Bioinformatics and Comparative Genome Analysis course

Institut Pasteur Paris - France

July 5 - July 17, 2010


Organizers/Contact:
  • Odile Kalogeropoulos, Institut Pasteur.
  • Julie Thompson,IGBMC.
  • Hugo Naya, Institut Pasteur de Montevideo.
  • Fredj Tekaia, Institut Pasteur Paris - France.
  • With the financial support from: International Network of Institut Pasteur.


  • Week 1 : Background: Material and Methods
  • Week 2 : Comparative Genomics (Methods - Applications) - What did we learn from genomes studies and perspectives

  • Week 1 (July 5 - July 17 ): Background: Material and Methods

    Day
    Date
    9H00-10H30
    11H00-12H30
    14H30-16H00
    16H30-18H00
    18H00-19H00
    Sunday
    July 4


    Hotel check in
    Hotel check in
    Hotel Check in
    Monday
    July 5
    Welcome address
    Anthony Pugsley
    Scientific Director

    Introduction and overview of the course
    Fredj Tekaia
    Students self introduction
    UNIX
    Tru Huynh
    Institut Pasteur Paris
    UNIX
    Tru Huynh
    Institut Pasteur Paris
    Unix/Perl
    Tru Huynh
    Institut Pasteur Paris
    Perl
    Fredj Tekaia
    Tuesday
    July 6
    Unix/Perl Minimum to know
    Fredj Tekaia
    Institut Pasteur Paris
    Unix/Perl (Practical: Genome Analysis)
    Fredj Tekaia
    Institut Pasteur Paris
    Whole Genome Databases (Review)
    Helene Chiapello
    INRA, Jouy en Josas - France
    Whole Genome Databases (Practical)
    Helene Chiapello
    INRA, Jouy en Josas - France
    Next Generation Sequencing:Technology and detecting stuctural variants (Review)
    Gary Benson
    Wednesday
    July 7
    Methods for Repeat Detection In Nucleotide Sequences (Review)
    Gary Benson
    Boston University
    Boston, USA
    Repeat Detection in Nucleotide Sequences (Practical)
    Gary Benson
    Boston University
    Boston, USA
    Multiple Sequence Alignments (Review)
    Julie Thompson
    IGBMC, Strasbourg - France
    Multiple Sequence Alignment (Practical)
    Julie Thompson
    IGBMC, Strasbourg - France
    Next Generation Sequencing: read mapping algorithms (Review)
    Gary Benson
    Thursday
    July 8
    Phylogenetic Reconstruction (Review)
    Julie Thompson
    IGBMC, Strasbourg - France
    Phylogenetic Reconstruction (Practical)
    Julie Thompson
    IGBMC, Strasbourg - France
    Large-scale genome comparisons (Practical)
    Fredj Tekaia
    Institut Pasteur Paris
    Large-scale genome comparisons (Practical)
    Fredj Tekaia
    Institut Pasteur Paris
    Large-scale genome comparisons (Practical)
    Friday
    July 9
    Whole genome alignment (Review)
    Inna Dubchak
    Genomic Division
    Lawrence Berkeley National Laboratory
    Berkeley, CA - USA
    Whole Genome Alignment (Practical)
    Inna Dubchak
    Genomic Division
    Lawrence Berkeley National Laboratory
    Berkeley, CA - USA
    Whole Genome Alignments (Practical)
    Inna Dubchak
    Genomic Division
    Lawrence Berkeley National Laboratory
    Berkeley, CA - USA
    Orthologs Prediction and Classification (Review)
    Christophe Dessimoz
    ETH, Zurich - Switzerland
    Social activities
    Saturday
    July 10
    Orthologs Prediction and Classification (Practical)
    Christophe Dessimoz
    ETH, Zurich - Switzerland
    Orthologs Prediction and Classification (Practical)
    Christophe Dessimoz
    ETH, Zurich - Switzerland
    Cytoscape (Review)
    Mathieu Michaud
    Cytoscape (Practical)
    Mathieu Michaud
    Extension - QA
    Sunday
    July 11
    Free

    Week 2 (July 12 - July 17 ): Comparative Genomics (Methods - Applications)

    Day
    Date
    9H00-10H30
    11H00-12H30
    14H30-16H00
    16H30-18H00
    18H00-19H00
    Monday
    July 12
    Comparing two-protein-coding DNA sequences/Codons Models and Positive Selection
    Ziheng Yang
    University College London UK
    Adaptive Molecular Evolution (PAML4)
    Ziheng Yang
    University College London - UK
    Visit to Pasteur Museum (1h)
    Adaptive Molecular Evolution
    Ziheng Yang
    University College
    London - UK
    Adaptive Molecular Evolution (Practical)
    Ziheng Yang
    University College
    London - UK
    Extension - QA
    Tuesday
    July 13
    Genomes Visualization with circos
    Course Plan and materials
    Visualization of Genomic Data
    Martin Krzywinski
    Genome Sciences Centre
    Vancouver - Canada
    Genomes Visualization with circos :
    Genome Visualization with CIRCOS - Introduction to CIRCOS - Circos preamble - Preamble to Practical session
    - Introduction to Ideogram Layout
    Martin Krzywinski
    Genome Sciences Centre
    Vancouver - Canada
    Genomes Visualization with circos:
    Data Tracks - Slides:Data Tracks
    Martin Krzywinski
    Genome Sciences Centre
    Vancouver - Canada
    Genomes Visualization with circos :
    Introduction to Links and Rules - Slides: Introduction to Links and Rules
    Martin Krzywinski
    Genome Sciences Centre
    Vancouver - Canada
    Extension - QA
    F
    Wednesday
    July 14
    Free

    Week 2 (July 15 - July 16 ): Lecturers on "What did we learn from genomes studies and perspectives"
    (Amphitheatre Jacques Monod: Access is free for interested research community.
    Note: Access to the Institut Pasteur is subject to an Identity document presentation)

    Day
    Date
    9H00-10H30
    11H00-12H30
    14H30-16H00
    16H30-18H00
    18H00-19H00
    Thursday
    July 15
    Realistic models and efficient algorithms in Bioinformatics/Biophysics
    Analysis of Genomes on stuctural bases

    Edouard Yeramian
    Institut Pasteur
    Bioinformatics and Genomics
    John Quackenbush
    Harvard School of Public Health - Boston - USA
    Bioinfromatics and Systems Biology Approaches for Disease Study
    Ueng-Cheng Yang
    National Yang-Ming University, Taipei - Taiwan
    Exploring rare variation in regions of association - tools and challenges
    Panagiotis Deloukas

    The Wellcome Trust Sanger Institute, Cambridge, UK
    Extension - QA
    Friday
    July 16
    Eukaryotic Genomes Evolution, an approach with hemiascomycetous yeasts
    Jean-Luc Souciet
    Universite de Strasbourg, France
    Origins and Evolution of Novel Genes
    Aoife Mclysaght
    Smurfit Institut of Genetics
    University of Dublin
    Trinity College
    Dublin - Ireland
    Ancient and Recent Evolution in Vertebrate Genomes
    Hugues Roest Crollius
    Institut de Biologie de l'Ecole Normale Superieur (IBENS)


    Social activities
    Saturday
    July 17
    Course evaluation (Students)
    Questionnaire
    (Organizers and Students)
    Course evaluation (Students)
    Questionnaire
    (Organizers and Students)
    Acknowledgements
    Free
    Free
    Free
    Sunday
    July 18
    Hotel check out
    Back to top program
    Course home page

    Fredj Tekaia
    Last Modified: July 1st, 2010 EST