Bioinformatics and Comparative Genome Analysis Fredj Tekaia Institut Pasteur Course Introduction:

Charles Nicolle The Nobel Prize in Physiology or Medicine Director of the : Institut Pasteur in Tunis:

Financial support distribution Institut Pasteur Paris EMBO French MFA - CNRS Institut Pasteur TunisTunisian MHESRT FEBS (4270€: 7 YTF grants) - CBBC (bags) 46% 25% 18% 5%

Financial support French Foreign Affairs - CNRS-NEPAD Bioinformatics Program - Tunisian Ministry of High Education, Scientific Research and Technology- CBBC.

I am Grateful to all the colleagues and administrative staff who devoted much of their time to efficiently help setting this course:

The Institut Pasteur Paris ( -Direction des affaires internationales Michèle Boccoz, Dr Jean-Luc Guesdon, Eliane Cöeffier; -Gestion du Budget Marie-Pierre Gratius; -Service Missions Michèle Leclerc, Murielle Dupuis; -Service Financier Martine Charbuy -Secretariat Martine Rambaud.

EMBO ( (Courses & Workshops/World Activities) Mary Gannon, Programme Manager; Mario Poth, Administrator; Lynne Turnbull, on line-Helpdesk Administrator. CNRS ( Chantal Pacteau (Afrique. et Moyen-Orient. CNRS-DRI); Mr François Bienenfeld. FEBS ( Prof. Karl Kuchler (Chairman FEBS Advanced Courses Committee; Max F. Perutz Laboratories, Vienna). Prof. Iain Mowbray (FEBS treasurer; Department of Biochemistry, University College London); Louise McSeveny (FEBS secretary).

Swiss Institute of Bioinformatics (SIB)( Lydie Bougueleret ( for helping invite speakers); European Bioinformatics Institute ( Abel Ureta-Vidal (for helping invite speakers);

Suggestion by Prof. Koussay Dellagi : April, 2005; Submission Institut Pasteur Paris : December 12, 2005; Submission CNRS - NEPAD : March, 2006; Submission EMBO : July 6, 2006; Submission FEBS : July 31, 2006; Course Announcement : November 01, 2006; Application deadline: December 31, 2006; Candidate evaluation and selection (20) : January 10, 2007; Conference registration deadline : February 28, 2007; Course starting : March, 19, 2007; Course end and evaluation : April 7, 2007; Course scientific and financial report : May 15, Milestones of the course organization

Applicants (99)/Country (37)/Sex 44 F / 55 M 79: ~ Biology; 20: ~ Bioinfo; Conference registrations: 55 (40 F / 15 M; 50 ~ Biology / 5 ~Bioinfo) Total: F / 11 M 13: ~ Biology; 7 : ~ Bioinfo; Selected (20)/country (14):

Why this course ?

Tree of life Complete genomes 2434 projects 520 published ( ) 1086 Bacteria 59 Archaea 696 eukaryotes 73 metagenomes 3 phylogenetic domains; Lifestyles: mesophiles; (hyper)thermophiles; psychrophiles; extreme conditions,...

Number of available completely sequenced genomes GOLD List and references List and references Completely sequenced Genomes that span the three domains of life are growing at a rapid rate

Recent genome studies show that: Access to entire genome sequences is revolutionizing our understanding of how genetic information is stored and organized in DNA, and how it has evolved over time. The sequence of a genome provides significant details of the gene catalogue within a species. Comparisons of complete genome sequences show the acceleration in the understanding of species organisation, links between genes, functions of the genes, evolution of genes, genomes and species. => Beyond fundamental biological and methodological interests, Expected applications include: Drug, Medical and Agricultural,… discoveries.

Few scientists are involved in generating data and much more are involved in data analyses

Genomics Is the study of genomes. (including the study of their genes, proteins, their sequences, functions, evolution,....)

Bioinformatics is needed to transform the flood of raw data (sequences) into scientific knowledge.

MathematicsStatistics Nucleotide & protein sequences and related informations Informatics Biology Bioinformatics

Information system: Bibliography

Bibliography:

The main objectives of the course are to familiarize you with bioinformatics and large scale genome data analyses skills by introducing: 1- advanced fundamental algorithms in Bioinformatics; 2- their application in genome analyses; 3- recent knowledge acquired from genomes studies and their perspectives. Bioinformatics and Comparative Genome Analysis

CDs: Bibliography Fundamental recent references in Bioinformatics and Comparative Genome Analysis (more than 1000 papers). Subdivided into items: Methods; Genomes; Comparative Genomics; Duplication; Evolution; Orthologs; Phylogeny; Selection; Tree of Life; …; Courses and conference presentations. Tables list the content of each directory.

Acknowledgements: We are grateful to all the colleagues for accepting our invitations and for devoting much of their time and efforts to participate to this course:

List of the invited speakers/tutors:

Sonia Abdelhak (Institut Pasteur Tunis); David Ardell (Linnaeus Centre for Bioinformatics, Uppsala, Sweden); Andrea Auchincloss (Swiss Institute of Bioinformatics, Geneva, Switzerland); Alia Benkahla (Institut Pasteur Tunis); Georgio Bernardi (Stazione Zoologica Anton Dohrn, Napoli, Italy); Jean-Michel Claverie (Information Génomique et Structurale - Marseille); Gorges Cohen (Institut Pasteur Paris); Stewart Cole (Institut Pasteur Paris); Stijn van Dongen (Sanger Institute, Hinxton, United Kingdom); Xose Fernandez-Suarez (EBI, Hinxton, United Kingdom);

André Goffeau (Université Catholique de Louvain, Louvain-la- Neuve, Belgium); Karin Eiglmeier (Institut Pasteur Paris); Najib El-Sayed (Maryland University - TIGR, USA); Ikram Guizani (Institut Pasteur Tunis); Ralf Herwig (Max Planck Institute, Berlin, Germany); Rym Kefi (Institut Pasteur Tunis); Alexander Kel (BIOBASE Gmbh, Germany); Heiki Lehväslaiho (SANBI - Cape Town University, South Africa); François Major (Université de Montréal, Canada);

Helmi Merdassi (Institut Pasteur Tunis); Burkhard Morgenstern (University of Göttingen, Germany); Grégory Nuel (Lab Stat and Genomes- Genoscope, Evry); Odile Ozier-Kalogeropoulos (Institut Pasteur Paris); Julian Parkhill (Sanger Institute, Hinxton, United Kingdom); Ahmed Rebai (Centre de Biotechnologie Sfax); Hugues Roest Crollius (Ecole Normale Supérieure, Paris); Todd Taylor (RIKEN, Tokyo, Japan); Fredj Tekaia (Institut Pasteur Paris); Edouard Yeramian (Institut Pasteur Paris);

Personal acknowledgements to : Prof. Koussay Dellagi who suggested the set up of this course.

We hope that this course and conferences will motivate some of you to take part in these fascinating domains: Bioinformatics and Genomics.

Enjoy this exiting program and your stay in Tunis.