Bioinformatic and Comparative Genome Analysis

Institut Pasteur Tunis - Tunisia

March 18 - April 7, 2007

Organizers/Contact:

Alia Benkahla
Institut Pasteur Tunis - Tunisia

Fredj Tekaia
Institut Pasteur Paris - France

Ahmed Rebai
Centre Biotechnologie Sfax - Tunisia

Edouard Yeramian
Institut Pasteur Paris - France
With the financial support from:
Institut Pasteur Paris - EMBO - FEBS - Institut Pasteur Tunis - Tunisian Ministry of High Education, Scienfitic Research and Technology - CBBC - French Foreign Affairs-CNRS-NEPAD Bioinformatics Program.

Final Program:
  • Week 1 : Background: Material and Methods
  • Week 2 : Practice of Comparative Genomics: Methods - Tools - Applications
  • Week 3 : What did we learn from genome studies

    • Week 1 (March 19 - March 25): Background: Material and Methods
    Day
    Date
    8H-9H45
    10H15-12H
    14H-15H45
    16H15-18H30
    Sunday
    March 18
    Installation in Hotel
    Installation in Hotel
    Monday
    March 19
    Welcome
    Alia Benkahla (Institut Pasteur Tunis)
    Course introduction
    Fredj Tekaia (Institut Pasteur Paris)
    Students introduction
    Molecular Biology story: DNA the queen molecule
    Odile Ozier-Kalogeropoulos
    Institut Pasteur Paris
    UniProtKB/Swiss-Prot and ExPASy: Protein sequence databases and proteomics tools developed at the Swiss Institute of Bioinformatics
    Andrea Auchincloss
    SIB
    Practical Exercises: UniProtKB/Swiss-Prot and ExPASy: Protein sequence databases and proteomics tools developed at the Swiss Institute of Bioinformatics
    Andrea Auchincloss
    SIB
    Tuesday
    March 20
    Genome databases and open access bibliographic resources
    Sonia Abdelhak (IPT)
    Ahmed Rebai (CBS)
    Suffix Trees, Automata and Pattern Matching
    Main Algorithms with Applications in Bioinformatics
    Gregory Nuel
    Lab. Stat & Genome, Evry
    Expectation-Maximization and Hidden Markov Models
    Main algorithms with applications in Bioinformatics
    Gregory Nuel
    Lab. Stat & Genome, Evry
    Dynamic Programming and Alignment
    Main algorithms with applications in Bioinformatic
    Gregory Nuel
    Lab. Stat & Genome, Evry
    Wednesday
    March 21
    Linux fundamentals
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical LINUX
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical LINUX
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical LINUX
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Thursday
    March 22
    Introduction to Perl and Bioperl
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical Perl
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical Perl
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Practical Perl
    Heikki Lehvaslaiho
    SANBI, U. Western Cape, SA
    Friday
    March 23
  • Introduction to Multivariate Statistical Analysis Methods
  • Useful Algorithms and Statistical Methods in Genome Data Analysis
    Ahmed Rebai
    CBS
    		•
  • Discriminant Analysis - Cluster Analysis
  • Principal Component Analysis
  • Correspondence Analysis
    Ahmed Rebai
    CBS
    		•
    Introduction to R langage


    Ahmed Rebai
    CBS
    R basics

    Ahmed Rebai
    CBS
    Saturday
    March 24
    Sequence comparisons: Substitution and scores
    David Ardell
    LCB, Uppsala
    Sequence Comparison: Alignments and Search
    David Ardell
    LCB, Uppsala
    Social and cultural activities
    Social and cultural activities
    Sunday
    March 25
    Social and cultural activities
    Back to top program

