Olivier Bastien Home Page
Publication List
Internationals journal with review committees
029. 2011 Glade N., Ballet P. and Bastien, 0.: "A Stochastic Process Approach of the Drake Equation Parameters".International Journal of Astrobiology.In Press. 
eprint
028. 2011 Villiers, F., Jourdain, A., Leonhard, N., Bastien, O. Parcy, F., Fujioka, S., Bourguignon, J. and Hugouvieux, V.: "Evidence for functional interaction between brassinosteroid and cadmium response in Arabidopsis thaliana". Journal Of Experimental Botany.In Press.
027. 2011 De Luca, G., Barakat, M., Ortet, P., Jourlin-Castelli, C., Ansaldi, M., Py, B., Fichant, G., Coutinho, P.M., Voulhoux, R., Bastien, O., Maréchal, E., Henrissat, B., Quentin, Y., Noirot, P., Filloux, A., Méjean, V., DuBow, M., Barras, F., Barbe, V., Weissenbach, J., Mihalcescu, I., Verméglio, A., Achouak, W. and Heulin, T.: "Genome analysis of the cyst-dividing proteobacterium Ramlibacter tataouinensis highlights original traits related to its adaptation to desert environment". PLoS ONE. 6(9): e23784. doi:10.1371/journal.pone.0023784. LINK
026. 2011 Botté, C., Deligny , M., Roccia , A., Bonneau , A.L., Saïdani , N., Hardré-Liénard , H., Aci , S., Jouhet , J., Dubots , E., Loizeau , K., Bastien , O., Bréhélin , L., Joyard , J., Cintrat , J.C., Falconet , D., Block , M.A., Rousseau , B., Lopez , R. and Maréchal, E.: "Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana". Nature Chemical Biology. 7: 834-842. LINK
025. 2011 Lespinats, S., Grando, D., Maréchal, E., Hakimi, M.A., Tenaillon, O. and Bastien, O.: "How Fitch-Margoliash algorithm can benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics. 7: 61-85. LINK
024. 2011 Moyroud, E., Minguet, E.G., Ott, F., Yant, L., Posé, D., Monniaux, M., Blanchet, S., Bastien, O., Thévenon, E., Weigel, D., Schmid, M. and Parcy, F. : "Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for the Arabidopsis LEAFY Transcription Factor". The Plant Cell. 23: 1293-1306. LINK
023. 2010 Ortet, P. and Bastien, O.: "Where does alignment score distribution shape come from?". Evolutionary Bioinformatics. 6: 159-187. LINK
022. 2010 Braun, L., Cannella, D., Ortet, P., Sautel, C.F., Barakat, M., Kieffer, S., Garin, J. , Bastien, O., Voinnet, O. and Hakimi M.A.: "A Complex Small RNA Repertoire Is Generated by a Plant/Fungal-Like Machinery and Effected by a Metazoan-Like Argonaute in the Single-Cell Human Parasite Toxoplasma gondii". Plos Path. 6(5): e1000920. LINK
021. 2010 Dubots, E., Audry, M., Yamaryo, Y., Bastien, O., Ohta, H., Maréchal, E. and Block, M.A.: "Activation of the chloroplast monogalactosyldiacylglycerol synthase, mgd1, by phosphatidic acid and phosphatidylglycerol". J. Biol. Chem. 285(9): 6003-6011. LINK
020. 2009 Curien, G., Bastien, O., Robert-Genthon, M., Cornish-Bowden, A., Cardenas, M.L. and Dumas, R.: "Understanding regulation of aspartate metabolism with a model based on measured kinetic parameters". Mol. Sys. Biol. 5: 271. LINK
019. 2009 Grando, D., Ortet, P., Jourbert, F., Maréchal, E. and Bastien, O.: "TULIP software and web server: automatic classification of protein sequences based on pairwise comparisons and Z-value statistics". Open Bioinformatics Journal. 3: 18-25. LINK
018. 2009 Bougdour, A., Maubon, D., Baldacci, P., Ortet, P., Bastien, O., Bouillon, A., Barale, J.C., Pelloux, H., Menard, R. And Hakimi, M.A.: "Drug-inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites". J. Exp. Med. 206(4) 953-966. LINK
017. 2008 Sautel, C.F., Ortet, P., Saksouk, N., Kieffer, S., Garin, J., Bastien, O. and Hakimi, M.A.: "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. LINK
016. 2008 Bastien, O. and Maréchal, E.: "Evolution of biological sequences implies Extreme Value Distribution of type I for both global and local pairwise alignment score". BMC Bioinformatics 9: 332. LINK
015. 2008 Saidani, N., Grando, D., Valadie, H., Bastien, O. and Maréchal, E.: "Potential and limits of in silico target discovery-Case study of the search for new antimalarial chemotherapeutic targets". Infect., Genet. and Evol. 9(3): 359-367. LINK
014. 2008 Bastien, O.: "A simple derivation of the distribution of pairwise local protein sequence alignment scores". Evolutionary Bioinformatics 4:41-45. LINK
013. 2007 Sautel, C.F., Cannella, D., Bastien O., Kieffer, S., Aldebert, D., Garin, J., Tardieux, I., Belrhali, H. and Hakimi, M.A.: "SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes". Mol. Cell. Biol. 27(16): 5711-5724. LINK
