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Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
Thieffry D, Salgado H, Huerta AM, Collado-Vides J. Thieffry D, et al. Bioinformatics. 1998 Jun;14(5):391-400. doi: 10.1093/bioinformatics/14.5.391. Bioinformatics. 1998. PMID: 9682052
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes.
Méndez-Cruz CF, Gama-Castro S, Mejía-Almonte C, Castillo-Villalba MP, Muñiz-Rascado LJ, Collado-Vides J. Méndez-Cruz CF, et al. Database (Oxford). 2017 Jan 1;2017:bax070. doi: 10.1093/database/bax070. Database (Oxford). 2017. PMID: 29220462 Free PMC article.
The EcoCyc Database.
Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I. Karp PD, et al. Among authors: collado vides j. EcoSal Plus. 2018 Nov;8(1):10.1128/ecosalplus.ESP-0006-2018. doi: 10.1128/ecosalplus.ESP-0006-2018. EcoSal Plus. 2018. PMID: 30406744 Free PMC article. Review.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899573 Free PMC article.
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo JS, Alquicira-Hernández K, Martínez-Flores I, Pannier L, Castro-Mondragón JA, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Pérez-Rueda E, Alquicira-Hernández S, Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, Del Moral-Chávez V, Rinaldi F, Collado-Vides J. Gama-Castro S, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43. doi: 10.1093/nar/gkv1156. Epub 2015 Nov 2. Nucleic Acids Res. 2016. PMID: 26527724 Free PMC article.
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.
Gama-Castro S, Rinaldi F, López-Fuentes A, Balderas-Martínez YI, Clematide S, Ellendorff TR, Santos-Zavaleta A, Marques-Madeira H, Collado-Vides J. Gama-Castro S, et al. Database (Oxford). 2014 Jun 4;2014:bau049. doi: 10.1093/database/bau049. Print 2014. Database (Oxford). 2014. PMID: 24903516 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. 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.
EcoCyc: a comprehensive view of Escherichia coli biology.
Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70. doi: 10.1093/nar/gkn751. Epub 2008 Oct 30. Nucleic Acids Res. 2009. PMID: 18974181 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. 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.
Multidimensional annotation of the Escherichia coli K-12 genome.
Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J. Karp PD, et al. Nucleic Acids Res. 2007;35(22):7577-90. doi: 10.1093/nar/gkm740. Epub 2007 Oct 16. Nucleic Acids Res. 2007. PMID: 17940092 Free PMC article.
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