François SERRA
29 years
[email protected]
Tel: +34 963289681 ext. 3004
Academic data
2007
MSc Structural Genomics and Bioinformatics . ULP, Strasbourg (France)2005
BSc Biology specialized in physiology and neurophysiology. ULP, Strasbourg (France)Professional background and research experience
since 09/2007
PhD student Genomics Unit at Centro de Investigación Príncipe Felipe (CIPF).. Valencia (Spain) Comparative02/2007-05/2007
Intern at Centro de Investigación Príncipe Felipe (CIPF). Functional Genomics Unit. Valencia (Spain).10/2006-01/2007
(200 hours)
Intern at Ecole Supérieur de Biotechnologie de Strasbourg (ESBS). Structural study on a membrane protein. Strasbourg (France).
Teaching Experience
06/2010
05/2008
06/2009
Course on Molecular Evolution, Phylogenetics, Phylogenomics & Adaptation.Centro de Investigación Príncipe Felipe, Valencia, Spain.CIPF, Valencia (Spain).Teaching assistant in a 5 days course.
09/2010
11/2009
02/2010
02/2009
A Primer on Molecular Evolution and Phylogenetics.
Department of Genetics, University of Cambridge (UK). Teaching assistant in a 3 days course.
04/2011
03/2009
02/2010
MEPA, Molecular Evolution, Phylogenetics and Adaptation.Gulbenkian Training Programme in Bioinformatics, Instituto Gulbenkian de Ciência. Oeiras (Portugal).Teaching assistant in a 5 days course.
03/2011 03/2010
Exploring genomes with Ensembl.Master Biología molecular celular y genética. Universitat de Valencia. Spain.Teaching assistant in a 2 hours course.
08/2011 08/2011
Introduction to Molecular Evolution and Adaptation.
Training course “Genómica y bioinformática: conceptos y usos de herramientas web” for teachers/lecturers in the program:
Centros de Formación, Innovación
y Recursos Educativos
(CEFIRE).Additional Merits and Experience
Specialized Courses and workshops
01-02/03/2011
Seminario de Formación sobre “Como redactar un articulo cientifico”.Centro de Investigacion Principe Felipe. Valencia (Spain)
31/05-04/06/2010
Montreal Spring School of Population Genomics and Genetic Epidemiology. Collège Jean-de-Brébeuf Montréal, Qc, (Canada). (with travel awards).09-19/07/2009
Computational Phyloinformatics - a GTPB-NESCent Collaboration.Instituto Gulbenkian de Ciência. Oeiras (Portugal)
14-25/01/2008
European course “Comparative Genomics”. Ecole Normale Supérieure de Lyon. Lyon (France)Other professional experience
since 09/2011
Journal Referee:BMC BioinformaticsComplementary skills
Informatics
• Python, R, Perl, Unix shell script, Java (initiate), PHP (initiate).
• Experience with version control Git/SVN.
• Database interaction with mySQL, PostgreSQL.
• Regular use of the CIPF’s computing cluster (200 CPUs) (European Award to the first
• computing cluster dedicated to bioinformatics running entirely on open-source
• software ).
• Experience with queue systems (Oracle Grid Engine) .
Bioinformatics
• Experience in computational analysis of molecularevolution and adaptation (PAML),
phylogenetics, phylogenomics, and functional genomics.
• Developmentofautomated pipelinesfor genome or large scale analysis integrating different data sources, resulting data management, analysis, and presentation of results.
• Familiarity with publicly available genomic data sets, standard biological databases, and APIs (sequence, functional, orthology, structural, expression, interaction)
Publications
Published Articles
Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments.
Gonçalves L, Borges N, Serra F, Fernandes P, Dopazo H and Santos H.
Environmental Microbiology, accepted (2011 Sep)
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics, and hypotheses testing.
Sánchez, R*, Serra F*, Tárraga J*, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H
Nucleic Acids Res., 39(Web Server issue):W470-4 (2011 Jul) * Authors contributed equally to this work.
Role of tomato BRANCHED1-like genes in the control of shoot branching .
Martín-Trillo M, González Grandío E , Serra F, Marcel F, Rodriguez-Buey M L, Schmitz G, Theres K, Bendahmane A, Dopazo H, Cubas P
The Plant Journal ,
67(4):701-714
(2011Jun)Natural Selection on Functional Modules, a Genome-Wide Analysis. Serra F, Arbiza L, Dopazo J, Dopazo H
PLoS Comput Biol, 7(3):e1001093(2011 Mar)
Recent human evolution has shaped geographical differences in susceptibility to disease.
