We are a multidisciplinary group that tries to apply new perspectives to biological problems especially focused to provide new findings with implications in human health.

Our Research group:

• Raquel Tobes. PhD in Medicine. Bioinformatics expert.
• Eduardo Pareja. PhD in Medicine. Immunologist. Theoretical Biology and Information Technologies expert.
• Isabel Aranda-Olmedo. PhD in Biology. Molecular Biology expert.
• Marina Manrique. Biochemistry student.
• Eduardo Pareja-Tobes. Mathematics student.
• Pablo Pareja-Tobes. Information Technologies student.

We actively participate in several collaborative scientific networks:

• Bacterial Genomics network
• Systems Biology network
• National Bioinformatics network
• Andalusian Bioinformatics network

Publications of the members of the group:

• Raquel Tobes

Tobes R, Pareja E.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
BMC Genomics. 2006 Mar 24;7:62.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
BMC Microbiol. 2006 Mar 15;6:29.

Yuste L, Hervas AB, Canosa I, Tobes R, Jimenez JI, Nogales J, Perez-Perez MM, Santero E, Diaz E, Ramos JL, de Lorenzo V, Rojo F.
Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray.
Environ Microbiol. 2006 Jan;8(1):165-77.

Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R.
The TetR family of transcriptional repressors.
Microbiol Mol Biol Rev. 2005 Jun;69(2):326-56. Review.

Tobes R, Pareja E.
Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
Res Microbiol. 2005 Apr;156(3):424-33.

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

Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.
BacTregulators: a database of transcriptional regulators in bacteria and archaea.
Bioinformatics. 2004 Nov 1;20(16):2787-91.

Martinez-Bueno MA, Tobes R, Rey M, Ramos JL.
Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01.
Environ Microbiol. 2002 Dec;4(12):842-55.

Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marques S.
Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
Nucleic Acids Res. 2002 Apr 15;30(8):1826-33.

Tobes R, Ramos JL.
AraC-XylS database: a family of positive transcriptional regulators in bacteria.
Nucleic Acids Res. 2002 Jan 1;30(1):318-21.

Tobes R, Pareja E, Nieto A, Martin J.
Two classes of MHC class II interactions with the TCR.
Immunol Today. 1998 Apr;19(4):192-3.

Pareja E, Tobes R, Martin J, Nieto A.
The tetramer model: a new view of class II MHC molecules in antigenic presentation to T cells.
Tissue Antigens. 1997 Nov;50(5):421-8. Review.

Nieto A, Tobes R, Martin J, Pareja E.
Allele walking: a new and highly accurate approach to HLA-DRB1 typing. Application to DRB1*04 alleles.
Tissue Antigens. 1997 Feb;49(2):141-51.

Tobes R, Martinez-Bueno M, Pareja E.
Are thymocytes positively selecting thymocytes?
Immunol Today. 1996 Jul;17(7):344-5.

Tobes R, Pareja E.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
BMC Genomics. 2006 Mar 24;7:62.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
BMC Microbiol. 2006 Mar 15;6:29.

Tobes R, Pareja E.
Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
Res Microbiol. 2005 Apr;156(3):424-33.

Martinez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.
BacTregulators: a database of transcriptional regulators in bacteria and archaea.
Bioinformatics. 2004 Nov 1;20(16):2787-91.

Tobes R, Pareja E, Nieto A, Martin J.
Two classes of MHC class II interactions with the TCR.
Immunol Today. 1998 Apr;19(4):192-3.

Vinasco J, Fraile A, Nieto A, Beraun Y, Pareja E, Mataran L, Martin J.
Analysis of LMP and TAP polymorphisms by polymerase chain reaction-restriction fragment length polymorphism in rheumatoid arthritis.
Ann Rheum Dis. 1998 Jan;57(1):33-7.

Pareja E, Tobes R, Martin J, Nieto A.
The tetramer model: a new view of class II MHC molecules in antigenic presentation to T cells.
Tissue Antigens. 1997 Nov;50(5):421-8. Review.

