Transcript Course Introduction: Bioinformatics and Comparative Genome Analysis Fredj Tekaia Institut Pasteur [email protected] Charles Nicolle The Nobel Prize in Physiology or Medicine 1928. Director of the : Institut Pasteur in Tunis: 1903-1936.

Course Introduction:
Bioinformatics and Comparative Genome
Analysis
Fredj Tekaia
Institut Pasteur
[email protected]
Charles Nicolle
The
Nobel
Prize
in
Physiology or Medicine
1928.
Director of the :
Institut Pasteur in Tunis:
1903-1936.
Bioinformatics and Comparative Genome Analysis
March 19 – April 7, 2007.
Institut Pasteur Tunis –Tunisia.
Organizers/Contact:
Alia Benkahla
Fredj Tekaia
Ahmed Rebai
Edouard Yeramian
Institut Pasteur of Tunis
[email protected]
Insitut Pasteur Paris
[email protected]
Centre Biotechnologie Sfax
ahm [email protected]
Insitut Pasteur Paris
[email protected]
With financial support from: Institut Pasteur Paris/EMBO/FEBS/Institut Pasteur Tunis/
Tunisian Ministry of High Education and the Ministry of Scientific Research/CBBC/ French
Foreign Affairs –CNRS – NEPAD Bioinformatics Program.
Program: http://www.pasteur.fr/~tekaia/BCGA.html
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 (http://www.pasteur.fr)
-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 (http://www.embo.org/projects/world/) (Courses &
Workshops/World Activities)
Mary Gannon, Programme Manager;
Mario Poth, Administrator;
Lynne Turnbull, on line-Helpdesk Administrator.
• CNRS (http://www.sg.cnrs.fr/)
Chantal Pacteau (Afrique. et Moyen-Orient. CNRS-DRI);
Mr François Bienenfeld.
• FEBS (http://www.febs.unibe.ch/)
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)(http://www.isb-sib.ch/)
Lydie Bougueleret (for helping invite speakers);
• European Bioinformatics Institute (http://www.ebi.ac.uk)
Abel Ureta-Vidal (for helping invite speakers);
Milestones of the course organization
• 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, 2007.
Applicants (99)/Country (37)/Sex
Female,
Total:
30
29
28
27
26
25
24
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15
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Selected (20)/country (14):
44 F / 55 M
9 F / 11 M
79: ~ Biology;
13: ~ Biology;
20: ~ Bioinfo;
7 : ~ Bioinfo;
3+1
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Venezuela
USA
Uruguay
Uganda
Tunisia
Tanzania
South Africa
Singapore
Sudan
Saudi
Russia
Romania
Poland
Pakistan
Oman
Morocco
Nigeria
Mexico
Mali
Kenya
Iran
Iraq
India
Greece
Germany
Ethiopia
Estonia
Egypt
Cuba
CAR
Cameroon
Brasil
Benin
Belarus
Austria
Algeria
Azerbaijan
Conference registrations: 55 (40 F / 15 M; 50 ~ Biology / 5 ~Bioinfo)
Why this course ?
433
36
Tree of life
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http://www.genomesonline.org/
Complete genomes
2434 projects
• 520 published
(01-03-07)
• 1086 Bacteria
• 59 Archaea
• 696 eukaryotes
• 73 metagenomes
• 3 phylogenetic
domains;
• Lifestyles:
mesophiles;
(hyper)thermophiles;
psychrophiles;
extreme conditions,...
Cumulated number of complete genomes
Number of available completely sequenced genomes
540
520
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480
460
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380
360
340
320
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280
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20
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500
523
323
224
165
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03-2007
Year
Completely sequenced Genomes that span the three
domains of life are growing at a rapid rate
List and references
GOLD
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.
Mathematics
Statistics
Bioinformatics
Nucleotide & protein
sequences and related
informations
Biology
Informatics
Bioinformatics and Comparative Genome
Analysis
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.
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:
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Speakers (29)/Institutions (17)
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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-laNeuve, 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.