012. 2007 Storozhenko, S., Navarette, O., Ravanel, S., De Brouwer, V., Chaerle, P., Zhang, G.F., Bastien, O., Lambert, W., Rébeillé, F.and Van Der Straeten D.: "Cytosolic Hydroxymethyldihydropterin Pyrophosphokinase/Dihydropteroate Synthase from Arabidopsis thaliana". J. Biol. Chem. 282 (14): 10749-10761. LINK
011. 2007 Bastien, O., Ortet, P., Roy, S. and Maréchal, E.: "The configuration space of homologous proteins: a theoretical and practical framework to reduce the diversity of the protein sequence space after massive all-by-all sequence comparisons". Future Generation Comput. Syst. 23:410-427. LINK
010. 2006 Birkholtz, L.M., Bastien, O., Wells, G., Grando, D., Joubert, F., Kasam, V., Zimmermann, M., Ortet, P., Jacq, N., Saidani, N., Hofmann-Apitius, S., Hofmann- Apitius, M., Breton, V., I Louw, A. and Marechal, E.: "Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?". Malaria Journal 5: 110. LINK
009. 2006 Le Lay, P., Isaure, M.P., Sarry, J.E., Khun, L., Fayard, B., Le Bail, J.L., Bastien, O., Garin, J., Roby, C., and Bourguignon, J.: "Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply." Biochimie 88 (11): 1533-1547. LINK
008. 2006 Rivasseau, C., Couram, G., Boisson, A.M., Bastien, O. and Bligny, R.: "Rapid analysis of organic acids in plant extracts by capillary electrophoresis with indirect UV detection Directed metabolic analyses during metal stress." J. Chromatographie A 1129 (2): 283-290. LINK
007. 2006 Sarry J.E., Kuhn L., Ducruix C., Lafaye A., Junot C., Hugouvieux V., Jourdain A., Bastien O., Vailhen D., Amekraz B., Moulin C., Ezan E., Garin J. and Bourguignon J.: "The early responses of Arabidopsis thaliana cells to Cd exposure explored by protein and metabolite profiling analyses". Proteomics 6 (7): 2180-2198. LINK
006. 2006 Bisanz C., Bastien O., Grando D., Jouhet J. , Maréchal E. and Cesbron-Delauw M.F.: "Toxoplasma gondii acyl-lipid metabolism: de novo synthesis from apicoplast generated fatty acids versus scavenging of host cell". Biochem. J. 394 (1): 197-206. LINK
005. 2005 Botté, C., Jeanneau, C., Snajdrova, L., Bastien, O., Imberty, A., Breton, C. and Maréchal, E.: "Molecular modelling and site directed mutagenesis of plant chloroplast MGDG synthase reveal critical residues for activity". J. Biol. Chem. 280 (41): 34691-34701. LINK
004. 2005 Bastien O., Roy S. and Maréchal E.: "Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions". C.R. Biol. 328 (5): 445-453. LINK
003. 2005 Bastien O., Ortet P., Roy, S. Maréchal E.: "A configuration space of homologous proteins, conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities". BMC Bioinformatics 6 (1): 49. LINK
002. 2004 Bastien O., Aude J.C., Roy S. and Maréchal E.: "Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics". Bioinformatics 20(4): 534-537. LINK
001. 2004 Bastien O., Lespinats S., Roy S., Métayer K., Fertil B., Codani J.J. and Maréchal E.: "Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference". Gene 336 (2): 163-173. LINK
Books chapters
003. 2009 Glade, N., Ben-Amor, H. abd Bastien, O.: "Trail Systems as fault tolerant wires and their use in bio-processors". Modelling Complex Biological Systems in The Context of Genomics. 85-119.
002. 2007 Block, M.A., Jouhet, J., Marechal, E. Bastien, O. and Joyard, J.: "Role of the envelope membranes in chloroplast glycerolipid biosynthesis". Photosynthesis: A Comprehensive Treatise Biochemistry, Biophysics and Molecular Biology. In press.
001. 2007 Bisanz, C., Botté, C., Saïdani, N, Bastien, O., Cesbron-Delauw, M.F., et Maréchal.: "Structure, function and biogenesis of the secondary plastid of apicomplexan parasites". Current Research in Plant Cell Compartments. In press.
Oral Communications
006. Atelier Formule de Drake, CNES, Paris 21-22 Novembre 2011. "Sur l'équation de Drake et les incertitudes liées à celles de ses paramètres".
005. Séminaire Matlab dans le domaine des Sciences de la Vie, Grenoble, 15 Novembre 2011. "Application de Simbiology à la régulation de la voie de biosynthèse des galactolipides dans la membrane des chloroplastes".
004. XXXIème Séminaire de la Société Francophone de Biologie Théorique, Autrans, 15-18 Mai 2011. "L'origine évolutive de la forme de la distribution des scores d'alignements de séquences biologiques".
003. SEMINAIRES Daniel Dautreppe 2010 (Société Française de Physique), Grenoble, 6-10 Décembre 2010. Conférencier invité. "L'origine évolutive de la forme de la distribution des scores d'alignements de séquences biologiques".
