Las siguientes son publicaciones de los miembros de Era7 Bioinformatics. Haga click en el título y podrá ver el abstract y los autores de Era7 resaltados en azul.

2016

 

Expression of Early Growth Response Gene-2 and Regulated Cytokines Correlates with Recovery from Guillain-Barré Syndrome.
01/02/2016

Expression of Early Growth Response Gene-2 and Regulated Cytokines Correlates with Recovery from Guillain-Barré Syndrome.

Doncel-Pérez E, Mateos-Hernández L, Pareja E, García-Forcada Á, Villar M, Tobes R, Romero Ganuza F, Vila Del Sol V, Ramos R, Fernández de Mera IG, de la Fuente J J Immunol. Feb 2016. doi: 10.4049/jimmunol.1502100 Guillain-Barré syndrome (GBS) is...

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2015

 

Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells.
02/12/2015

Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells.

Villar M, Ayllón N, Alberdi P, Moreno A, Moreno M, Tobes R, Mateos-Hernández L, Weisheit S, Bell-Sakyi L, de la Fuente J Mol Cell Proteomics. Dec 2015. doi: 10.1074/mcp.M115.051938 Anaplasma phagocytophilum is an emerging zoonotic pathogen that...

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Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence.
20/11/2015

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence.

de la Fuente J, Díez-Delgado I, Contreras M, Vicente J, Cabezas-Cruz A, Tobes R, Manrique M, López V, Romero B, Bezos J, Dominguez L, Sevilla IA, Garrido JM, Juste R, Madico G, Jones-López E, Gortazar C PLoS Negl Trop Dis. Nov 2015. doi: 10.1371/journal.pntd.0004232 Mycobacteria...

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Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.
25/06/2015

Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.

de la Fuente J, Díez-Delgado I, Contreras M, Vicente J, Cabezas-Cruz A, Manrique M, Tobes R, López V, Romero B, Domínguez L, Garrido JM, Juste R, Gortazar C Genome Announc. 2015. doi: 10.1128/genomeA.00247-15e00247-15 Here we report the complete...

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Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines.
28/05/2015

Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines.

Calderon-Gonzalez R, Tobes R, Pareja E, Frande-Cabanes E, Petrovsky N, Alvarez-Dominguez C J Immunol Methods. Sep 2015. doi: 10.1016/j.jim.2015.05.009S0022-1759(15)30002-8 Dendritic cells loaded with antigenic peptides, because of their safety and...

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Response to
06/05/2015

Response to "In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response".

López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M, Tobes R, Máiz L, Cantón R, Baquero F, del Campo R Mucosal Immunol. May 2015. doi: 10.1038/mi.2015.10 ...

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Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.
06/05/2015

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.

Jiménez E, de Andrés J, Manrique M, Pareja-Tobes P, Tobes R, Martínez-Blanch JF, Codoñer FM, Ramón D, Fernández L, Rodríguez JM J Hum Lact. Aug 2015. doi: 10.1177/0890334415585078 Some studies have been conducted to assess the composition of the...

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Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).
02/03/2015

Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).

Ouma WZ, Mejia-Guerra MK, Yilmaz A, Pareja-Tobes P, Li W, Doseff AI, Grotewold E Sci Rep. 2015. doi: 10.1038/srep08635 Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively...

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In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response.
01/03/2015

In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response.

López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M, Tobes R, Máiz L, Cantón R, Baquero F, Del Campo R Mucosal Immunol. Mar 2015. doi: 10.1038/mi.2014.73 Methicillin-resistant...

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Complete Genome Sequence of Ehrlichia mineirensis, a Novel Organism Closely Related to Ehrlichia canis with a New Host Association.
23/01/2015

Complete Genome Sequence of Ehrlichia mineirensis, a Novel Organism Closely Related to Ehrlichia canis with a New Host Association.

Cabezas-Cruz A, Zweygarth E, Broniszweska M, Passos LM, Ribeiro MF, Manrique M, Tobes R, de la Fuente J Genome Announc. 2015. doi: 10.1128/genomeA.01450-14e01450-14 We report here the complete genome sequencing of Ehrlichia mineirensis, an Ehrlichia...

