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Items: 1 to 50 of 127

1.

Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.

Ledezma-Tejeida D, Altamirano-Pacheco L, Fajardo V, Collado-Vides J.

Nucleic Acids Res. 2019 Jun 13. pii: gkz525. doi: 10.1093/nar/gkz525. [Epub ahead of print]

PMID:
31194874
2.

Similarity corpus on microbial transcriptional regulation.

Lithgow-Serrano O, Gama-Castro S, Ishida-Gutiérrez C, Mejía-Almonte C, Tierrafría VH, Martínez-Luna S, Santos-Zavaleta A, Velázquez-Ramírez D, Collado-Vides J.

J Biomed Semantics. 2019 May 22;10(1):8. doi: 10.1186/s13326-019-0200-x.

3.

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

Santos-Zavaleta A, Pérez-Rueda E, Sánchez-Pérez M, Velázquez-Ramírez DA, Collado-Vides J.

BMC Genomics. 2019 Apr 16;20(1):299. doi: 10.1186/s12864-019-5619-z.

4.

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.

Rioualen C, Charbonnier-Khamvongsa L, Collado-Vides J, van Helden J.

Curr Protoc Bioinformatics. 2019 Feb 20:e72. doi: 10.1002/cpbi.72. [Epub ahead of print]

PMID:
30786165
5.

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.

EcoSal Plus. 2018 Nov;8(1). doi: 10.1128/ecosalplus.ESP-0006-2018. Review.

6.

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.

Santos-Zavaleta A, Salgado H, Gama-Castro S, Sánchez-Pérez M, Gómez-Romero L, Ledezma-Tejeida D, García-Sotelo JS, Alquicira-Hernández K, Muñiz-Rascado LJ, Peña-Loredo P, Ishida-Gutiérrez C, Velázquez-Ramírez DA, Del Moral-Chávez V, Bonavides-Martínez C, Méndez-Cruz CF, Galagan J, Collado-Vides J.

Nucleic Acids Res. 2019 Jan 8;47(D1):D212-D220. doi: 10.1093/nar/gky1077.

7.

MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.

Tierrafría VH, Mejía-Almonte C, Camacho-Zaragoza JM, Salgado H, Alquicira K, Ishida C, Gama-Castro S, Collado-Vides J.

Bioinformatics. 2019 Mar 1;35(5):856-864. doi: 10.1093/bioinformatics/bty689.

PMID:
30137210
8.

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J.

BMC Biol. 2018 Aug 16;16(1):91. doi: 10.1186/s12915-018-0555-y.

9.

Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.

Salgado H, Martínez-Flores I, Bustamante VH, Alquicira-Hernández K, García-Sotelo JS, García-Alonso D, Collado-Vides J.

Curr Protoc Bioinformatics. 2018 Mar;61(1):1.32.1-1.32.30. doi: 10.1002/cpbi.43.

10.

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.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax070.

11.

Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli.

Ledezma-Tejeida D, Ishida C, Collado-Vides J.

Front Microbiol. 2017 Aug 3;8:1466. doi: 10.3389/fmicb.2017.01466. eCollection 2017.

12.

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis.

Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides J, Selman M, Pardo A.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax030.

13.

Strategies towards digital and semi-automated curation in RegulonDB.

Rinaldi F, Lithgow O, Gama-Castro S, Solano H, López-Fuentes A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax029. No abstract available.

14.

Effect of genomic distance on coexpression of coregulated genes in E. coli.

Pannier L, Merino E, Marchal K, Collado-Vides J.

PLoS One. 2017 Apr 18;12(4):e0174887. doi: 10.1371/journal.pone.0174887. eCollection 2017.

15.

Strategies towards digital and semi-automated curation in RegulonDB.

Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax012. Erratum in: Database (Oxford). 2017 Jan 1;2017:null.

16.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28.

17.

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD.

Martínez-Flores I, Pérez-Morales D, Sánchez-Pérez M, Paredes CC, Collado-Vides J, Salgado H, Bustamante VH.

Sci Rep. 2016 Nov 25;6:37858. doi: 10.1038/srep37858.

18.

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.

Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.

Nucleic Acids Res. 2016 Jan 4;44(D1):D620-3. doi: 10.1093/nar/gkv1251. Epub 2015 Nov 19.

19.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43. doi: 10.1093/nar/gkv1156. Epub 2015 Nov 2.

20.

Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli.

Alvarez-Vasquez FJ, Freyre-González JA, Balderas-Martínez YI, Delgado-Carrillo MI, Collado-Vides J.

Mol Biosyst. 2015 Apr;11(4):994-1003. doi: 10.1039/c4mb00561a.

PMID:
25683745
21.

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.

Database (Oxford). 2014 Jun 4;2014. pii: bau049. doi: 10.1093/database/bau049. Print 2014.

22.

The EcoCyc Database.

Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I.

EcoSal Plus. 2014 May;6(1). doi: 10.1128/ecosalplus.ESP-0009-2013.

23.

Structural properties of prokaryotic promoter regions correlate with functional features.

Meysman P, Collado-Vides J, Morett E, Viola R, Engelen K, Laukens K.

PLoS One. 2014 Feb 7;9(2):e88717. doi: 10.1371/journal.pone.0088717. eCollection 2014.

24.

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.

Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K.

Nucleic Acids Res. 2014 Jan;42(Database issue):D649-53. doi: 10.1093/nar/gkt1086. Epub 2013 Nov 8.

25.

In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes.

