Main.Research History

Hide minor edits - Show changes to markup

November 16, 2011, at 05:08 PM by 193.52.105.131 -
Changed line 10 from:

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.\\

to:

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.\\

Restore
November 16, 2011, at 05:07 PM by 193.52.105.131 -
Added lines 8-12:
  • 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, 419–423 (22 September 2011).
Restore
April 10, 2011, at 05:11 PM by 192.124.26.250 -
Changed lines 10-11 from:

Int. J. of Bioinformatics Research and Applications (2011), 7(1), pages 43-62.

to:

Int. J. of Bioinformatics Research and Applications (2011), 7(1), pages 43-62.

Changed lines 14-16 from:

Curr. Protoc. Bioinform. (2010), 32:11.6.1-11.6.38.

to:

Curr. Protoc. Bioinform. (2010), 32:11.6.1-11.6.38.

Changed lines 19-21 from:

Genome Research (2009) 19, pages 1696-1709.

to:

Genome Research (2009) 19, pages 1696-1709.

Changed lines 24-25 from:

Journal of Computational Biology (2009) 16(9), pages 1267-84.

to:

Journal of Computational Biology (2009) 16(9), pages 1267-84.

Changed line 41 from:
  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. (poster)\\
to:
  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. \\
Changed lines 43-46 from:

JOBIM 2010, Montpellier, France, September 7-9, 2010.

  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. (poster)\\
to:

JOBIM 2010, Montpellier, France, September 7-9, 2010. (poster)

  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. \\
Changed lines 48-49 from:

ISMB 2010, Boston, USA, July 11-13, 2010.

to:

ISMB 2010, Boston, USA, July 11-13, 2010. (poster)

Changed lines 74-75 from:

Journée satellite GTGC des Journées Ouvertes Biologie Informatique Mathématiques, Marseille, July, 2007.

to:

Journée satellite GTGC des Journées Ouvertes Biologie Informatique Mathématiques, Marseille, July, 2007.

Restore
April 10, 2011, at 05:09 PM by 192.124.26.250 -
Added lines 41-48:
  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. (poster)
    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.
  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. (poster)
    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.
Restore
April 10, 2011, at 05:04 PM by 192.124.26.250 -
Changed line 7 from:

Publications

to:

Journals

Restore
April 10, 2011, at 04:58 PM by 192.124.26.250 -
Changed lines 22-23 from:
  • Mining the semantics of genome super-blocks to infer ancestral architectures.
    G. Jean, D.J. Sherman, M. Nikolski.\\
to:
  • Mining the semantics of genome super-blocks to infer ancestral architectures.
    G. Jean, D.J. Sherman, M. Nikolski.\\
Restore
April 10, 2011, at 04:58 PM by 192.124.26.250 -
Changed lines 8-9 from:
  • SyDiG: Uncovering Synteny in Distant Genomes.
    G. Jean, M. Nikolski.\\
to:
  • SyDiG: Uncovering Synteny in Distant Genomes.
    G. Jean, M. Nikolski.\\
Changed line 18 from:

The G\'enolevures Consortium.\\

to:

The Genolevures Consortium.\\

Deleted line 19:
Restore
April 10, 2011, at 04:56 PM by 192.124.26.250 -
Changed lines 10-11 from:

Int. J. of Bioinformatics Research and Applications (2011), 7(1), pages 43-62.

to:

Int. J. of Bioinformatics Research and Applications (2011), 7(1), pages 43-62.

Changed lines 13-16 from:

G. Jean, A. Kahles, V.T. Sreedharan, F. De Bona, G. Raetsch, Curr. Protoc. Bioinform. (2010), 32:11.6.1-11.6.38.

to:

G. Jean, A. Kahles, V.T. Sreedharan, F. De Bona, G. Raetsch.
Curr. Protoc. Bioinform. (2010), 32:11.6.1-11.6.38.

Changed lines 18-22 from:

The G\'enolevures Consortium.\\ Genome Research (2009) 19, pages 1696-1709.\\

to:

The G\'enolevures Consortium.
Genome Research (2009) 19, pages 1696-1709.

Changed line 25 from:

Journal of Computational Biology (2009) 16(9), pages 1267-84.\\

to:

Journal of Computational Biology (2009) 16(9), pages 1267-84.

Restore
April 10, 2011, at 04:53 PM by 192.124.26.250 -
Changed lines 8-16 from:
  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    Genome Research, online access ahead of print.
  • Mining the semantics of genome super-blocks to infer ancestral architectures.
    G. Jean, D.J. Sherman, M. Nikolski.
    To appear in Journal of Computational Biology.
to:
  • 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 G\'enolevures 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.