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20/01/2015

A Dendritic Cell-Targeted Vaccine Loaded with Glyceraldehyde-3-Phosphate Dehydrogenase Peptides Proposed for Individuals at High Risk of Listeriosis

Calderon-Gonzalez G, Frande-Cabanes E, Tobes R, Pareja E, Alaez-Alvarez L, et al. (2015) J Vaccines Vaccin 6:266. doi: 10.4172/2157-7560.1000266 Objective: Individuals at risk of Listeria infection lacked vaccines to prevent the development of severe...

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Gene calling and bacterial genome annotation with BG7.
01/01/2015

Gene calling and bacterial genome annotation with BG7.

Tobes R, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Kovach E, Alekhin A, Pareja E Methods Mol Biol. 2015. doi: 10.1007/978-1-4939-1720-4_12 New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but...

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2014

 

Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines.

Calderon-Gonzalez R, Tobes R, Pareja E, Frande-Cabanes E, Petrovsky N, Alvarez-Dominguez C.

J Immunol Methods. 2015 May 29. pii: S0022-1759(15)30002-8. doi: 10.1016/j.jim.2015.05.009. 

  • Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.

    de la Fuente J, Díez-Delgado I, Contreras M, Vicente J, Cabezas-Cruz A, Manrique M, Tobes R, López V, Romero B, Domínguez L, Garrido JM,Juste R, Gortazar C

    Genome Announc. 2015 Jun 25;3(3). pii: e00247-15. doi: 10.1128/genomeA.00247-15.

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.

Jiménez E, de Andrés J, Manrique M, Pareja-Tobes P, Tobes R, Martínez-Blanch JF, Codoñer FM, Ramón D, Fernández L, Rodríguez JM.

J Hum Lact. 2015 May 6. pii: 0890334415585078.

  • A Dendritic Cell-Targeted Vaccine Loaded with Glyceraldehyde-3-Phosphate Dehydrogenase Peptides Proposed for Individuals at High Risk of Listeriosis

    Ricardo Calderon-Gonzalez, Elisabet Frande-Cabanes, Raquel Tobes, Eduardo Pareja, Lidia Alaez-Alvarez and Carmen Alvarez-Dominguez

    J Vaccines Vaccin 2015, 6: 266

    http://omicsonline.org/vaccines-vaccination-abstract.php?abstract_id=40246

  • Response to "In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response"

    López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M,Tobes R, Máiz L, Cantón R, Baquero F, Del Campo R

    Mucosal Immunology , (4 March 2015) | doi:10.1038/mi.2015.10

    http://www.ncbi.nlm.nih.gov/pubmed/25736458

Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq)

Wilberforce Zachary Ouma, Maria Katherine Mejia-Guerra, Alper Yilmaz, Pablo Pareja-Tobes, Wei Li, Andrea I. Doseff & Erich Grotewold

Scientific Reports 5, Article number: 8635, doi:10.1038/srep08635 

Received 12 October 2014, Accepted 12 January 2015, Published 02 March 2015

http://www.nature.com/srep/2015/150302/srep08635/full/srep08635.html

  • Complete Genome Sequence of Ehrlichia mineirensis, a Novel Organism Closely Related to Ehrlichia canis with a New Host Association.

    Cabezas-Cruz A, Zweygarth E, Broniszweska M, Passos LM, Ribeiro MF, Manrique M, Tobes R, de la Fuente J.

    Genome Announc. 2015 Jan 22;3(1). pii: e01450-14. doi: 10.1128/genomeA.01450-14.

    http://www.ncbi.nlm.nih.gov/pubmed/25614563

  • Gene Calling and Bacterial Genome Annotation with BG7.

    Tobes R, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Kovach E, Alekhin A, Pareja E.

    Methods Mol Biol. 2015;1231:177-89. doi: 10.1007/978-1-4939-1720-4_12.

    http://www.ncbi.nlm.nih.gov/pubmed/25343866

  • In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response.

    López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M, Tobes R, Máiz L, Cantón R, Baquero F, Del Campo R.

    Mucosal Immunol. 2014 Aug 13. doi: 10.1038/mi.2014.73

    http://www.ncbi.nlm.nih.gov/pubmed/25118167

  • Genomic Resources Notes accepted 1 April 2014 - 31 May 2014

    Genomic Resources Development Consortium, Contreras M, de la Fuente J, Estrada-Peña A, Grubhoffer L, Tobes R.

