Wednesday, August 26, 2009

Interview with Evolutionary Bioinformatics editorial board member Dr Olivier Bastien

This interview is with Evolutionary Bioinformatics editorial board member Dr Olivier Bastien. Evolutionary Bioinformatics is an open access journal published by Libertas Academica.

Editor in Chief Dr Dennis Wall has recently issued a
call for papers.

What is the primary focus of your work and main areas of expertise?

I began to work on the development of theoretical and numerical mathematical tools for the genome comparison. The main goal of these work was to applied to the study of the malaria genome, namely Plasmodium falciparum, and its evolution. Rapidly, I have extend my research area to the fundamentals and the theoretical basis of the genome comparison and the sequence comparison.

In addition to these topics, I work on applied dynamical systems to regulatory metabolism network and on the development of bioinformatics tools for new biological technologies like Chip-On-Chip. One way to summarize my work is to say that I'm working on application of the Information Theory on Biological Systems.

What are the most exciting and cutting-edge developments in your area?

I have developed a new model for understanding the origin of the form of the pairwise alignment scores distribution based on a new approach using both reliability theory and information theory. The development of a new set of tools called Genobrower and GenoChip for epigenetic studies is also an recent important which have contribute to important advances in the Toxoplasma gondii epigenetic research field.

Who are your main formal and informal collaborators and/or networks? Please describe your work with them.

I am affiliated with the Institut National de la Recherche Agronomique (INRA). My main collaborators include Dr. Mohamed-Ali Hakimi (INSERM, for all epigenetic works), Dr Nicolas Glade (Grenoble University, for Theoretical Biology) and Dr Sylvain Lespinats (CEA, for Theoretical Biology). Based on Grenoble (France), I have developped a strong collaboration within my laboratory (The Laboratoire de Physiologie Cellulaire Végétale) including Dr Eric Maréchal, Dr Maryse Block, Dr Gilles Curien and Dr Fabrice Rébeillé.

How did you come to be working in your research area?

I come to work in my research area with the observation that theoretical biologists were really wanted by Molecular Biology. It was a great wish of René Thom, the father of the catastrophe theory.

What do you think about the development of open access publishing? Have you published in an open access journal? What motivated you to do so?

I have published in many open access journals. I was first motivated because I think it is a great improvement for developing countries' scientists. Moreover, as said by Jean Hladik, knowledge is the only things that future generations can inherit without charge. It is a way to ensure the free diffusion of knowledge all over the world.

What articles and/or books have you published recently?
  • Glade, N., Ben-Amor, H. and Bastien, O. (2009): “Trail Systems as fault tolerant wires and their use in bio-processors”. Epigenomic Program Spring School, La Colle sur Loup, France.
  • Curien, G., Bastien, O., Robert-Genthon, M., Cornish-Bowden, A., Cardenas, M.L. and Dumas, R. (2009): “Understanding regulation of aspartate metabolism with a model based on measured kinetic parameters”. Mol. Sys. Biol. 5: 271.
  • Grando, D., Ortet, P., Jourbert, F., Maréchal, E. and Bastien, O. (2009): “TULIP software and web server: automatic classification of protein sequences based on pairwise comparisons and Z-value statistics”. Open Bioinformatics Journal. In Press.
  • Bougdour, A., Maubon, D., Baldacci, P., Ortet, P., Bastien, O., Bouillon, A., Barale, J.C., Pelloux, H., Menard, R. And Hakimi, M.A. (2009): “Drug-inhibition of HDAC3 and epigenetic control of differentiation in Apicimplexa parasites”. J. Exp. Med. In Press.
  • Sautel, C.F., Ortet, P., Saksouk, N., Kieffer, S., Garin, J., Bastien, O. and Hakimi, M.A. (2008): “The histone methylase KMTox interacts with 1 the redox-sensor peroxiredoxin-1 and targets genes involved in Toxoplasma gondii antioxidant defenses”. Mol. Micro. 71(1): 212-226.
  • Bastien, O. and Maréchal, E. (2008): “Evolution of biological sequences implies Extreme Value Distribution of type I for both global and local pairwise alignment score”. BMC Bioinformatics 9: 332.
  • Saidani, N., Grando, D., Valadie, H., Bastien, O. and Maréchal, E. (2008): “Potential and limits of in silico target discovery--Case study of the search for new antimalarial chemotherapeutic targets”. Infect., Genet. and Evol., In Press.
  • Bastien, O. (2008): “A simple derivation of the distribution of pairwise local protein sequence alignment scores”. Evolutionary Bioinformatics 4:41-45
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