Marigorta UM, Lao O, Casals F, Calafell F, Morcillo-Suárez C, Faria R, Bosch E, Serra F, Bertranpetit J, Dopazo H, Navarro A
BMC Genomics, 12(1):55(2011 Jan)
Submitted Articles (2011)
Sexual Selection and the Evolution of Protamines in Primates and Rodents. Serra F, Roldán E, Dopazo H, Gomendio M.
Evolutionary genomics of genes involved in olfactory behavior in the Drosophila
melanogaster species group: timing of expression and position in the signal transduction pathway.
Lavagnino N, Serra F, Arbiza, L, Dopazo H, Hasson E.
Sexual selection halts the relaxation of Protamine 2 among Rodents.
Lüke L, Vicens A, Serra F, Luque-Larena J J, Dopazo H, Roldán E, and Gomendio M.
On the Universal Random-like Structure of Genomes.
Becher V, Barenbaum P, Deymonnaz A, Halsband M, Ariel Heiber P, Sánchez R, Herrero J,
Book chapters
Genómica Comparativa y Selección Natural. Aplicaciones en el Genoma Humano.
Serra F, Arbiza L y Dopazo H.
Capítulo 1.6. En: "Evolución y Adaptacón. 150 años después del Origen de las Especies". Hernán Dopazo y Arcadi Navarro (Eds). Pp. 51-59.Obrapropia. Valencia. España. (2009)
Oral communications and Posters
Presentations
The influence of sexual selection upon sperm design in mammals: integrating phenotypic and genomic approaches.
Gomendio M, Tourmente M, Lueke L, Gomez-Montoto L, Vicens A, Serra F, Dopazo H, & Roldan E.
NEW DIRECTIONS IN SEXUAL SELECTION RESEARCH: Unifying behavioural & genomic approaches. University of Bath (UK). (01-04/09/2010)
Duplication and divergence of branched1-like genes and the evolution of the control of shoot branching in tomato.
Martín Trillo M, González Grandío E , Serra F, Rodriguez Buey ML, Dopazo H , Cubas P.
XVII Congress of the Federation of European Societies of Plant Biology (FESPB). Valencia (Spain). (05/07/2010)
Genome Scale Adaptation by Selection on Functional Modules. Serra F, DopazoH.
Segundo Congreso de la Sociedad Española de Biología Evolutiva. Valencia, Spain.
(02/12/2009)
Refocusing genome scale analysis of adaptation at functional level. Serra F, Dopazo H.
GDRE - RA Comparative genomics Fourth meeting. Lyon, France. (16/10/2009)
Presentation of Phylemon, the suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Serra F, Arbiza L, Dopazo H.
INB ROADSHOW. Sevilla, Spain. (14-15/01/2009)
Posters
Phylogenomics and Evolution of Paralogs in Drosophila Species.
Serra F, Huerta-Cepas J, Gabaldón T, Dopazo H. GDRE-RA Comparative genomics Fifth meeting. Barcelona, Spain.(16-17/11/2010)
Phylogenomics and Evolution of Paralogs in Drosophila Species. Serra F, Huerta-Cepas J, Gabaldón T, Dopazo H.
Xth Spanish Symposium on Bioinformatics (JBI2010). Málaga, Spain. (17-19/10/2010)
Phylogenomics and Evolution of Paralogs in Drosophila Species. Serra F, Huerta-Cepas J, Gabaldón T, Dopazo H.
Frontiers in Biodiversity: a Phylogenetic Perspective. Barcelona, Spain. (01-02-2010)
Molecular evolution of olfactory behavior genetic basis in Drosophila.
Lavagnino N, Serra F, Arbiza L, Dopazo H, and Hasson E.
Comparative Analysis of Genes under Alternative Selective Strength during Primates and Murid Evolution.
Serra F, Arbiza L, Dopazo H.
8th Spanish Symposium on Bioinformatics and Computational Biology. Valencia, Spain.
(01/02/2008)
Phylemon 2.0: New resources in a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Tarraga J, Medina I, Huertas-Cepas J, Serra F, Arbiza L, Gabaldón T, Dopazo J, Dopazo H.
8th Spanish Symposium on Bioinformatics and Computational Biology. Valencia, Spain.