    Mol Ecol Resour. 2014 Jun 27. doi: 10.1111/1755-0998.12298

    http://www.ncbi.nlm.nih.gov/pubmed/24976445

  • A Systems Biology Approach to the Characterization of Stress Response in Dermacentor reticulatus Tick Unfed Larvae.

    Margarita Villar, Marina Popara,  Nieves Ayllón,  Isabel G. Fernández de Mera, Lourdes Mateos-Hernández,  Ruth C. Galindo,  Marina Manrique, Raquel Tobes,  José de la Fuente. February 21, 2014DOI: 10.1371/journal.pone.0089564

Ver también: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089564

  • Cellular vaccines in listeriosis: role of the Listeria antigen GAPDH.

    Calderón-González R, Frande-Cabanes E, Bronchalo-Vicente L, Lecea-Cuello MJ, Pareja E, Bosch-Martínez A, Fanarraga ML, Yañez-Díaz S, Carrasco-Marín E and Álvarez-Domínguez C. Front. Cell. Infect. Microbiol., 21 February 2014 | doi: 10.3389/fcimb.2014.00022

Ver también: http://journal.frontiersin.org/Journal/10.3389/fcimb.2014.00022/full

  • Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance.

    López-Camacho E, Gómez-Gil R, Tobes R, Manrique M, Lorenzo M, Galván B, Salvarelli E, Moatassim Y, Salanueva IJ, Pareja E, Codoñer FM, Alvarez-Tejado M, Garcillán-Barcia MP, De la Cruz F, Mingorance J.

    J Antimicrob Chemother. 2014 Mar;69(3):632-6. doi: 10.1093/jac/dkt419.

    http://www.ncbi.nlm.nih.gov/pubmed/24155060

2013

  • Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population

    María-Carmen Turrientes, Bruce R. Levin,  José-Luis Martínez,  Aida Ripoll,  José-María González-Alba,  Raquel Tobes, Marina Manrique,  Maria-Rosario Baquero,  Mario-José Rodríguez-Domínguez, Rafael Cantón, Juan-Carlos Galán

     2013 PLoS ONE 8(9): e72963. doi:10.1371/journal.pone.0072963

Ver también: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072963

  • Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning Outbreak in Switzerland

    Raquel Tobes, Marina Manrique, Marta Brozynska, Roger Stephan, Eduardo Pareja, Sophia Johler

    Genome Announc. 1(3):e00214-13.doi:10.1128/genomeA.00214-13.

Ver también: http://genomea.asm.org/content/1/3/e00214-13.long

  • Bloody coli: a Gene Cocktail in Escherichia coli O104:H4

    Baquero F, Tobes R.

    MBio. 2013 Feb 19;4(1). doi:pii: e00066-13. 10.1128/mBio.00066-13.

Ver también: http://mbio.asm.org/content/4/1/e00066-13.long

  • Genome Sequence of Klebsiella pneumoniae KpQ3, a DHA-1 β-Lactamase-Producing Nosocomial Isolate

    Raquel Tobes, Francisco M. Codoñer, Elena López-Camacho, Iñigo J. Salanueva, Marina Manrique, Marta Brozynska, Rosa Gómez-Gil, Juan F. Martínez-Blanch, Miguel Álvarez-Tejado, Eduardo Pareja, Jesús Mingorance

    Genome Announc. 1(1):e00167-12. doi:10.1128/genomeA.00167-12.

Ver también: http://genomea.asm.org/content/1/1/e00167-12.long

2012

  • Phagosomes induced by cytokines function as anti-Listeria vaccines: novel role for functional compartmentalization of STAT-1 protein and cathepsin-D.

    Carrasco-Marín E, Rodriguez-Del Rio E, Frande-Cabanes E, Tobes R, Pareja E, Lecea-Cuello MJ, Ruiz-Sáez M, Madrazo-Toca F, Hölscher C, Alvarez-Dominguez C.

    J Biol Chem. 2012 Apr 27;287(18):14310-24. doi: 10.1074/jbc.M112.348615. Epub 2012 Feb 15.

Ver también: http://www.jbc.org/content/287/18/14310.long

  • BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data.

    Pareja-Tobes P, Manrique M, Pareja-Tobes E, Pareja E, Tobes R.

    PLoS One. 2012;7(11):e49239. doi: 10.1371/journal.pone.0049239. Epub 2012 Nov 21.

