CURRICULUM VITAE

Claudine MÉDIGUE-ROUSSEAU

Nationality: French

Present position: investigator at the National Center of Scientific Research

Phone: +33 (0) 60 74 79 31
E-mail: cmedigue@infobiogen.fr


EDUCATION

o 2000 Accreditation to supervise research in Biological Science – University of Versailles St Quentin (France)
o 1991 Ph.D. in Biological Science – University of Paris VI (France)
o 1987 Master degree in Bio-Informatics – University of Paris VI (France)
o 1986 Master degree in Biological Science – University of Paris VII (France)

RESEARCH EXPERIENCE

o Since 1999
Setting up, at the Genopole of Evry, 91000 (France), a research team working on the genome annotation of pathogenic micro-organisms and of their models.
o 1992 to 1999
Unité de Régulation de l’Expression Génétique (Institut Pasteur - France) and Atelier de Bio-Informatique (Univ of Paris VI, France): Development of an integrated computer environment for prokaryotic genomes annotation (Imagene).
o 1989 to 1991
Unité de Régulation de l’Expression Génétique (Institut Pasteur - France) and Atelier de Bio-Informatique (Univ of Paris VI, France): Development of a specialized data base for the study of the Escherichia coli genome (Colibri).

SUPERVISING EXPERIENCE

o 2001 Géraldine Pascal (Master degree) – University of Toulouse
Jean-François Vincent (engineer IEE in computer science) – Evry
Christophe Devine(engineer IEE in computer science) – Evry
o 2000 David Vallenet (Master degree) – University of Clermont-Ferrand
Laurent Labarre (Ph.D.) – University of Versailles St Quentin
o 1999 Stéphanie Bocs (Ph.D.) – University of Paris VI
Stéphane Declère (Master degree/engineer) – University of Paris VI
o 1999 Céline Lefèbvre (Master degree) – University of Paris VI
o 1997 Corinne Millerat (engineer CNAM in computer science) –Paris

TEACHING EXPERIENCE

o Lecture on genome annotation in the context of Master degree:
DESS d'Informatique Appliquée à la Biologie - University of Paris VI
DESS Ingénierie génomique fonctionnelle - University of Paris VII and Evry
o Lecture on genome annotation at the ISTM (Marne La Vallée, 94000).
o Lecture on the in silico sequence analysis in the context of Master degree:
DESS d'Informatique Appliquée à la Biologie - University of Paris VI
DEA de Génétique des Populations - University of Marseille

PUBLICATIONS

[1] Médigue C., Bouché, J.P., Hénaut A. and Danchin A. (1990) Mapping of sequenced genes (700 kbp) on the restriction map of the E. coli chromosome. Mol. Microbiol., 4, 169-187.

[2] Médigue C., Hénaut A. and Danchin A. (1990) Escherichia coli molecular genetic map (1000 kb): update I. Mol. Microbiol., 4, 1443-1454.

[3] Danchin A., Médigue C., Gascuel O., Soldano H., and Hénaut A. (1991) From data banks to data bases. Research in Microbiology, 142, 913-916.

[4] Médigue C., Viari A., Hénaut A. and Danchin A. (1991) Escherichia coli molecular genetic map (1500 kb): update II. Mol. Microbiol., 5, 2629-2640.

[5] Médigue C., Rouxel T., Vigier P., Hénaut A., and Danchin A. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol., 222, 851-856.

[6] Médigue C. (1992) COLIBRI, une base de données spécialisée dédiée a l'analyse du génome d' Escherichia coli. In Traitement de l'Information des séquences biologiques, vol II; Cahiers IMABIO, 5, 5-13.

[7] Médigue C., Viari A., Hénaut A. and Danchin A. (1993) Colibri : a functionnal database for the Escherichia coli genome. Microbiol. Rev., 57, 623-654.

[8] Schmeltzer O., Médigue C., Perrière G. and Rechenmann F. (1993) Building large knowledge bases in molecular biology. Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. AAAI/MIT Press, Menlo Park A., pp 345-353.

[9] Médigue C., Willamowski J., Chevenet F. and Rechenmann F. (1993) Modeling tasks for problem solving in molecular biology. Proceedings of the IJCAI’93 Workshop "Artificial intelligence and genome", pp 67-76.

[10] Borodovsky M., McIninch J., Médigue C., Rudd K. and Danchin A. (1995) Detection of new genes in the bacterial genome using Markov models for three gene classes. Nucleic. Acids Res, 17, 3554-3562.

[11] Médigue C., Vermat T., Bisson G., Viari A. and Danchin A. (1995) Cooperative computer system for genome sequence analysis. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI/MIT Press, Menlo Park A., pp. 249-258.

[12] Médigue C., Moszer I., Viari A. and Danchin A. (1995) Analysis of a B. subtilis genome fragment using a cooperative computer system prototype. Gene, 165, GC37-GC51.

[13] Kunst, F., N. Ogasawara, I. Moszer, A.M. Albertini, G. Alloni, V. Azevedo, M.G. Bertero, P. Bessières, A. Bolotin, S. Borchert, ...C. Médigue, ... & Danchin A. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.

[14] Danchin A., Médigue C. and Rechenmann F. (1998) Integrated Genome Informatics. In Bacterial Genome : Physical Structure and Analysis, Ed Chapman & Hall, pp: 567-582.

