<![CDATA[Era7 Bioinformatics - Publications]]> <![CDATA[Era7 Bioinformatics - Publications]]> http://era7bioinformatics.com/assets/logo_asnc.jpg http://era7bioinformatics.com/web/page.cfm?id=388 <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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

]]> <![CDATA[REP code: defining bacterial identity in extragenic space]]> Tobes R, Ramos JL.
Environ Microbiol. 2005 Feb;7(2):225-8.

]]> <![CDATA[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

]]> <![CDATA[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

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements]]> Tobes R, Pareja E.
BMC Genomics. 2006 Mar 24;7:62. Review.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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.

]]> <![CDATA[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. 

]]> <![CDATA[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.

]]> <![CDATA[]]> These are publications of members of Era7 Bioinformatics (in blue):

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