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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Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients
01/01/2016

Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients

Marina Manrique, Eduardo Pareja-Tobes, Eduardo Pareja, Pablo Pareja-Tobes, Raquel Tobes. doi: https://doi.org/10.1101/039107.   Evolution and clinical manifestations of Ebola virus (EBOV) infection overlap with the pathologic processes...

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2015

 

Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells.
01/12/2015

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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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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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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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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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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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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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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A Dendritic Cell-Targeted Vaccine Loaded with Glyceraldehyde-3-Phosphate Dehydrogenase Peptides Proposed for Individuals at High Risk of Listeriosis
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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Biographika: rich interactive data visualizations on the web for the research community
17/06/2015

Biographika: rich interactive data visualizations on the web for the research community

Pablo Pareja Tobes, Eduardo Pareja Tobes, Marina Manrique, Eduardo Pareja, Raquel Tobes doi: https://doi.org/10.1101/021063 When visualizing scientific data one of the current bottlenecks is the lack...

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MG7: Configurable and scalable 16S metagenomics data analysis
01/01/2015

MG7: Configurable and scalable 16S metagenomics data analysis

Alexey Alekhin, Evdokim Kovach, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes; doi: https://doi.org/10.1101/027714   As part of...

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Bio4j: a high-performance cloud-enabled graph-based data platform
20/03/2015

Bio4j: a high-performance cloud-enabled graph-based data platform

Pablo Pareja-Tobes, Raquel Tobes, Marina Manrique, Eduardo Pareja, Eduardo Pareja-Tobes doi: https://doi.org/10.1101/016758 Background. Next Generation Sequencing and other high-throughput technologies...

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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

 

Genomic resources notes accepted 1 April 2014 - 31 May 2014.
14/09/2014

Genomic resources notes accepted 1 April 2014 - 31 May 2014.

Contreras M, de la Fuente J, Estrada-Peña A, Grubhoffer L, Tobes R Mol Ecol Resour. Sep 2014. doi: 10.1111/1755-0998.12298 This article documents the public availability of a global transcriptome comparison between Lyme disease tick vectors, Ixodes...

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Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance.
01/03/2014

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. Mar 2014. doi: 10.1093/jac/dkt419 To...

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A systems biology approach to the characterization of stress response in Dermacentor reticulatus tick unfed larvae.
21/02/2014

A systems biology approach to the characterization of stress response in Dermacentor reticulatus tick unfed larvae.

Villar M, Popara M, Ayllón N, Fernández de Mera IG, Mateos-Hernández L, Galindo RC, Manrique M, Tobes R, de la Fuente J PLoS One. 2014. doi: 10.1371/journal.pone.0089564 Dermacentor reticulatus (Fabricius, 1794) is distributed in Europe and Asia...

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Cellular vaccines in listeriosis: role of the Listeria antigen GAPDH.
21/02/2014

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, Alvarez-Domínguez C Front Cell Infect Microbiol. 2014. doi: 10.3389/fcimb.2014.00022 The use of...

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Statika: managing cloud resources, bioinformatics tools and data.
07/04/2014

Statika: managing cloud resources, bioinformatics tools and data.

Alexey Alekhin, Evdokim Kovach, Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes Next Generation Sequencing (NGS) has brought a revolution to the bioinformatics landscape, definitely reshaping fields such as genomics...

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Bio4j: bigger, faster, leaner
07/04/2014

Bio4j: bigger, faster, leaner

Pablo Pareja-Tobes, Alexey Alekhin, Evdokim Kovach, Marina Manrique, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes Bio4j (http://bio4j.com) is a high-performance cloud-enabled graphbased bi oinformatics da ta pl atform. I t i s one of t he first...

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MG7: A fast horizontally scalable tool based on cloud computing and graph databases for microbial community profiling.
07/04/2014

MG7: A fast horizontally scalable tool based on cloud computing and graph databases for microbial community profiling.

Evdokim Kovach, Alexey Alekhin, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes Methods: MG7 i s a n ope n s ource t ool i mplemented i n J ava a nd Scala, ba sed on c loud c omputing ( Amazon W eb S ervices)....

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2013

Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population
12/09/2013

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; doi:  10.1371/journal.pone.0072963 The...

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Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning Outbreak in Switzerland.
27/06/2013

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

Tobes R, Manrique M, Brozynska M, Stephan R, Pareja E, Johler S Genome Announc. May 2013. doi: 10.1128/genomeA.00214-13e00214-13 We present the first complete genome sequence of a Staphylococcus aureus strain assigned to clonal complex 12. The strain...

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Bloody coli: a gene cocktail in Escherichia coli O104: H4
01/03/2013

Bloody coli: a gene cocktail in Escherichia coli O104: H4

Fernando Baquero, Raquel Tobes; doi:  10.1128/mBio.00066-13 A recent study published in mBio [Y. H. Grad et al., mBio 4(1):e00452-12, 2013] indicates that a rapid introgressive evolution has occurred in Escherichia coli O104:H4...

