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Items: 22

1.

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico.

Godoy-Lozano EE, Escobar-Zepeda A, Raggi L, Merino E, Gutierrez-Rios RM, Juarez K, Segovia L, Licea-Navarro AF, Gracia A, Sanchez-Flores A, Pardo-Lopez L.

Front Microbiol. 2018 Oct 18;9:2528. doi: 10.3389/fmicb.2018.02528. eCollection 2018.

2.

Reactant pairs and reaction organization patterns produced by a new rule-based approach.

Vazquez-Hernandez C, Loza A, Gutierrez-Rios RM.

BMC Res Notes. 2018 Aug 24;11(1):608. doi: 10.1186/s13104-018-3724-8.

3.

Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics.

Escobar-Zepeda A, Godoy-Lozano EE, Raggi L, Segovia L, Merino E, Gutiérrez-Rios RM, Juarez K, Licea-Navarro AF, Pardo-Lopez L, Sanchez-Flores A.

Sci Rep. 2018 Aug 13;8(1):12034. doi: 10.1038/s41598-018-30515-5.

4.

Identification of reaction organization patterns that naturally cluster enzymatic transformations.

Vazquez-Hernandez C, Loza A, Peguero-Sanchez E, Segovia L, Gutierrez-Rios RM.

BMC Syst Biol. 2018 May 30;12(1):63. doi: 10.1186/s12918-018-0583-9.

5.

BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously.

Pedraza-Pérez Y, Cuevas-Vede RA, Canto-Gómez ÁB, López-Pliego L, Gutiérrez-Ríos RM, Hernández-Lucas I, Rubín-Linares G, Martínez-Laguna Y, López-Olguín JF, Fuentes-Ramírez LE.

G3 (Bethesda). 2018 Jul 2;8(7):2167-2172. doi: 10.1534/g3.118.200220.

6.

CRISPR-Cas system presents multiple transcriptional units including antisense RNAs that are expressed in minimal medium and upregulated by pH in Salmonella enterica serovar Typhi.

Medina-Aparicio L, Rebollar-Flores JE, Beltrán-Luviano AA, Vázquez A, Gutiérrez-Ríos RM, Olvera L, Calva E, Hernández-Lucas I.

Microbiology. 2017 Feb;163(2):253-265. doi: 10.1099/mic.0.000414.

PMID:
28270274
7.

Analysis of Spo0M function in Bacillus subtilis.

Vega-Cabrera LA, Guerrero A, Rodríguez-Mejía JL, Tabche ML, Wood CD, Gutiérrez-Rios RM, Merino E, Pardo-López L.

PLoS One. 2017 Feb 24;12(2):e0172737. doi: 10.1371/journal.pone.0172737. eCollection 2017.

8.

The Salmonella enterica serovar Typhi ltrR-ompR-ompC-ompF genes are involved in resistance to the bile salt sodium deoxycholate and in bacterial transformation.

Villarreal JM, Becerra-Lobato N, Rebollar-Flores JE, Medina-Aparicio L, Carbajal-Gómez E, Zavala-García ML, Vázquez A, Gutiérrez-Ríos RM, Olvera L, Encarnación S, Martínez-Batallar AG, Calva E, Hernández-Lucas I.

Mol Microbiol. 2014 Jun;92(5):1005-24. doi: 10.1111/mmi.12610. Epub 2014 Apr 24.

9.

Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium.

Cortés-Tolalpa L, Gutiérrez-Ríos RM, Martínez LM, de Anda R, Gosset G, Bolívar F, Escalante A.

Microb Cell Fact. 2014 Feb 21;13(1):28. doi: 10.1186/1475-2859-13-28.

10.

PhyloFlu, a DNA microarray for determining the phylogenetic origin of influenza A virus gene segments and the genomic fingerprint of viral strains.