    Week 2 (March 26 - March 31 ): Practice of Comparative Genomics: Methods - Tools - Applications
    Day
    Date
    8H-9H45
    10H15-12H
    14H-15H45
    16H15-18H30
    Monday
    March 26
    Practical on genomes comparisons Using Stand-alone BLAST
    David Ardell
    LCB, Uppsala
    Practical: genomes comparisons
    David Ardell
    LCB, Uppsala
    Practical: genomes comparisons
    David Ardell
    LCB, Uppsala
    Practical: genomes comparisons
    David Ardell
    LCB, Uppsala
    Tuesday
    March 27
    Multiple Alignment and Motif Searching
    Burkhard Morgenstern
    Bioinformatics, Univ Gottingen
    Multiple Alignment
    Burkhard Morgenstern
    Bioinformatics, Univ Gottingen
    Motif searching
    Burkhard Morgenstern
    Bioinformatics, Univ Gottingen
    Motif searching
    Burkhard Morgenstern
    Bioinformatics, Univ Gottingen
    Wednesday
    March 28
    Phylogenetic Analysis Methods
    Fredj Tekaia
    Institut Pasteur Paris
    Practical-Phylogeny
    Fredj Tekaia
    Institut Pasteur Paris
    Molecular Evolution Methods
    Fredj Tekaia
    Institut Pasteur Paris
    Practical Mol. evol.
    Fredj Tekaia
    Institut Pasteur Paris
    Thursday
    March 29
    Clustering of orthologs and paralogs
    Stijn van Dongen
    Sanger Institute
    Graph Clustering with MCL
    Stijn van Dongen
    Sanger Institute
    Gene annotation
    Alia Benkahla
    Institut Pasteur Tunis
    Gene annotation
    Alia Benkahla
    Institut Pasteur Tunis
    Friday
    March 30
    Gene annotation
    Alia Benkahla
    Institut Pasteur Tunis
  • Gene regulatory code
  • Regulatory sequences (basics)
    Alexander Kel
    BIOBASE
    		•
    Regulatory sequence Analysis
    tools and approaches
    Alexander Kel
    BIOBASE
    Comparative genomic and function analysis for the identification and or characterization of Leishmania targets for intervention and control
    Ikram Guizani
    Institut Pasteur Tunis
    Saturday
    March 31
    Browsing Genomes with Ensembl
    Xose Fernandez-Suarez
    EBI
  • Access to genes and genomes with Ensembl
  • Data Mining in Ensembl with Biomart
    Xose Fernandez-Suarez
    EBI
    		•
    Social and cultural activities
    Social and cultural activities
    Sunday
    April 1
    Social and cultural activities
    Back to top program

    Week 3 (April 2 - April 7 ): Conferences: What did we learn from genome studies
    Day
    Date
    8H-9H45
    10H15-12H
    14H-15H45
    16H15-18H30
    Monday
    April 2
    What have we learned from 10 years of yeast genomology
    Andre Goffeau
    Universite Catholique Louvain
    Yeast Genomology
    Andre Goffeau
    Universite Catholique Louvain
    Understanding Human genome (Structural) evolution through chimpanzee and mouse comparisons
    Todd Taylor
    RIKEN
    Resources, tools and Methods for Systems biology
    Ralf Herwig
    Max Planck Institute for Molecular Genetics, Bioinformatics, Berlin
    Tuesday
    April 3
    Reconstructing Ancestral Vertebrate Genomes by in silico Paleogenomics
    Hugues Roest Crollius
    Dyogen ENS Paris
    Anopheles gambiae: A genetic Approach
    Karin Eiglmeier
    Institut Pasteur Paris
    Bridges between Biophysics and Bioinformatics: applications to Genomics
    Edouard Yeramian
    Institut Pasteur Paris
    Open discussion
    Wednesday
    April 4
    Computational tools for disease gene identification
    Sonia Abdelhak
    Institut Pasteur Tunis
    Exploring evolutionary trends in Proteomes
    Fredj Tekaia
    Institut Pasteur Paris
    Human population phylogenetic studies using mithochondrial DNA
    Rym Kefi
    Institut Pasteur Tunis
    Data mining and annotation validation (Text of talk)
    Georges Cohen
    Institut Pasteur Paris
    Thursday
    April 5
  • On the evolution of pathogenic mycobacteria (and their antigens)
  • Evolutionary genomics of mycobacterial pathogens (on the origin of tuberculosis)
    Stewart Cole
    Institut Pasteur Paris
    		•
    Putative Biology of PE/PPE multigene families of Mycobacteria and their Relevance with Regard to Evolution
    Helmi Mardassi
    Institut Pasteur Tunis
    Genome dynamics in bacterial pathogens
    Julian Parkhill
    Sanger Intitute
    Genome organization and evolution
    Gerogio Bernardi
    SZAD Napoli
    Friday
    April 6
    RNA structure
    Francois Major
    U Montreal
    Current hypothesis on the origin and evolution of large DNA viruses
    Larger than bacteria: the mystery of giant viruses
    Jean-Michel Claverie
    Information Genomique et Structurale - Marseille
    Open discussion on Bioinformatics and Genomics
    Open discussion on Bioinformatics and Genomics
    Saturday
    April 7
    Course evaluation
    Farewell
    Sunday
    April 8
    Last leaving the Hotel
    Back to top program
    Course home page
    Fredj Tekaia
    Last Modified: Friday, March 09, 2007 EST