Practical Course on. Bioinformatics and Comparative Genomes Analyses. University of La Réunion 2013 May 6-18

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1 Practical Course on Bioinformatics and Comparative Genomes Analyses University of La Réunion 2013 May Abstract The course will be organized within the frame of Run-Emerge objectives in order to train in La Réunion local, regional and international young scientists and PHD students in Bioinformatics and Genomics. An emphasis will be put on methods suitable for large data analysis provided by Next Generation Sequencing. The course will stress comparative analyses on bacterial and viral pathogens. In the context of large-scale genome comparisons, the main objectives of this proposed practical course are to strengthen capacities of students in Bioinformatics and data analyses skills by introducing reviews on advanced fundamental algorithms and statistical methods used in Bioinformatics and their applications in genome studies. Theoretical presentations will be followed by practical sessions, so that the same speaker will ensure links between theory and practice. Reviews on each suggested topic will include their corresponding research perspectives, aiming to help young scientists to gain insights into ongoing research in this domain. The course will involve genome comparisons, evolutionary analyses, phylogenomics and statistical methods needed in RNAiseq data analyses and Next Generation sequencing methods. The students will have to manipulate large amounts of data (raw data and results obtained from data analyses) using UNIX shell and perl scripting. The course program includes a series of lectures related to recent hot topics in Bioinformatics and Genome studies. These lectures are open for all local interested local colleagues and students (see programme). In summary: the proposed practical course will deal with conceptual methods in analysing genome data and expected biological results. Organizers: Pablo Tortosa, Université de la Réunion, Saint-Denis, France Koussay Dellagi, CRVOI, Saint-Denis, France,, France

2 Objectives: The main objectives of the course are to familiarize young scientists (Biologists, Computer Scientists, Mathematicians or Statisticians) with Bioinformatics and genome data analysis skills and to encourage multi-disciplinarity by introducing: 1- advanced fundamental algorithms in bioinformatics, 2- their application in genome analyses, 3- and recent knowledge acquired from genome studies and perspectives. Duration: Full time from May 6 th to 18 th, 2013 Location: Université de la Réunion, Saint-Denis Reunion Island Accommodation and Meals: All selected applicants will be offered accommodation and meals. In addition, flight tickets will be offered for the regional selected applicants (from countries in the south western Indian Ocean region). Target participants: The course is aimed at motivated Ph.D students and Post-docs, as well as young assistant professors in Academic Institutions with background in Mathematics, Statistics, Biology or Computing, who are involved in Bioinformatics and Genomes studies. Twenty (20) full time places are available for the course. Application to participate to this training: Candidates are invited to send a one page CV and a carefully completed application form to: : tekaia@pasteur.fr Pablo Tortosa: pablo.tortosa@univ-reunion.fr Marion Maire: marion.maire@univ-reunion.fr Acceptance will be subject to an evaluation process. Selection criteria include confirmed initial experience in Bioinformatics and Genomics, running projects and expressed motivations. Practical sessions in Linux environment will involve Unix shell and Perl scripting - Students are assumed to be familiar with this environment. Gender balance between selected students will be guaranteed as far as possible. Application deadline : March, 30th 2013 Selected candidates will be informed by April, 6th 2013

3 Final programme: Week 1 (May 6 - May 12 ): Bioinformatics and Genome Analyses I Day Date 8:30-10:00 10:30-12:00 14:00-15:30 16:00-17:30 Monday May 6 Welcome Koussay Dellagi - Pablo Tortosa Course Introduction and overview Pablo Tortosa - Computing Network Environment Tru Huynh Participants self-introduction Students Complete Genomes Databases and Bibliographics resources Large-scale Genomes Comparisons Tuesday May 7 Large-scale Genomes Comparisons (Practical) Large-scale Genomes Comparisons (Practical) Large-scale Genomes Comparisons (Practical) Large-scale Genomes Comparisons (Practical) Wednesday May 8 Multiple Sequence Alignments (Review) Centre de Regulacio Multiple Sequence Alignments (Practical) CRG, Barcelona - Spain Multiple Sequence Alignments (Review) CRG, Barcelona - Spain Multiple Sequence alignments (Practical) CRG, Barcelona - Spain

