Curriculum Vitae Sylvain Gaudan

Address 18 Orchard Street CB1 1JS Cambridge United Kingdom Phone: +44 7877611549 Email: [email protected]

Personal Details Gender: Male Date of birth: 9th of March, 1976 Place of birth: Oloron Sainte Marie, France Present Citizenship: French

Working Experience 04/2000 – 09/2003 Software Engineer at Lion Bioscience AG Heidelberg, Germany Development of tools for the extraction, the statistical analysis and the visualization of information from the biomedical literature. Integration of bio-molecular databases with SRS(Sequence Retrieval System). 07/1999–10/1999 Development of a project management tool at Jouve in Mayenne, France 05/1999–10/1999 Development of an application for the management of plane’s components at Sogerma in Bordeaux, France

Education 11/1996 – 06/2000 Master in Computer Science at the University of Bordeaux, France Specialization: Software Engineering Thesis: System Checking: Simulation of hierarchical automaton; Image Processing: morphing with multi-warping grids.

01/2004 – Today Ph.D. student at the European Bioinformatics Institute, delivered by the University of Cambridge, United Kingdom.

Thesis My thesis consists of exploring and applying linguistic methods to automatically extract information from biomedical publications. This involves the development of machine learning techniques and statistical methods to handle the complexity of the language and the properties of the biomedical terminology.

Computer Science Skills XML

SAX and DOM parsing, XSLT transformation, DTD and xmlschema validation Web CSS, XHTML, JSP, Servlets and Tomcat Lang C, Ocaml, Java, Lisp, Python, Shell-script Theory Trees, Graphs, Automata, data mining, classification and information theory NLP Ontology, Parsing and Tagging.

Language Knowledge French English German

native fluent fair

Publications S. Gaudan, A. Jimeno Yepes, V. Lee, D. Rebholz-Schuhmann Identifying Gene Ontology terms in text. Submitted. Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich RebholzSchuhmann Protein Function Predicted from Conserved Protein Interaction Graphs and Validated by the Literature. Submitted. Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P. EBIMed–text crunching to gather facts for proteins from Medline. Bioinformatics. 2007 Jan 15;23(2):e237-44. Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Rynbeek M, Stoehr P. Protein annotation by EBIMed. Nat Biotechnol. 2006 Aug;24(8):902-3.

Rebholz-Schuhmann,D., Kirsch,H., Gaudan,S., Arregui,M., and Nenadic,G. (2006) Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition. Workshop on multidimensional markup with Xml (XMLNLP), EACL 2006, Trente, Italy. S. Gaudan, H. Kirsch, D. Rebholz-Schuhmann. Resolving abbreviations to their senses in Medline. Bioinformatics. 2005 Sep 15;21(18):3658-64. H. Kirsch, S. Gaudan, D. Rebholz-Schuhmann Distributed modules for text annotation and IE applied to the biomedical domain. International Journal of Medical Informatics. 2005 Aug 4. Sylvie Albert, Sylvain Gaudan, Heidrun Knigge, Andreas Raetsch, Asuncion Delgado, Bettina Huhse, Harald Kirsch, Michael Albers, Dietrich Rebholz-Schuhmann and Manfred Koegl. Computer-Assisted Generation of a ProteinInteraction Database for Nuclear Receptors. Mol Endocrinol. 2003 Aug;17(8):1555-67. Christian Gieger, Sylvain Gaudan and Maik Kscischo. Managing biological knowledge using text clustering and feature extraction. Proceedings of the Conference CompStat 2002.

Awards Best Poster Award, In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot, July 2006, Brazil.

References These persons are familiar with my professional qualifications and my character: Dr. D. Rebholz-Schuhmann Thesis supervisor European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom

Cambridge (UK), July 4, 2007

Phone: Fax: Email:

+44 (0)1223 492 594 +44 (0)1223 494 468 [email protected]