002. COLLOQUE PPF, Tours, 9-10 Mars 2006. Conférencier invité. "Le théorème TULIP et l'espace de configuration des protéines homologues".
001. ALPHY/GTGC, Lyon, 23-24 janvier 2006. "Le théorème TULIP et l'espace de configuration des protéines homologues".
Scientific Communications (Poster)
012. XXXIème Séminaire de la Société Francophone de Biologie Théorique, Autrans, 15-18 Mai 2011. Ballet, P., Bastien O. and Glade, N.: "Sédimentation, agitation, turn-over, évolution et biodiversité dans des écosystèmes artificiels: la vie est belle".
011. 7ième Congrès de Lipomique du Groupe d'Etude et de Recherche en Lipidomique, GERLI 2010, Anglet Biarritz 03-06 Octobre 2010. Ben Amor, H., Block, M.A., Maréchal, E., Glade, N. and Bastien, O.: "Implication of both positive and negative feedback circuits in plastid envelope membrane galactolipid biosynthetic pathway stability".
010. 7ième Congrès de Lipomique du Groupe d'Etude et de Recherche en Lipidomique, GERLI 2010, Anglet Biarritz 03-06 Octobre 2010. Dubots, E., Audry, M., Yamaryo, Y., Bastien, O., Ohta, H., Breton, C., Maréchal, E. and Block, M.A.: "Regulation of the Chloroplast Monogalactosyldiacylglycerol Synthase, MGD1, by Phosphatidic Acid and Phosphatidylglycerol".
009 19th International Symposium on Plant Lipids, Cairns 11-16 Juillet 2010. Dubots, E., Audry, M., Yamaryo, Y., Bastien, O., Ohta, H., Breton, C., Maréchal, E. and Block, M.A.: "Regulation of the Chloroplast Monogalactosyldiacylglycerol Synthase, MGD1, by Phosphatidic Acid and Phosphatidylglycerol".
008. X Reunion de Biologia Molecular de Plantas, Valencia 08-10 Juillet 2010. Minguet, E.G., Moyroud, E., Blanchet, S., Yant, L., Padilla, D.J., Ott, F., Monniaux, M., Bastien, O., Schmid, M. and Parcy, F.: "modelizacion cuantitativa de la union de los factores de transcripcion al adn: el ejemplo de leafy".
007. 1rst Viruses of Microbes Congress 2010, Paris, 21-25 Juin 2010. Ginevra, C., Bastien, O., Vandenesch, F., Etienne, J., and Jarraud, S.: "Diversity of CRISPR/cas complex in Legionella pneumophila contrasting with a lack of phage signature".
006. 3rd CNRS-MPG joint worshop on Systems Biology, Grenoble, 24-25 Novembre 2008. Glade N. et Bastien O.: "On the Self-organizing Properties of Trail Systems and Their Possible Use as Structurally Programmable Bio-Processors".
005. Réaumur Meeting 2007, Grenoble, 28-31 Octobre 2007. Bastien O. et Maréchal E.: "Reliability theory provide a strong link between protein evolution and alignment score probabilities".
004. Réaumur Meeting 2007, Grenoble, 28-31 Octobre 2007. Lespinats S., Grando D., Sautel C.F., Hakimi M.A. et Bastien O.: "Pointing out complex phylogenic relationships from apicomplexan methytransferase SET domain data by Multi Dimensional Scaling methods".
003. Journées Ouvertes Biologie, Informatique et Mathématiques 2004 (JOBIM), Montréal, 28-30 Juin 2004. Bastien O., Ortet P., Roy, S. et Maréchal E.: "Building-up of a Configuration Space of Homologous Proteins".
002. European Conference on Computational Biology 2003 (ECCB), Paris, 27-30 Septembre 2003. Bastien O., Aude J.C., Roy S., Codani J.J. et Maréchal E.: "Genome-Scale comparative analysis of the G+C content and amino acid composition of homologous coding sequences from Plasmodium falciparum and Arabidopsis thaliana".
001. Congrès de l'European Life Scientist Organization (ELSO), Nice, 29 juin - 3 juillet 2002. Bastien O., Monier B, Viari A., Joyard J., Maréchal E. et Roy S.: "Development of bioinformatic tools devoted to the trans-species comparison of non-biased and nucleotide-biased genomes. A case study of data-mining in Plasmodium falciparum databases".
My PhD thesis (in french)
Titre: Bastien, O.: "Développements théoriques et méthodes numériques pour les analyses comparatives de génomes et protéomes biaisés. Application a la comparaison des génomes et protéomes de Plasmodium falciparum et d'Arabidopsis thaliana". Soutenue le 26 Avril 2006 à l'université Joseph Fourier de Grenoble I.
Title: Bastien, O.: "Theoretical advances and numerical methods for genomes comparisons. Application to the Plasmodium falciparum/Arabidopsis thaliana genomes and proteomes comparison". Presented the 26 April 2006 at the Joseph Fourier University (Grenoble, France).
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Mise à jour le 07 décembre 2011
par Olivier Bastien.