4 Genomica, Barcelona - Spain Thursday May 9 Phylogenetic trees construction (Review) Institute of Genetics and Molecular and Cellular Biology, Strasbourg - France Phylogenetic trees construction (Practical) IGBMC, Strasbourg - France Phylogenic Trees Construction (Review) IGBMC, Strasbourg - France Phylogenetic Trees Construction (Practical) IGBMC, Strasbourg - France Friday May 10 Phylogenomics (Review) Phylogenomics (Practical) Horizontal Gene Transfer (Review) Horizontal Gene Transfer (Practical) Saturday May 11 Open questions about giant viruses (Part I) Jean-Michel Claverie Information Genomique et Structurale, Marseille - France Open questions about giant viruses (Part II) Jean-Michel Claverie Information Genomique et Structurale, Marseille - France Free time Free time Gala Sunday May 12 Social activities

5 Week 2 (May 13 - May 18 ): Bioinformatics and Genome Analyses II Day Date 8:30-10:00 10:30-12:00 14:00-15:30 16:00-17:30 Monday May 13 NGS Technology, Mapping and Analysis Boston University - USA NGS Technology, Mapping and Analysis (Practical) Boston University - USA Read Mapping Algorithms Boston University - USA Read mapping algorithms Boston University - USA Tuesday May 14 RNAseq data processing: mapping, functional analysis and gene finding (Review) Andrea Tanzer Institute for Theoretical Chemistry, Vienna - Austria RNAseq data processing (Practical) Andrea Tanzer Institute for Theoretical Chemistry, Vienna - Austria RNAseq data processing (Review) Andrea Tanzer Institute for Theoretical Chemistry, Vienna - Austria RNAseq data processing (Practical) Andrea Tanzing Institute for Theoretical Chemistry Wednesday May 15 Inferring Orthologs (Review) EBI, Cambridge - UK Inferring Orthologs (Practical) EBI, Cambridge - UK Inferring Orthologs (Review) EBI, Cambridge - UK Inferring Orthologs (Practical) EBI, Cambride - UK

6 Thursday May 16 Ancient and Recent Evolution Ancient and Recent in Vertebrate Genomes Evoloution in Vertebrate (Review) Genomes (Practical) Hugues Roest Crollius Hugues Roest Crollius Institut de Biologie, Ecole Institut de Biologie, Ecole Normale Superieure Paris Normale Superieure Paris Genome Evolution in Vertebrates (Review) Hugues Roest Crollius Institut de Biologie, Ecole Normale Superieure Paris Genome Evolution in Vertebrates (Practical) Hugues Roest Crollius Institut de Biologie, Ecole Normale Superieure Paris Friday May 17 Eukaryotic Genomes (Part 1) Bernard Dujon Eukaryotic Genomes (Part 2) Bernard Dujon Bioinformatics, Biophysics, Genomics: convergent approaches illustrated with case studies. PartI Edouard Yeramian Bioinformatics, Biophysics, Genomics: convergent approaches illustrated with case studies. PartII Edouard Yeramian Special Saturday May 18 Course evaluation Participants Acknowledgements Free Free Free Sunday May 19 Hotel check out NOTE: Lectures on Sunday May 11 and Friday May 17, 2013 are public. They are open for local interested colleagues and students.

7 Lecturers and Tutors: Tru Huynh Centre de Regulacio Genomica (CRG) Dr. Aiguader, Barcelona, Spain Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, France. simonetta.gribaldo@pasteur.fr Jean-Michel Claverie Laboratoire Information Génomique et Structurale (IGS) CNRS - UMR7256 Institut de Microbiologie de la Méditerranée (IMM, FR3479) Parc Scientifique de Luminy 163 Avenue de Luminy - Case 934 FR , Marseille cedex 09 Tel : +33/ Jean-Michel.Claverie@igs.cnrs-mrs.fr

8 Department of Computer Science, Boston University, Boston, MA, USA Dr. Andrea Tanzer Institute for Theoretical Chemistry University of Vienna Währinger Straße 17, 3rd floor, room Vienna, Austria e-mmail: EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom dessimoz@ebi.ac.uk Hugues Roest Crollius Institut de Biologie Ecole Normale Supérieure Paris, France hrc@ens.fr Bernard Dujon bdujon@pasteur.fr Edouard Yeramian yeramian@pasteur.fr