[15] Médigue C., F. Rechenmann, A. Danchin, and Viari A. (1999) Imagene : an integrated computer environment for sequence annotation and analysis. Bioinformatics, 15, 2-15.

[16] Médigue, C., M. Rose, A. Viari and Danchin A. (1999) Detecting and Analysing Sequencing Errors: Toward a High Quality of the Bacillus subtilis Genome Sequence. Genome Research, 9, 1116-1127.
[17] Rocha E., I. Moszer, M. Klaerr-Blachard, A. Sekowska, C. Médigue, A. Viari and A. Danchin (2000) In silico genome analysis. In Functionnal Analysis of Bacterial Genes: A Practical Manual, Ed W. Schumann, S.D. Ehrlich & N. Ogasawara, pp:
[18] Labarre L., Declère S., Danchin A., and Médigue, C. "Frameshift sequencing errors detection in DNA sequences: what about complete bacterial genomes ?". (submitted to EMBO Report).
[19] Bocs S., Blazy S., Frangeul L., Danchin A., and Médigue, C "Re-annotation of microbial genomes CoDing Sequences : finding new genes and wrongly annotated genes" (sumitted to Nucleic Acid Research).
[20] Médigue C., Bocs S., Labarre L., Mathé C., Vallenet D. "L’annotation in silico des séquences génomiques". Médecine et Sciences, numéro spécial Bio-informatique (in press).
[21] Labarre L., Vallenet D., Lefèbvre C., Viari A., Moszer I., and Médigue, C "PkGDB: a Prokaryotic Genomes Data Base for comparative genomics in bacteria". (En préparation).

CONFERENCES AND SYMPOSIA

Médigue C., Hénaut A. and Danchin A. (1989) Localisation d'un segment du génome d’ E coli sur la carte physique totale du chromosome. Workshop "RBMI". ENS Paris, 8-9 juin.
Médigue C., Delorme M.O., Hénaut A. and Danchin A. (1990) Self-consistency of the Escherichia coli genome. Workshop "Computer applications in biosciences". Munich, 15-17 novembre 1990.
Médigue C., Hénaut A. and Danchin A. (1991) Data bases for Escherichia coli and Bacillus subtilis genomes. Meeting " Genome analysis in the EC". Elounda, Crète, 15-17 mai.
Médigue C., Viari A., Hénaut A. and Danchin A. (1992) COLIBRI, a data base dedicated to the analysis of Escherichia coli genome. Meeting " Genome mapping and sequencing". Cold Spring Harbor Laboratory, 6-10 mai.
Médigue C., Willamowski J., Viari A., and Danchin A. (1996) PowerGene : une plateforme informatique dédiée à l’analyse des séquences biologiques. Journées départementales de l’Institut Pasteur, 2-3 avril.
Viari A. and Médigue C. (1997) ImaGene : Un environnement intégré pour l’annotation et l’analyse de séquences génomiques. 7ème Rencontre INRIA Industrie "Technologies de l’information et santé". 22 Octobre.
Médigue C., Rocha E., Danchin A., and Viari A. (1997) PowerGene :An integrated Computer Environment for Sequence Annotation and Analysis. 1st annual conference on Computational Genomics, Herndon VA. 1-4 november.
L. Jones, I Moszer, M. Klaerr-Blanchard, C. Médigue, A. Viari, and A. Danchin (1999) GenomeList : a web based microbial genome browser. 3rd annual Microbial Genome Conference, Virginia. January 29- February 1.
Viari A., Rocha E.P.C, Médigue C., and A. Danchin (1999) Replication-induced Constraints on Genes and Proteins Composition in Bacteria. 3rd annual Microbial Genome Conference, Virginia. January 29- February 1.
Médigue C., Viari A., Rose M., and A. Danchin (1999) Finding sequencing errors in DNA sequences based on intrinsic properties of coding regions: what about available complete prokaryotic genomes? The Second Georgia Tech International Conference on Bioinformatics. "In silico Biology Sequence & Structure & Function", Atlanta, Georgia, November 11-14.
Bocs S., Blazy S., Glaser P., and Médigue C. (2000) An Automatic Detection of Prokaryotic CoDing Sequences Combining Several Independant Methods. Genome 2000 : International Conference on Microbial and Model Genomes. Paris, April 11-15.
Declère S., Lefebvre C., Viari A., and Médigue C. (2000) A simple strategy to Compare Bacterial Genomic Contexts. Genome 2000 : International Conference on Microbial and Model Genomes. Paris, April 11-15.
Médigue C. (2000) Annotation des génomes de micro-organismes pathogènes : objectifs et moyens. Journées Péri-Bio : rencontre informaticiens, statisticiens et bio-informaticiens. Evry, 25 et 26 Avril.
Bocs S. et Médigue C. (2000) Annotation automatique des régions codantes de génomes bactériens. Colloque T.A.S Evry, 22, 23 et 24 Novembre
Médigue C. (2001) Annotation de régions codantes et détection d’erreurs frameshifts dans les génomes bactériens : application à l’analyse du génome de Yersinia pestis. Colloque IMPG : Détection de Gènes - Méthodes et Outils. Gif-sur-Yvette, 5 et 6 Mars.


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