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Items: 17

1.

Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae.

Solano-De la Cruz MT, Adame-García J, Gregorio-Jorge J, Jiménez-Jacinto V, Vega-Alvarado L, Iglesias-Andreu LG, Escobar-Hernández EE, Luna-Rodríguez M.

BMC Genomics. 2019 Nov 8;20(1):826. doi: 10.1186/s12864-019-6229-5.

2.

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes.

González LM, Estrada K, Grande R, Jiménez-Jacinto V, Vega-Alvarado L, Sevilla E, Barrera J, Cuesta I, Zaballos Á, Bautista JM, Lobo CA, Sánchez-Flores A, Montero E.

PLoS Negl Trop Dis. 2019 Aug 19;13(8):e0007680. doi: 10.1371/journal.pntd.0007680. eCollection 2019 Aug.

3.

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis.

Jiménez-Jacinto V, Sanchez-Flores A, Vega-Alvarado L.

Front Genet. 2019 Mar 29;10:279. doi: 10.3389/fgene.2019.00279. eCollection 2019.

4.

Whole-exome sequencing in maya indigenous families: variant in PPP1R3A is associated with type 2 diabetes.

Sánchez-Pozos K, Ortíz-López MG, Peña-Espinoza BI, de Los Ángeles Granados-Silvestre M, Jiménez-Jacinto V, Verleyen J, Tekola-Ayele F, Sanchez-Flores A, Menjivar M.

Mol Genet Genomics. 2018 Oct;293(5):1205-1216. doi: 10.1007/s00438-018-1453-2. Epub 2018 Jun 11.

PMID:
29948331
5.

Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment.

Chowdhury-Paul S, Pando-Robles V, Jiménez-Jacinto V, Segura D, Espín G, Núñez C.

J Proteomics. 2018 Jun 15;181:47-59. doi: 10.1016/j.jprot.2018.03.031. Epub 2018 Mar 29. No abstract available.

PMID:
29605291
6.

Differential transcriptome regulation by 3,5-T2 and 3',3,5-T3 in brain and liver uncovers novel roles for thyroid hormones in tilapia.

Olvera A, Martyniuk CJ, Buisine N, Jiménez-Jacinto V, Sanchez-Flores A, Sachs LM, Orozco A.

Sci Rep. 2017 Nov 8;7(1):15043. doi: 10.1038/s41598-017-14913-9.

7.

Global transcriptional start site mapping in Geobacter sulfurreducens during growth with two different electron acceptors.

González G, Labastida A, Jímenez-Jacinto V, Vega-Alvarado L, Olvera M, Morett E, Juárez K.

FEMS Microbiol Lett. 2016 Sep;363(17). pii: fnw175. doi: 10.1093/femsle/fnw175. Epub 2016 Aug 3.

PMID:
27488344
8.

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.

9.

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.

10.

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].

11.

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.

12.

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.

13.

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.

14.

The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons.

González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, Dávila G.

Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3834-9. Epub 2006 Feb 27.

15.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.

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.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D394-7.

16.

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
17.

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.

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.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D303-6.

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