Ver también: http://dx.plos.org/10.1371/journal.pone.0049239

Archivo: BG7_journal_pone_0049239.pdf 

 

2011

  • Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.

    Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R; E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium. (**Marina Manrique from Era7 is a member of the Genome Analysis Crowd-Sourcing Consortium)

    N Engl J Med. 2011 Aug 25;365(8):718-24. Epub 2011 Jul 27. 

Ver también: http://www.ncbi.nlm.nih.gov/pubmed?term=21793736

  • The intact structural form of LLO in endosomes cannot protect against listeriosis.

    Rodriguez-Del Rio E, Frande-Cabanes E, Tobes R, Pareja E, Lecea-Cuello MJ, Ruiz-Sáez M, Carrasco-Marín E, Alvarez-Dominguez C.

    Int J Biochem Mol Biol. 2011;2(3):207-18. Epub 2011 Jul 15.

Ver también: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193297/

2009 - 2002

  • The innate immunity role of cathepsin-D is linked to Trp-491 and Trp-492 residues of listeriolysin O

    Carrasco-Marín E, Madrazo-Toca F, de Los Toyos JR, Cacho-Alonso E, Tobes R, Pareja E, Paradela A, Albar JP, Chen W, Gomez-Lopez MT, Alvarez-Dominguez C.
    Mol Microbiol. 2009 Apr 6.

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/19389128

  • Search spaces representation in optimization problems

    P. Pareja-Tobes, David A. Pelta, Alejandro Sancho-Royo, José L. Verdegay

    Expert Syst. Appl. 01/2008; 34:2891-2895.

  • Characterization of a Listeria monocytogenes protein interfering with Rab5a

    Alvarez-Dominguez C, Madrazo-Toca F, Fernandez-Prieto L, Vandekerckhove J, Pareja E, Tobes R, Gomez-Lopez MT, Del Cerro-Vadillo E, Fresno M, Leyva-Cobián F, Carrasco-Marín E.
    Traffic. 2008 Mar;9(3):325-37.

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/18088303

  • Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9

    Magnusson M, Tobes R, Sancho J, Pareja E.
    J Immunol. 2007 Jul 1;179(1):31-5.

Ver también: http://www.jimmunol.org/content/179/1/31.long

  • Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements

    Tobes R, Pareja E.
    BMC Genomics. 2006 Mar 24;7:62. Review.

Ver también: http://www.biomedcentral.com/1471-2164/7/62

  • ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms

    Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
    BMC Microbiol. 2006 Mar 15;6:29.

Ver también: http://www.biomedcentral.com/1471-2180/6/29

  • The TetR family of transcriptional repressors

    Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R.

    Microbiol Mol Biol Rev. 2005 Jun;69(2):326-56

Ver también: http://mmbr.asm.org/content/69/2/326.long

  • Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation

    Tobes R, Pareja E.
    Res Microbiol. 2005 Apr;156(3):424-33. Epub 2005 Jan 28.

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/15808947

  • Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray

    Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, Díaz E, Ramos JL, de Lorenzo V, Rojo F.
    Environ Microbiol. 2006 Jan;8(1):165-77

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/16343331

  • REP code: defining bacterial identity in extragenic space

    Tobes R, Ramos JL.
    Environ Microbiol. 2005 Feb;7(2):225-8.

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/15658989

  • BacTregulators: a database of transcriptional regulators in bacteria and archaea

    Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.
    Bioinformatics. 2004 Nov 1;20(16):2787-91

Ver también: http://bioinformatics.oxfordjournals.org/content/20/16/2787.long

  • Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01

    Martínez-Bueno MA, Tobes R, Rey M, Ramos JL.
    Environ Microbiol. 2002 Dec;4(12):842-55.

Ver también: http://www.ncbi.nlm.nih.gov/pubmed/12534467

  • Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida

    Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marqués S.
    Nucleic Acids Res. 2002 Apr 15;30(8):1826-33.

Ver también: http://nar.oxfordjournals.org/content/30/8/1826.long

  • AraC-XylS database: a family of positive transcriptional regulators in bacteria

    Tobes R, Ramos JL.
    Nucleic Acids Res. 2002 Jan 1;30(1):318-21.

Ver también: http://nar.oxfordjournals.org/content/30/1/318.long