Changed lines 32-37 from:

Submitted papers and manuscripts

  • SyDiG: Uncovering Synteny in Distant Genomes.
    G. Jean, D.J. Sherman, M. Nikolski.
    Submitted to Int. J. of Bioinformatics Research and Applications.
to:

Manuscript

Restore
June 24, 2009, at 02:42 PM by 147.210.129.124 -
Changed line 11 from:

To appear in Genome Research.

to:

Genome Research, online access ahead of print.

Restore
April 28, 2009, at 05:20 PM by 147.210.129.124 -
Changed lines 48-49 from:

G. Jean, M. Nikolski.\\ ''Yeast Genome 10th anniversary, Brussels, Belgium, September 7-8, 2006.

to:

G. Jean, M. Nikolski.
Yeast Genome 10th anniversary, Brussels, Belgium, September 7-8, 2006.

Restore
April 28, 2009, at 05:19 PM by 147.210.129.124 -
Changed line 48 from:

G. Jean, M. Nikolski.

to:

G. Jean, M. Nikolski.\\

Restore
April 22, 2009, at 01:56 PM by 147.210.129.124 -
Changed lines 9-12 from:
to:
  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    To appear in Genome Research.
Deleted lines 28-30:
  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    Submitted to Genome Research.
Restore
March 30, 2009, at 10:13 PM by 127.0.0.1 -
Changed line 30 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf) Δ\\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf)\\
Changed line 54 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf)\\
Restore
March 30, 2009, at 10:10 PM by 127.0.0.1 -
Changed line 30 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction (pdf) Δ\\
Restore
March 30, 2009, at 09:37 PM by 127.0.0.1 -
Changed line 30 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
Restore
March 25, 2009, at 02:41 PM by 127.0.0.1 -
Changed line 14 from:
  • Genome rearrangements : a correct algorithm for optimal capping. \\
to:
  • Genome rearrangements : a correct algorithm for optimal capping. (here)\\
Restore
March 25, 2009, at 02:38 PM by 127.0.0.1 -
Changed line 30 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
Changed line 54 from:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction \\
Restore
March 25, 2009, at 11:06 AM by 127.0.0.1 -
Deleted lines 37-41:
  • '''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.

Added lines 39-42:

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. \\
Changed lines 73-74 from:
  • '''Comparing genomic architectures to reconstruct ancestral 
  genomes.''' \\
to:
  • Comparing genomic architectures to reconstruct ancestral genomes. \\
Restore
March 25, 2009, at 11:03 AM by 127.0.0.1 -
Changed line 38 from:
  • blue '''Reconstruction and visualization of genome rearrangements
to:
  • '''Reconstruction and visualization of genome rearrangements
Changed line 43 from:
  • blue Reconstruction and visualization of genome rearrangements within the Kluyveromyces. \\
to:
  • Reconstruction and visualization of genome rearrangements within the Kluyveromyces. \\
Changed line 48 from:
  • blue Reconstruction of ancestral genomes within Hemiascomycetes. \\
to:
  • Reconstruction of ancestral genomes within Hemiascomycetes. \\
Changed line 59 from:
  • blue Reconstruction d'architectures ancestrales. \\
to:
  • Reconstruction d'architectures ancestrales. \\
Changed line 62 from:
  • blue De la reconstruction d'un génome médian au calcul de scénarii évolutifs corrects. \\
to:
  • De la reconstruction d'un génome médian au calcul de scénarii évolutifs corrects. \\
Changed line 67 from:
  • blue Parcimonious distance and scenario for multichromosomal genomes \\
to:
  • Parcimonious distance and scenario for multichromosomal genomes \\
Changed line 71 from:
  • blue Reconstruction of ancestral genomes. \\
to:
  • Reconstruction of ancestral genomes. \\
Changed line 74 from:
  • blue '''Comparing genomic architectures to reconstruct ancestral
to:
  • '''Comparing genomic architectures to reconstruct ancestral
Restore
March 25, 2009, at 11:02 AM by 127.0.0.1 -
Changed lines 41-42 from:

First German/French/European meeting yeast and Filamentous Fungi, May ,2008.

to:

First German/French/European meeting yeast and Filamentous Fungi, Strasbourg, France, May 29-31, 2008.

Changed lines 45-47 from:

ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution, October ,2007.

to:

ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution, Sant Feliu, Spain, October 20-25, 2007.

Changed lines 50-51 from:

''Yeast Genome 10th anniversary, ,2006.

to:

''Yeast Genome 10th anniversary, Brussels, Belgium, September 7-8, 2006.

Changed lines 56-58 from:

PhD Defense, December 9, 2008.

to:

PhD Defense, Bordeaux, December 9, 2008.

