These are publications of members of Era7 Bioinformatics (Click on "see publication" to see the abstract and the Era7's members highlighted in blue):

2016

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Expression of Early Growth Response Gene-2 and Regulated Cytokines Correlates with Recovery from Guillain-Barré Syndrome.
30/12/2015

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. Dec 2015 Guillain-Barré syndrome (GBS) is an immune-mediated peripheral...

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2015

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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.
19/11/2015

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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Integrated metabolomics, transcriptomics and proteomics identifies metabolic pathways affected by Anaplasma phagocytophilum infection in tick cells.
07/10/2015

Integrated metabolomics, transcriptomics and proteomics identifies metabolic pathways affected by Anaplasma phagocytophilum infection in tick cells.

Villar M, Ayllon N, Alberdi P, Moreno A, Moreno M, Tobes R, Mateos-Hernandez L, Weisheit S, Bell-Sakyi L, de la Fuente J Mol Cell Proteomics. Sep 2015 Anaplasma phagocytophilum is an emerging zoonotic pathogen that causes human granulocytic anaplasmosis....

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Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).
07/10/2015

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.
07/10/2015

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.
07/10/2015

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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Response to
07/10/2015

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.
07/10/2015

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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Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines.
07/10/2015

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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Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.
07/10/2015

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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Gene calling and bacterial genome annotation with BG7.
08/10/2015

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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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

2014

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  • 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, 2014. DOI: 10.1371/journal.pone.0089564

    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

    http://www.ncbi.nlm.nih.gov/pubmed/24600592

  • 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

    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.

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

    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.

    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.

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

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. 

    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.

    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.

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

  • 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.

    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.

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

  • 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.

    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

    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.

    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

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

  • 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.

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