ohnosequences!

era7 bioinformatics R&D group

publications

group members publications, (more or less accurate) reverse chronological order:

  • 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
    Journal of Vaccines & Vaccination | 2015 | journal link

  • 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 | 2015 | pubmed

  • 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 Announcements | 2015 | pubmed

  • 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 in Molecular Biology | 2015 | pubmed

  • 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 | 2015 | pubmed

  • 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.
    Molecular Ecology Resources | 2014 | pubmed

  • 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
    PLOS ONE | 2014 | pubmed

  • 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.
    Frontiers in Cellular and Infection Microbiology, | 2014 | pubmed

  • Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance. Elena López-Camacho, Rosa Gómez-Gil, Raquel Tobes, Marina Manrique, María Lorenzo, Beatriz Galván, Estefanía Salvarelli, Youssef Moatassim, Iñigo J. Salanueva, Eduardo Pareja, Francisco M. Codoñer, Miguel Alvarez-Tejado, María Pilar Garcillán-Barcia, Fernando De la Cruz, Jesús Mingorance
    Journal of Antimicrobial Chemotherapy | 2013 | pubmed

  • Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population María-Carmen Turrientes, Fernando Baquero, 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
    PLOS ONE | 2013 | pubmed

  • 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 Announcements | 2013 | pubmed

  • Bloody coli: a gene cocktail in Escherichia coli O104:H4 Fernando Baquero, Raquel Tobes
    mBio | 2013 | pubmed

  • 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 Announcements | 2013 | pubmed

  • BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Eduardo Pareja, Raquel Tobes
    PLoS One | 2012 | pubmed

  • Phagosomes Induced by Cytokines Function as anti-Listeria Vaccines: a novel role for functional compartmentalization of STAT-1 and cathepsin-D. Eugenio Carrasco-Marín, Estela Rodriguez-Del Rio, Elisabet Frande-Cabanes, Raquel Tobes, Eduardo Pareja, M. Jesús Lecea-Cuello, Marta Ruiz-Sáez, Fidel Madrazo-Toca, Christoph Hölscher, and Carmen Alvarez-Dominguez.
    The Journal of biological chemistry | 2012 | pubmed

  • Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system. Raquel Tobes, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja-Tobes, and Eduardo Pareja.
    Nature Precedings | 2011 | doi

  • The intact structural form of LLO in endosomes cannot protect against listeriosis. Estela Rodriguez-Del Rio, Elisabet Frande-Cabanes, Raquel Tobes, Eduardo Pareja, M. Jesús Lecea-Cuello, Marta Ruiz-Sáez, Eugenio Carrasco-Marín, and Carmen Alvarez-Dominguez.
    International journal of biochemistry and molecular biology | 2011 | pubmed

  • Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. Rohde, Holger, Junjie Qin, Yujun Cui, Dongfang Li, Nicholas J. Loman, Moritz Hentschke, Wentong Chen, et al.
    The New England journal of medicine | 2011 | pubmed

  • The innate immunity role of cathepsin-D is linked to Trp-491 and Trp-492 residues of listeriolysin O. Eugenio Carrasco-Marín, Fidel Madrazo-Toca, Juan R. de los Toyos, Eva Cacho-Alonso, Raquel Tobes, Eduardo Pareja, Alberto Paradela, et al.
    Molecular microbiology | 2009 | pubmed

  • Characterization of a Listeria monocytogenes protein interfering with Rab5a. Carmen Alvarez-Dominguez, Fidel Madrazo-Toca, Lorena Fernandez-Prieto, Joël Vandekerckhove, Eduardo Pareja, Raquel Tobes, Maria Teresa Gomez-Lopez, et al.
    Traffic | 2008 | pubmed

  • symmetric monoidal (bi)categories with feedback and biological networks. Eduardo Pareja-Tobes, Marina Manrique, Raquel Tobes, and Eduardo Pareja. 2008.
    4th Meeting of the Spanish Systems Biology Network (REBS). | 2008 | slides

  • Cutting Edge: Natural DNA Repetitive Extragenic Sequences from Gram-Negative Pathogens Strongly Stimulate TLR9. Mattias Magnusson, Raquel Tobes, Jaime Sancho, and Eduardo Pareja
    Journal of Immunology | 2007 | pubmed

  • Search spaces representation in optimization problems Pablo Pareja-Tobes, D. Pelta, A. Sancho Royo, and J. Verdegay.
    Expert Systems with Applications | 2007 | doi

  • Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. Raquel Tobes and Eduardo Pareja.
    BMC genomics | 2006 | pubmed

  • ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. Eduardo Pareja, Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Javier Bonal, and Raquel Tobes.
    BMC microbiology | 2006 | pubmed

  • Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Luis Yuste, Ana B. Hervás, Inés Canosa, Raquel Tobes, José Ignacio Jiménez, Juan Nogales, Manuel M. Pérez-Pérez, et al.
    Environmental microbiology | 2006 | pubmed

  • Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. Raquel Tobes and Eduardo Pareja.
    Research in microbiology | 2005 | pubmed

  • REP code: defining bacterial identity in extragenic space. Raquel Tobes and Juan-Luis Ramos.
    Environmental microbiology | 2005 | pubmed

  • The TetR family of transcriptional repressors. Juan L. Ramos, Manuel Martínez-Bueno, Antonio J. Molina-Henares, Wilson Terán, Kazuya Watanabe, Xiaodong Zhang, María Trinidad Gallegos, Richard Brennan, and Raquel Tobes.
    Microbiology and molecular biology reviews  | 2005 | pubmed

  • MicrobialTREE: A user friendly tool for bacterial taxonomy navigation.Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Raquel Tobes, and Eduardo Pareja.
    1st International Student Symposium in Computational Biology | 2005

  • BacTregulators: a database of transcriptional regulators in bacteria and archaea. Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, and Raquel Tobes.
    Bioinformatics | 2004 | pubmed

  • Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Isabel Aranda-Olmedo, Raquel Tobes, Maximino Manzanera, Juan L. Ramos, and Silvia Marqués.
    Nucleic Acids Research | 2002 | pubmed

  • AraC-XylS database: a family of positive transcriptional regulators in bacteria. Raquel Tobes and Juan L. Ramos.
    Nucleic acids research | 2002 | pubmed

  • Two classes of MHC class II interactions with the TCR. Raquel Tobes, Eduardo Pareja, Antonio Nieto, and Javier Martín.
    Immunology today | 1998 | pubmed

  • Allele walking: a new and highly accurate approach to HLA-DRB1 typing. Application to DRB1*04 alleles. Antonio Nieto, Raquel Tobes, Javier Martín, and Eduardo Pareja.
    Tissue antigens | 1997 | pubmed

  • The tetramer model: a new view of class II MHC molecules in antigenic presentation to T cells Eduardo Pareja, Raquel Tobes, Javier Martín, and Antonio Nieto. 1997.
    Tissue antigens | 1997 | pubmed

  • Are thymocytes positively selecting thymocytes?. Raquel Tobes, M. Martìnez-Bueno, and Eduardo Pareja.
    Immunology today | 1996 | pubmed

  • HLA DRB104 alleles typing by allele walking. Antonio Nieto, Raquel Tobes, Javier Vinasco, Javier Martin, and Eduardo Pareja.
    Human Immunology | 1996 | pubmed