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Bio4J: An Open source biological data integration platform.
18/03/2013

Bio4J: An Open source biological data integration platform.

Pablo Pareja-Tobes, Eduardo Pareja-Tobes, Marina Manrique, Eduardo Pareja, Raquel Tobes Today’s biology involves many times the use of different omics approaches, in particular, data and information from genomes and proteins are frequently difficult...

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Net7: a new tool for bacterial comparative genomics: massive tracing of vertical and horizontal gene flux between genome elements.
18/03/2013

Net7: a new tool for bacterial comparative genomics: massive tracing of vertical and horizontal gene flux between genome elements.

Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja-Tobes, Marta Brozynska, Eduardo Pareja, Raquel Tobes Identification and epidemiologic studies of pathogenic bacteria are mainly based on genotyping of a set of selected genes. The availability of...

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Genome sequence of Klebsiella pneumoniae KpQ3, a DHA-1 β-lactamase-producing nosocomial isolate
28/02/2013

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; doi:  10.1128/genomeA.00167-12 Klebsiella...

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2012

Phagosomes induced by cytokines function as anti-Listeria vaccines: novel role for functional compartmentalization of STAT-1 protein and cathepsin-D.
27/04/2012

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. Apr 2012. doi: 10.1074/jbc.M112.348615 Phagosomes are critical compartments for...

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BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.
21/11/2012

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. doi: 10.1371/journal.pone.0049239 BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating...

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2011

The intact structural form of LLO in endosomes cannot protect against listeriosis.
15/07/2011

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 LLO is the major immuno-dominant antigen in listeriosis and is also required for protective...

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Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
05/06/2011

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,...

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2009 - 2002

The innate immunity role of cathepsin-D is linked to Trp-491 and Trp-492 residues of listeriolysin O.
01/05/2009

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. May 2009. doi: 10.1111/j.1365-2958.2009.06673.x Listeriolysin O (LLO) is a thiol-activated...

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Search spaces representation in optimization problems
15/05/2008

Search spaces representation in optimization problems

P. Pareja-Tobes , D. Pelta , A. Sancho-Royo, J.L. Verdegay; http://dx.doi.org/10.1016/j.eswa.2007.05.046 We present formally a search space representation method in combinatorial optimization problems, as well as a tool for the...

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Characterization of a Listeria monocytogenes protein interfering with Rab5a.
01/03/2008

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. Mar 2008 Listeria monocytogenes (LM) phagocytic strategy implies...

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Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9.
01/07/2007

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

Magnusson M, Tobes R, Sancho J, Pareja E J Immunol. Jul 2007 Bacterial DNA exerts immunostimulatory effects on mammalian cells via the intracellular TLR9. Although broad analysis of TLR9-mediated immunostimulatory potential of synthetic oligonucleotides...

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Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
01/07/2007

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

Tobes R, Pareja E BMC Genomics. Mar 2006 Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been...

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ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
15/03/2006

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. Mar 2006 Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory...

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The TetR family of transcriptional repressors.
01/06/2005

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. Jun 2005 We have developed a general profile for the proteins of the TetR family of repressors. The stretch that...

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Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
03/04/2005

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

Tobes R, Pareja E Res Microbiol. Apr 2005 Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears...

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Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray.
01/01/2006

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. Jan 2006 Bacterial transcriptional networks are built on a hierarchy of regulators, on top of which...

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REP code: defining bacterial identity in extragenic space.
01/02/2005

REP code: defining bacterial identity in extragenic space.

Tobes R, Ramos JL Environ Microbiol. Feb 2005 Through the analysis of 57 bacterial genomes we have detected repetitive extragenic palindromic DNA sequences (REPs) in 11 species. For a sequence to be considered as REP, the following criteria should...

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BacTregulators: a database of transcriptional regulators in bacteria and archaea.
01/11/2004

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

Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R Bioinformatics. Nov 2004 The BacTregulators database is intended to collect and to integrate information on proteins belonging to defined families of transcriptional regulators in...

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Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01.
01/12/2002

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. Dec 2002 Pseudomonas putida KT2440 is highly successful in colonizing a variety habitats, including aquatic and edaphic niches. In accordance with this ability and with the need to adapt...

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Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
15/04/2002

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

Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marqués S Nucleic Acids Res. Apr 2002 Pseudomonas putida KT2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. Its genome...

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AraC-XylS database: a family of positive transcriptional regulators in bacteria.
01/01/2002

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

Tobes R, Ramos JL Nucleic Acids Res. Jan 2002 The AraC-XylS database contains information about a family of positive transcriptional regulators broadly distributed in bacteria. This specific database focuses on protein sequences and on the biological...

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