RegulonDB RegulonDB 10.0: RegulonDB Papers  

RegulonDB Papers

Please cite the most recent paper describing progress in RegulonDB:

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, Moral-Chávez VD, Rinaldi F, Collado-Vides J. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 2016 Jan 4; 44(Database issue): D133-D143. PMID: 26527724

Previous RegulonDB papers:

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. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. PMID: 23203884
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. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. PMID: 21051347
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. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. PMID: 18158297
Salgado H, Gama-Castro S, Peralta-Gil M, Díaz-Peredo E, Sánchez-Solano F, Santos-Zavaleta A, Martínez-Flores I, Jiménez-Jacinto V, Bonavides-Martínez C, Segura-Salazar J, Martínez-Antonio A, Collado-Vides J. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D394-7. PMID: 16381895
Salgado H, Gama-Castro S, Martínez-Antonio A, Díaz-Peredo E, Sánchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jiménez-Jacinto V, Santos-Zavaleta A, Bonavides-Martínez C, Collado-Vides J. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D303-6. PMID: 14681419
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. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 2001 Jan 1;29(1):72-4. PMID: 11125053 .
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millán-Zárate D, Blattner FR, Collado-Vides J. RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 2000 Jan 1;28(1):65-7. PMID: 10592182
Salgado H, Santos A, Garza-Ramos U, van Helden J, Díaz E, Collado-Vides J. RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 1999 Jan 1;27(1):59-60. PMID: 9847141
Huerta AM, Salgado H, Thieffry D, Collado-Vides J. RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 1998 Jan 1;26(1):55-9. PMID: 9399800


RegulonDB Related Papers

RegulonDB has been used in the laboratory  to generate computational methods to predict transcriptional regulators, operons, promoters, and  regulatory sites. These predictions enrich the content of RegulonDB. Here is the list of the corresponding papers:

1.- Evidence classification

Weiss V, Medina-Rivera A, Huerta AM, Santos-Zavaleta A, Salgado H, Morett E, Collado-Vides J. Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database (Oxford). 2013 Jan 17;2013:bas059. PMID: 23327937

2. Regulatory proteins:

Pérez-Rueda E, Collado-Vides J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 2000 Apr 15;28(8):1838-47. PMID: 10734204
Pérez-Rueda E, Gralla JD, Collado-Vides J. Genomic position analyses and the transcription machinery. J Mol Biol. 1998 Jan 16;275(2):165-70. PMID: 9466899
3. Binding sites:
Salgado H, Santos-Zavaleta A, Gama-Castro S, Peralta-Gil M, Peñaloza-Spínola MI, Martínez-Antonio A, Karp PD, Collado-Vides J. The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics. 2006 Jan 6;7:5. PMID: 16398937
Guía MH, Pérez AG, Angarica VE, Vasconcelos AT, Collado-Vides J. Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. In Silico Biol. 2005;5(2):209-19. PMID: 15972018
González AD, Espinosa V, Vasconcelos AT, Pérez-Rueda E, Collado-Vides J. TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Res. 2005 Jan 1;33 PMID: 15608293
Benítez-Bellón E, Moreno-Hagelsieb G, Collado-Vides J. Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol. 2002;3(3):RESEARCH0013. Epub 2002 Feb 21. PMID: 11897025
Thieffry D, Salgado H, Huerta AM, Collado-Vides J. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics. 1998 Jun;14(5):391-400. PMID: 9682052
Thieffry D, Rosenblueth DA, Huerta AM, Salgado H, Collado-Vides J. Definite-clause grammars for the analysis of cis-regulatory regions in E. coli. Pac Symp Biocomput. 1997:441-52. PMID: 9390313
Rosenblueth DA, Thieffry D, Huerta AM, Salgado H, Collado-Vides J. Syntactic recognition of regulatory regions in Escherichia coli. Comput Appl Biosci. 1996 Oct;12(5):415-22. PMID: 8996790
4. Operons:
Moreno-Hagelsieb G, Collado-Vides J. Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context. In Silico Biol. 2002;2(2):87-95. PMID: 12066843
Moreno-Hagelsieb G, Treviño V, Pérez-Rueda E, Smith TF, Collado-Vides J. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends Genet. 2001 Apr;17(4):175-7. PMID: 11275307
Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6652-7. PMID: 10823905
5. Promoters:
Huerta AM, Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol. 2003 Oct 17;333(2):261-78. PMID: 14529615
6. Nebulon:
Janga SC, Collado-Vides J, Moreno-Hagelsieb G. Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res. 2005 May 2;33(8):2521-30. Print 2005. PMID: 15867197
7. Tools:
Huerta A.M., Glasner J.D., Jin H., Blattner F.D., Gutiérrez-Ríos R.M. and Collado-Vides J. GETools: gene expression tool for analysis of transcriptome experiments in E. coli. Trends in Genetics, Volume 18, Issue 4, 217-218, 1 April 2002 PDF
Web site: GETools
van Helden J, André B, Collado-Vides J. A web site for the computational analysis of yeast regulatory sequences. Yeast. 2000 Jan 30;16(2):177-87. PMID: 10641039
Web site: RSA-tools
8. RegulonDB has also provided the basis for additional studies performed in our laboratory, such as:
Martínez-Antonio A, Salgado H, Gama-Castro S, Gutiérrez-Ríos RM, Jiménez-Jacinto V, Collado-Vides J. Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach. Biotechnol Bioeng. 2003 Dec 30;84(7):743-9. PMID: 14708114
Gutiérrez-Ríos RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, Blattner FR, Collado-Vides J. Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res. 2003 Nov;13(11):2435-43. PMID: 14597655
van Helden J, Rios AF, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 2000 Apr 15;28(8):1808-18. PMID: 10734201
van Helden J, André B, Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol. 1998 Sep 4;281(5):827-42. PMID: 9719638
Thieffry D, Huerta AM, Pérez-Rueda E, Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays. 1998 May;20(5):433-40. PMID: 9670816
9. List of other papers generated in the Lab.