Martínez LC, Martínez-Flores I, Salgado H, Fernández-Mora M, Medina-Rivera A, Puente JL, Collado-Vides J, Bustamante VH.

J Bacteriol. 2014 Jan;196(2):325-36. doi: 10.1128/JB.00806-13. Epub 2013 Nov 1.

26.

Transcription factors in Escherichia coli prefer the holo conformation.

Balderas-Martínez YI, Savageau M, Salgado H, Pérez-Rueda E, Morett E, Collado-Vides J.

PLoS One. 2013 Jun 12;8(6):e65723. doi: 10.1371/journal.pone.0065723. Print 2013. Erratum in: PLoS One. 2013;8(8). doi:10.1371/annotation/96d7b9a4-aa2e-4593-ae8a-7c14d134e29c.

27.

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.

Database (Oxford). 2013 Jan 17;2013:bas059. doi: 10.1093/database/bas059. Print 2013.

28.

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.

Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29.

29.

EcoCyc: fusing model organism databases with systems biology.

Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D605-12. doi: 10.1093/nar/gks1027. Epub 2012 Nov 9.

30.

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.

Pauling J, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J.

Integr Biol (Camb). 2012 Jul;4(7):728-33. doi: 10.1039/c2ib00132b. Epub 2012 Feb 9.

PMID:
22318347
31.

Extracting regulatory networks of Escherichia coli from RegulonDB.

Salgado H, Martínez-Flores I, López-Fuentes A, García-Sotelo JS, Porrón-Sotelo L, Solano H, Muñiz-Rascado L, Collado-Vides J.

Methods Mol Biol. 2012;804:179-95. doi: 10.1007/978-1-61779-361-5_10.

PMID:
22144154
32.

EcoCyc: a comprehensive database of Escherichia coli biology.

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD.

Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21.

33.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

34.

Theoretical and empirical quality assessment of transcription factor-binding motifs.

Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J.

Nucleic Acids Res. 2011 Feb;39(3):808-24. doi: 10.1093/nar/gkq710. Epub 2010 Oct 4.

35.

The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].

36.

Structural and functional map of a bacterial nucleoid.

Martínez-Antonio A, Medina-Rivera A, Collado-Vides J.

Genome Biol. 2009;10(12):247. doi: 10.1186/gb-2009-10-12-247. Epub 2009 Dec 11. Review.

37.

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.

PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526.

38.

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters.

Pérez AG, Angarica VE, Collado-Vides J, Vasconcelos AT.

BMC Mol Biol. 2009 Sep 22;10:92. doi: 10.1186/1471-2199-10-92.

39.

The condition-dependent transcriptional network in Escherichia coli.

Lemmens K, De Bie T, Dhollander T, Monsieurs P, De Moor B, Collado-Vides J, Engelen K, Marchal K.

Ann N Y Acad Sci. 2009 Mar;1158:29-35. doi: 10.1111/j.1749-6632.2008.03746.x.

PMID:
19348629
40.

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.

Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, Schoofs G, De Weerdt A, De Moor B, Vanderleyden J, Collado-Vides J, Engelen K, Marchal K.

Genome Biol. 2009;10(3):R27. doi: 10.1186/gb-2009-10-3-r27. Epub 2009 Mar 6.

41.

Regulation by transcription factors in bacteria: beyond description.

Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J.

FEMS Microbiol Rev. 2009 Jan;33(1):133-51. doi: 10.1111/j.1574-6976.2008.00145.x. Review.

42.

Bioinformatics resources for the study of gene regulation in bacteria.

Collado-Vides J, Salgado H, Morett E, Gama-Castro S, Jiménez-Jacinto V, Martínez-Flores I, Medina-Rivera A, Muñiz-Rascado L, Peralta-Gil M, Santos-Zavaleta A.

J Bacteriol. 2009 Jan;191(1):23-31. doi: 10.1128/JB.01017-08. Epub 2008 Oct 31. Review. No abstract available.

43.

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.

Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70. doi: 10.1093/nar/gkn751. Epub 2008 Oct 30.

44.

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach.

Freyre-González JA, Alonso-Pavón JA, Treviño-Quintanilla LG, Collado-Vides J.

Genome Biol. 2008 Oct 27;9(10):R154. doi: 10.1186/gb-2008-9-10-r154.

45.

Prediction of TF target sites based on atomistic models of protein-DNA complexes.

Angarica VE, Pérez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B.

BMC Bioinformatics. 2008 Oct 16;9:436. doi: 10.1186/1471-2105-9-436.

46.

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes.

Janga SC, Collado-Vides J, Babu MM.

Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15761-6. doi: 10.1073/pnas.0806317105. Epub 2008 Oct 7.

47.

The role of DNA-binding specificity in the evolution of bacterial regulatory networks.

Lozada-Chávez I, Angarica VE, Collado-Vides J, Contreras-Moreira B.

J Mol Biol. 2008 Jun 6;379(3):627-43. doi: 10.1016/j.jmb.2008.04.008. Epub 2008 Apr 9.

48.

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

González Pérez AD, González González E, Espinosa Angarica V, Vasconcelos AT, Collado-Vides J.

BMC Genomics. 2008 Mar 17;9:128. doi: 10.1186/1471-2164-9-128.

49.

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.

Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.

50.

Structure and evolution of gene regulatory networks in microbial genomes.

Janga SC, Collado-Vides J.

Res Microbiol. 2007 Dec;158(10):787-94. Epub 2007 Oct 15.

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