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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. 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
Genomic position analyses and the transcription machinery.
Pérez-Rueda E, Gralla JD, Collado-Vides J. Pérez-Rueda E, et al. J Mol Biol. 1998 Jan 16;275(2):165-70. doi: 10.1006/jmbi.1997.1465. J Mol Biol. 1998. PMID: 9466899
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
Pérez-Rueda E, Collado-Vides J. Pérez-Rueda E, et al. Nucleic Acids Res. 2000 Apr 15;28(8):1838-47. doi: 10.1093/nar/28.8.1838. Nucleic Acids Res. 2000. PMID: 10734204 Free PMC article.
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millán-Zárate D, Díaz-Peredo E, Sánchez-Solano F, Pérez-Rueda E, Bonavides-Martínez C, Collado-Vides J. Salgado H, et al. Nucleic Acids Res. 2001 Jan 1;29(1):72-4. doi: 10.1093/nar/29.1.72. Nucleic Acids Res. 2001. PMID: 11125053 Free PMC article.
Transcription unit conservation in the three domains of life: a perspective from Escherichia coli.
Moreno-Hagelsieb G, Treviño V, Pérez-Rueda E, Smith TF, Collado-Vides J. Moreno-Hagelsieb G, et al. Trends Genet. 2001 Apr;17(4):175-7. doi: 10.1016/s0168-9525(01)02241-7. Trends Genet. 2001. PMID: 11275307
Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria.
Pérez-Rueda E, Collado-Vides J. Pérez-Rueda E, et al. J Mol Evol. 2001 Sep;53(3):172-9. doi: 10.1007/s002390010207. J Mol Evol. 2001. PMID: 11523004
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.
González AD, Espinosa V, Vasconcelos AT, Pérez-Rueda E, Collado-Vides J. González AD, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D98-102. doi: 10.1093/nar/gki054. Nucleic Acids Res. 2005. PMID: 15608293 Free PMC article.
Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach.
Moreno-Campuzano S, Janga SC, Pérez-Rueda E. Moreno-Campuzano S, et al. BMC Genomics. 2006 Jun 13;7:147. doi: 10.1186/1471-2164-7-147. BMC Genomics. 2006. PMID: 16772031 Free PMC article.
A network perspective on the evolution of metabolism by gene duplication.
Díaz-Mejía JJ, Pérez-Rueda E, Segovia L. Díaz-Mejía JJ, et al. Genome Biol. 2007;8(2):R26. doi: 10.1186/gb-2007-8-2-r26. Genome Biol. 2007. PMID: 17326820 Free PMC article.
Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins.
Hernandez-Mendoza A, Quinto C, Segovia L, Perez-Rueda E. Hernandez-Mendoza A, et al. Comput Biol Chem. 2007 Apr;31(2):115-23. doi: 10.1016/j.compbiolchem.2007.02.003. Epub 2007 Feb 11. Comput Biol Chem. 2007. PMID: 17416336
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