Publications

These are publications of members of Era7 Bioinformatics (in blue):

2013

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. 2013 Oct 23.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

REP code: defining bacterial identity in extragenic space

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

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

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.

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.

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.