Santi Garcia-Vallvé Biochemistry and Biotechnology Department Rovira i Virgili University. Tarragona. Contact adress: Santi Garcia-Vallve Departament de Bioquímica i Biotecnologia Universitat Rovira i Virgili (URV) Campus Sescelades c/ Marcel·li Domingo s/n 43007 TARRAGONA SPAIN Phone:+34 977558778 Fax:+34 977558232 Email: santi.garcia-vallve at urv.cat

ACADEMIC RECORD

2003-present: Lecturer (Dept. Bioquímica i Biotecnologia, URV) 2001-2003: Assistant Professor (Dept. Bioquímica i Biotecnologia, URV) 2001: EMBO-fellow at the Computational Genomics Group, European Bioinformatic Institute (EBI), Cambridge, UK 2000: Associate Professor (Dept. Bioquímica i Biotecnologia, URV) 1996-1999: PhD degree in Biochemistry (Dept. Bioquímica i Biotecnologia, URV) 1990-1995: B.Sc degree in Chemistry (URV)

RESEARCH INTERESTS

Horizontal Gene Transfer (HGT): There is a recent awareness that horizontal gene transfer, defined as the transmission of DNA between species, is a is a potent evolutionary force in prokaryotes. I have characterizated several cases of transferred genes, sometimes identifying the putative donor species. I have also developed a statistical procedure, based on compsotional parameters (like analysis of G+C contents, codon usage and amino acid usage) and gene position, for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. With these results I have created the Horizontal Gene Transfer Database (HGT-DB). Evolutionary Genomics and Phylogenomics: Development of new Bioinformatic tools for Genome Analysis:

PhD STUDENTS

Eduard Guzmán Descarrega Pere Puigbò Avalos

COLLABORATORS

Dr. Ignacio G. Bravo (Deutsches Krebsforschungszentrum, Infection and Cancer, Heidelberg, Germany) Members of the "Red Nacional de Genómica Bacteriana"

SOCIETY MEMBER

Sociedad Española de Bioquímica y Biología Molecular (SEBBM) Red Nacional de Bioinformática Red Nacional de Genómica Bacteriana Xarxa Catalana de Bioinformàtica Xarxa Catalana de Genòmica i Proteòmica

PEER-REVIEWER JOURNALS

Bioinformatics, BMC Evolutionary Biology, BMC Genomics, Genome, Gene, Journal of Molecular Evolution, Molecular Biology and Evolution, Nucleic Acids Research, Trends in Genetics

PUBLICATIONS

- Puigbò P., Garcia-Vallvé S. and McInerney J.O. (2007) TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 23(12):1556-1558. - Puigbò P., Guzmán E., Romeu A. and Garcia-Vallvé S. 2007 OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research 35:W126-W131. - Guzmán E., Romeu A. and Garcia-Vallve S. 2007 Completely sequenced genomes of pathogenic bacteria: a review. Enfermedades infecciosas y microbiologia clinica. In press. - Rojas A, Montero MA, Guzmán E, Pallejà A, Puigbò P, Garcia-Vallvé S and Romeu A. Thodosius Dobzhansky (1900-1975). El naixement de la teoria sintètica. Actes de la VIII trobada d'història de la ciència i de la tècnica. Barcelona, SCHCT, 2006. 349-354. - Pasamontes A. and Garcia-Vallve S. 2006. Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. BMC Bioinformatics 7:257. - Garcia-Vallve S, Iglesias-Rozas JR, Alonso A, Bravo IG. 2006. Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region. BMC Evol. Biol. 6:20 - Garcia-Vallve, S., Alonso, A. and Bravo, I.G. 2005. Papillomaviruses: different genes have different histories. Trends in Microbiology 13(11):514-21. - Bravo, I.G., Garcia-Vallvé, S., Romeu, A. and Reglero, A. 2004. Prokaryotic origin of cytidylyltransferases and alpha-ketoacid synthases. Trends in Microbiology 12:120-8. - Garcia-Vallve, S. 2004. Contribution of each complex of the mitochondrial respiratory chain in the generation of the proton-motive force. Biochemistry and Molecular Biology Education 32:17-19. - Rojas, A., Garcia-Vallvé, S., Montero, M.A., Arola, Ll. and Romeu, A. 2003. Frameshift mutation events in beta-glucosidases. GENE 314: 191-199.. - Garcia-Vallve, S, Guzman, E., Montero, MA. and Romeu, A. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Research 31: 187-189 - Garcia-Vallve, S, Janssen, P i Ouzounis CA. 2002. Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends in Microbiology 10:445-447. - Garcia-Vallve, S, Simó, FX, Montero, MA, Arola, Ll and Romeu, A. 2002. Simultaneous horizontal gene transfer of a gene coding for ribosomal protein L27 and operational genes in Arthrobacter sp. Journal Molecular and Evolution 55: 632-637. - Garcia-Vallve, S., Romeu, A. and Palau, J. 2000. Horizontal gene transfer in bacterial and archeal complete genomes. Genome Research 10:1719-1725. - Garcia-Vallve, S., Romeu, A. and Palau, J. 2000. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Molecular Biology and Evolution 17:352-361. - Garcia-Vallve, S., Palau, J. and Romeu, A. 1999. Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtili. Molecular Biology and Evolution 16:1125-1134. - Rojas, A., Garcia-Vallve, S., Palau, J. and Romeu, A. 1999. Circular permutation in proteins. Biologia 54:255-277. - Garcia-Vallve, S., Rojas, A., Palau, J. and Romeu, A. 1998. Circular permutants in b-glucosidases (family 3) within a predicted double-domain topology which includes a (b/a)8-barrel. Proteins 31:214-223. - Palau, J., Pujadas, G., Negrete, JA., Viñuales, Y. and Garcia-Vallve, S. 1998. La tecnologia computacional com a eina d’anàlisi per a l’evolució molecular i per al desxiframent d’estructures de proteïnes. Dinàmica Estructural de Macromolècules. Treballs de la Societat Catalana de Biologia 48:93-141 15:665-682. - Garcia-Vallve, S. and Palau, J. 1998. Nuclear receptors, nuclear receptor factors, and nuclear recepetor-like orphans form a large paralog cluster in Homo sapiens. Molecular Biology and Evolution 15:665-682.