC article.
Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.
Huerta AM, Francino MP, Morett E, Collado-Vides J. Huerta AM, et al. PLoS Genet. 2006 Nov 10;2(11):e185. doi: 10.1371/journal.pgen.0020185. Epub 2006 Sep 12. PLoS Genet. 2006. PMID: 17096598 Free PMC article.
Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes.
Espinosa V, González AD, Vasconcelos AT, Huerta AM, Collado-Vides J. Espinosa V, et al. Among authors: huerta am. J Mol Biol. 2005 Nov 18;354(1):184-99. doi: 10.1016/j.jmb.2005.09.037. Epub 2005 Oct 4. J Mol Biol. 2005. PMID: 16236313
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.
Huerta AM, Collado-Vides J. Huerta AM, et al. J Mol Biol. 2003 Oct 17;333(2):261-78. doi: 10.1016/j.jmb.2003.07.017. J Mol Biol. 2003. PMID: 14529615
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