Vinasco J, Beraun Y, Nieto A, Fraile A, Pareja E, Mataran L, Martin J.
Heat shock protein 70 gene polymorphisms in rheumatoid arthritis.
Tissue Antigens. 1997 Jul;50(1):71-3.

Nieto A, Tobes R, Martin J, Pareja E.
Allele walking: a new and highly accurate approach to HLA-DRB1 typing. Application to DRB1*04 alleles.
Tissue Antigens. 1997 Feb;49(2):141-51.

Vinasco J, Beraun Y, Nieto A, Fraile A, Mataran L, Pareja E, Martin J.
Polymorphism at the TNF loci in rheumatoid arthritis.
Tissue Antigens. 1997 Jan;49(1):74-8.

Tobes R, Martinez-Bueno M, Pareja E.
Are thymocytes positively selecting thymocytes?
Immunol Today. 1996 Jul;17(7):344-5..

Fraile A, Vinasco J, Nieto A, Pareja E, Martin J.
Typing for TAP alleles using PCR-RFLP with amplification-created restriction sites.
Tissue Antigens. 1996 Apr;47(4):346-52.

Nieto A, Pareja E.
HLA typing by amplification-created restriction site.
Lancet. 1992 Sep 19;340(8821):735-6.

Aranda-Olmedo I, Marin P, Ramos JL, Marques S.
Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures.
Appl Environ Microbiol. 2006 Nov;72(11):7418-21.

Marques S, Aranda-Olmedo I, Ramos JL.
Controlling bacterial physiology for optimal expression of gene reporter constructs.
Curr Opin Biotechnol. 2006 Feb;17(1):50-6.

Aranda-Olmedo I, Ramos JL, Marques S.
Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0.
Appl Environ Microbiol. 2005 Aug;71(8):4191-8.

Ruíz R, Aranda-Olmedo I, Domínguez-Cuevas P, Ramos-González MI, Marqués S.
Transcriptional regulation of the toluene catabolic pathways.
R. JL (ed.), Pseudomonas, vol. 2, p. 509-537.2004. Kluwer Academic/Plenum Publishers, London.

Dinamarca MA, Aranda-Olmedo I, Puyet A, Rojo F.
Expression of the Pseudomonas putida OCT plasmid alkane degradation pathway is modulated by two different global control signals: evidence from continuous cultures.
J Bacteriol. 2003 Aug;185(16):4772-8.

Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marques S.
Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
Nucleic Acids Res. 2002 Apr 15;30(8):1826-33.

Camacho JP, Bakkali M, Corral JM, Cabrero J, Lopez-Leon MD, Aranda I, Martin-Alganza A, Perfectti F.
Host recombination is dependent on the degree of parasitism.
Proc Biol Sci. 2002 Oct 22;269(1505):2173-7.

Manzanera M, Aranda-Olmedo I, Ramos JL, Marques S.
Molecular characterization of Pseudomonas putida KT2440 rpoH gene regulation.
Microbiology. 2001 May;147(Pt 5):1323-30.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
BMC Microbiol. 2006 Mar 15;6:29

MicrobialTREE: A user friendly tool for bacterial taxonomy navigation. Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Raquel Tobes y Eduardo Pareja.

1st International Student Symposium in Computational Biology. Madrid 2005.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
BMC Microbiol. 2006 Mar 15;6:29.

MicrobialTREE: A user friendly tool for bacterial taxonomy navigation. Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Raquel Tobes y Eduardo Pareja.

1st International Student Symposium in Computational Biology. Madrid 2005.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
BMC Microbiol. 2006 Mar 15;6:29.

MicrobialTREE: A user friendly tool for bacterial taxonomy navigation. Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Raquel Tobes y Eduardo Pareja.

1st International Student Symposium in Computational Biology. Madrid 2005.

Représentation des espaces de recherche dans problèmes d'optimisation" by Pablo Pareja-Tobes, David Pelta, Alejandro Sancho-Royo, and José Luis Verdegay.

IPMU Paris Julio 2007