Bioinformatics and Comparative Genome Analysis

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

Course home page

Fredj Tekaia
Last Modified: July 1st, 2010 EST

Bioinformatics and Comparative Genome Analysis course

Institut Pasteur Paris - France

July 5 - July 17, 2010

With the financial support from: International Network of Institut Pasteur.

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

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

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)

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)