Sylvain Gaudan
Home
Past and present
About Me

I did my PhD at the University of Cambridge, doing my research work at the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) based in Heidelberg (Germany). I was previously working for Lion Bioscience AG, also based in Heidelberg.

My research work at the EBI consisted of developing and applying linguistic methods to automatically extract information from biomedical publications. This involved the development of machine learning techniques and statistical methods to handle the complexity of the language and the properties of the biomedical terminology.

For more details, see my CV [pdf].

Contact
Sylvain Gaudan
Appt 1, BAT A, 14 rue Caussade
31400 Toulouse
France
sylvain dot gaudan at gmail dot com
Between you and me
Photography

You can find my tries with black and white photography development on my blog. I developed these prints in the dark room of the Universite of Cambridge (Wolfson College). I mainly use ILFORD FP4 PLUS 125 films and develop on ILFORD MULTIGRADE IV RC paper.
Publications, Posters and Talks
Publications

S. Gaudan, A. Jimeno Yepes, V. Lee, and D. Rebholz-Schuhmann Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text EURASIP Journal on Bioinformatics and Systems Biology Volume 2008 (2008), Article ID 342746, 9 pages doi:10.1155/2008/342746

Jaeger, S., Gaudan, S., Leser, U. and Rebholz-Schuhmann, D. Integrating Protein-Protein Interactions and Text Mining for Protein Function Prediction Workshop on Data Integration for the Life Sciences (DILS), Evry, France, (to appear).

Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga and Dietrich Rebholz-Schuhmann Assessment of disease named entity recognition on a corpus of annotated sentences BMC Bioinformatics 2008, 9(Suppl 3):S3doi:10.1186/1471-2105-9-S3-S3

Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through Web services: calling Whatizit. Bioinformatics. 2008 Jan 15;24(2):296-8. Epub 2007 Nov 15.

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.

Dietrich Rebholz-Schuhmann, Harald Kirsch, Sylvain Gaudan, Miguel Arregui and Goran Nenadic Annotation and Disambiguation of Semantic Types in Biomedical Text: A Cascaded Approach to Named Entity Recognition 11th Conference of the European Chapter of the Association for Computational Linguistics Proceedings of the 5th Workshop on NLP and XML (NLPXML-2006).

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 Protein-Interaction 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
Posters

S. Gaudan, Vivian Lee, Miguel Arregui, Harald Kirsch, Dietrich Rebholz-Schuhmann Indexing text with proteins names under their UniProt PANs In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Award for the Best Poster of the conference. See Abstract. See the poster.

Talks

S. Gaudan EbiMed Centre for Genomic Regulation, Barcelona, Spain - December 2005

S. Gaudan Abbreviation disambiguation in Medline Computer Laboratory, William Gates Building, University of Cambridge, UK - November 2005.

S. Gaudan Resolving abbreviations to their senses in Medline Max Planck Institute for Molecular Genetics, Germany - April 2005.