Changed line 68 from:

Groupe de Travail Bioinformatique, Bordeaux, February, 2007.\\

to:

Groupe de Travail Bioinformatique, LaBRI, Bordeaux, February, 2007.\\

Restore
March 25, 2009, at 10:59 AM by 127.0.0.1 -
Deleted line 18:
Changed lines 55-58 from:
to:
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction
    PhD Defense, December 9, 2008.
Added lines 65-69:
  • blue Parcimonious distance and scenario for multichromosomal genomes
    Groupe de Travail Bioinformatique, Bordeaux, February, 2007.
Restore
March 25, 2009, at 10:55 AM by 127.0.0.1 -
Changed line 10 from:
  • SyDiG: Uncovering Synteny in Distant Genomes. \\
to:
  • Mining the semantics of genome super-blocks to infer ancestral architectures. \\
Deleted lines 11-18:

Submitted to Int. J. of Bioinformatics Research and Applications.

  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    Submitted to Genome Research.
  • Mining the semantics of genome super-blocks to infer ancestral architectures.
    G. Jean, D.J. Sherman, M. Nikolski.\\
Changed lines 20-29 from:

Manuscripts

Conferences

Other talks

to:

Submitted papers and manuscripts

  • SyDiG: Uncovering Synteny in Distant Genomes.
    G. Jean, D.J. Sherman, M. Nikolski.
    Submitted to Int. J. of Bioinformatics Research and Applications.
  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    Submitted to Genome Research.
  • In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction
    G. Jean.
    PhD Thesis, 2008.

International conferences

  • blue '''Reconstruction and visualization of genome rearrangements

within the Kluyveromyces.'''
G. Jean.\\ First German/French/European meeting yeast and Filamentous Fungi, May ,2008.

  • blue 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, October ,2007.
  • blue Reconstruction of ancestral genomes within Hemiascomycetes.
    G. Jean, M. Nikolski.

''Yeast Genome 10th anniversary, ,2006.

Other talks

  • blue Reconstruction d'architectures ancestrales.
    GDR Génolevures, Institut Pasteur, Paris, December, 2007.
  • blue 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.

  • blue Reconstruction of ancestral genomes.
    GDR Génolevures, ENS, Paris, April, 2006.
  • blue '''Comparing genomic architectures to reconstruct ancestral 
  genomes.''' 
GDR Génolevures, Institut Pasteur, Paris, February, 2006.
Restore
March 25, 2009, at 10:37 AM by 127.0.0.1 -
Changed lines 9-27 from:

SyDiG: Uncovering Synteny in Distant Genomes.
G. Jean, D.J. Sherman, M. Nikolski. Submitted to Int. J. of Bioinformatics Research and Applications.

Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
The G\'enolevures Consortium. Submitted to Genome Research.

Mining the semantics of genome super-blocks to infer ancestral architectures.
G. Jean, D.J. Sherman, M. Nikolski. Accepted in Journal of Computational Biology.

Genome rearrangements : a correct algorithm for optimal capping.
G. Jean, M. Nikolski. In Information Processing Letters (2007) 104 (1), pages 14-20.

to:
  • SyDiG: Uncovering Synteny in Distant Genomes.
    G. Jean, D.J. Sherman, M. Nikolski.
    Submitted to Int. J. of Bioinformatics Research and Applications.
  • Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
    The Génolevures Consortium.
    Submitted to Genome Research.
  • Mining the semantics of genome super-blocks to infer ancestral architectures.
    G. Jean, D.J. Sherman, M. Nikolski.
    To appear in Journal of Computational Biology.
  • Genome rearrangements : a correct algorithm for optimal capping.
    G. Jean, M. Nikolski.
    Information Processing Letters (2007) 104 (1),pages 14-20.
Added line 31:
Added lines 33-34:
Restore
March 24, 2009, at 05:16 PM by 127.0.0.1 -
Added lines 8-24:

SyDiG: Uncovering Synteny in Distant Genomes.
G. Jean, D.J. Sherman, M. Nikolski. Submitted to Int. J. of Bioinformatics Research and Applications.

Comparative genomics of protoploid genomes of Saccharomycetaceae defines the orthologous gene set and basic yeast proteome repertoire.
The G\'enolevures Consortium. Submitted to Genome Research.

Mining the semantics of genome super-blocks to infer ancestral architectures.
G. Jean, D.J. Sherman, M. Nikolski. Accepted in Journal of Computational Biology.

Genome rearrangements : a correct algorithm for optimal capping.
G. Jean, M. Nikolski. In Information Processing Letters (2007) 104 (1), pages 14-20.

Restore
March 24, 2009, at 05:10 PM by 127.0.0.1 -
Changed line 17 from:

Other talks

to:

Other talks

Restore
March 24, 2009, at 05:10 PM by 127.0.0.1 -
Changed lines 7-17 from:

Publications

to:

Publications

Manuscripts

Conferences

Other talks

Restore
March 24, 2009, at 05:08 PM by 127.0.0.1 -
Changed line 7 from:

Publications

to:

Publications

Restore
March 24, 2009, at 05:07 PM by 127.0.0.1 -
Added lines 1-7:

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.

Publications

Restore
GlossyBlue theme adapted by David Gilbert
Powered by PmWiki