I am mainly interested in the definition of mathematic models describing genome at gene scale and in the development of algorithmic and combinatoric methods based on the study of genome rearrangements for the comparison of genomes:
- Identification of common markers between different species,
- Rearrangement distance and parsimonious scenarios,
- Reconstruction of ancestral genome architecture.
Journals
- Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan, X, Stegle, O, Behr, J, Steffen, JG, Drewe, P, Hildebrand, KL, Lyngsoe, R, Schultheiss, SJ, Osborne, EJ, Sreedharan, VT, Kahles, A, Bohnert, R, Jean, G, Derwent, P, Kersey, P, Belfield, EJ, Harberd, NP, Kemen, E, Toomajian, C, Kover, PX, Clark, RM, Ratsch, G, and Mott, R.
Nature 477, 419423 (22 September 2011). - SyDiG: Uncovering Synteny in Distant Genomes.
G. Jean, M. Nikolski.
Int. J. of Bioinformatics Research and Applications (2011), 7(1), pages 43-62. - RNA-Seq Read Alignments with PALMapper.
G. Jean, A. Kahles, V.T. Sreedharan, F. De Bona, G. Raetsch.
Curr. Protoc. Bioinform. (2010), 32:11.6.1-11.6.38. - Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire
The Genolevures Consortium.
Genome Research (2009) 19, pages 1696-1709. - Mining the semantics of genome super-blocks to infer ancestral architectures.
G. Jean, D.J. Sherman, M. Nikolski.
Journal of Computational Biology (2009) 16(9), pages 1267-84. - Genome rearrangements : a correct algorithm for optimal capping. (here)
G. Jean, M. Nikolski.
Information Processing Letters (2007) 104 (1),pages 14-20.
Manuscript
- In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf)
G. Jean.
PhD Thesis, 2008.
International conferences
- PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads.
G. Raetsch, G. Jean, A. Kahles, S. Sonnenburg, F. De Bona, K. Schneeberger, J. Hagmann, D. Weigel.
JOBIM 2010, Montpellier, France, September 7-9, 2010. (poster) - PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads.
G. Raetsch, G. Jean, A. Kahles, S. Sonnenburg, F. De Bona, K. Schneeberger, J. Hagmann, D. Weigel.
ISMB 2010, Boston, USA, July 11-13, 2010. (poster) - Reconstruction and visualization of genome rearrangements within the Kluyveromyces.
G. Jean.
First German/French/European meeting yeast and Filamentous Fungi, Strasbourg, France, May 29-31, 2008. - Reconstruction and visualization of genome rearrangements within the Kluyveromyces.
G. Jean, D.J. Sherman, M. Nikolski.
ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution, Sant Feliu, Spain, October 20-25, 2007. - Reconstruction of ancestral genomes within Hemiascomycetes.
G. Jean, M. Nikolski.
Yeast Genome 10th anniversary, Brussels, Belgium, September 7-8, 2006.
Other talks
- In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf)
PhD Defense, Bordeaux, December 9, 2008. - Reconstruction d'architectures ancestrales.
GDR Génolevures, Institut Pasteur, Paris, December, 2007. - De la reconstruction d'un génome médian au calcul de scénarii évolutifs corrects.
Journée satellite GTGC des Journées Ouvertes Biologie Informatique Mathématiques, Marseille, July, 2007. - Parcimonious distance and scenario for multichromosomal genomes
Groupe de Travail Bioinformatique, LaBRI, Bordeaux, February, 2007.
- Reconstruction of ancestral genomes.
GDR Génolevures, ENS, Paris, April, 2006. - Comparing genomic architectures to reconstruct ancestral genomes.
GDR Génolevures, Institut Pasteur, Paris, February, 2006.