Paulin LF, de los D Soto-Del Río M, Sánchez I, Hernández J, Gutiérrez-Ríos RM, López-Martínez I, Wong-Chew RM, Parissi-Crivelli A, Isa P, López S, Arias CF.

J Clin Microbiol. 2014 Mar;52(3):803-13. doi: 10.1128/JCM.03134-13. Epub 2013 Dec 18.

11.

Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.

Freyre-González JA, Manjarrez-Casas AM, Merino E, Martinez-Nuñez M, Perez-Rueda E, Gutiérrez-Ríos RM.

BMC Syst Biol. 2013 Nov 16;7:127. doi: 10.1186/1752-0509-7-127.

12.

Prokaryotic regulatory systems biology: Common principles governing the functional architectures of Bacillus subtilis and Escherichia coli unveiled by the natural decomposition approach.

Freyre-González JA, Treviño-Quintanilla LG, Valtierra-Gutiérrez IA, Gutiérrez-Ríos RM, Alonso-Pavón JA.

J Biotechnol. 2012 Oct 31;161(3):278-86. doi: 10.1016/j.jbiotec.2012.03.028. Epub 2012 Jun 20.

PMID:
22728391
13.

Transcriptional profiling of fetal hypothalamic TRH neurons.

Guerra-Crespo M, Pérez-Monter C, Janga SC, Castillo-Ramírez S, Gutiérrez-Rios RM, Joseph-Bravo P, Pérez-Martínez L, Charli JL.

BMC Genomics. 2011 May 10;12:222. doi: 10.1186/1471-2164-12-222.

14.

The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi.

Medina-Aparicio L, Rebollar-Flores JE, Gallego-Hernández AL, Vázquez A, Olvera L, Gutiérrez-Ríos RM, Calva E, Hernández-Lucas I.

J Bacteriol. 2011 May;193(10):2396-407. doi: 10.1128/JB.01480-10. Epub 2011 Mar 11.

15.

New insights into the regulatory networks of paralogous genes in bacteria.

Martínez-Núñez MA, Pérez-Rueda E, Gutiérrez-Ríos RM, Merino E.

Microbiology. 2010 Jan;156(Pt 1):14-22. doi: 10.1099/mic.0.033266-0. Epub 2009 Oct 22. Review.

PMID:
19850620
16.

Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli.

Vázquez CD, Freyre-González JA, Gosset G, Loza JA, Gutiérrez-Ríos RM.

BMC Microbiol. 2009 Aug 24;9:176. doi: 10.1186/1471-2180-9-176.

17.

The repABC plasmid family.

Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM.

Plasmid. 2008 Jul;60(1):19-37. doi: 10.1016/j.plasmid.2008.03.001. Epub 2008 Apr 22. Review.

PMID:
18433868
18.

Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli.

Gutierrez-Ríos RM, Freyre-Gonzalez JA, Resendis O, Collado-Vides J, Saier M, Gosset G.

BMC Microbiol. 2007 Jun 8;7:53.

19.

Modular analysis of the transcriptional regulatory network of E. coli.

Resendis-Antonio O, Freyre-González JA, Menchaca-Méndez R, Gutiérrez-Ríos RM, Martínez-Antonio A, Avila-Sánchez C, Collado-Vides J.

Trends Genet. 2005 Jan;21(1):16-20.

PMID:
15680508
20.

Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach.

Martínez-Antonio A, Salgado H, Gama-Castro S, Gutiérrez-Ríos RM, Jiménez-Jacinto V, Collado-Vides J.

Biotechnol Bioeng. 2003 Dec 30;84(7):743-9.

PMID:
14708114
21.

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

Gutiérrez-Ríos RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, Blattner FR, Collado-Vides J.

Genome Res. 2003 Nov;13(11):2435-43.

22.

Networks of transcriptional regulation encoded in a grammatical model.

Collado-Vides J, Gutièrrez-Ríos RM, Bel-Enguix G.

Biosystems. 1998 Jun-Jul;47(1-2):103-18.

PMID:
9715754

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