Mathematique Informatique et Genome

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[1] Aubin, S., Nazarenko, A. and Nedellec, C. (2005). Adapting a general parser to a sublanguage. In Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP'05), 89-93, Borovets, Bulgaria.
[2] Bossy, R., Loux, V., Bryson, K., Nicolas, P., Bessières, P. and Gibrat, J.-F. (2005). Agmial: a distributed genome annotation based on cooperative web services. In Journ Nies Ouvertes Biologie Informatique Math Nimatiques (JOBIM 2005), (G. P. Nhre, A. G. Ninoche, and C. Geourjon, ed.), 371-381, Lyon, France.
[3] Chiapello, H., Bourgait, F., I.and Sourivong, Jacquemard, A., Petit, M.-A. and El Karoui, M. (2005a). Mosaic: an online database for systematic determination of the mosaic structure of bacterial genomes. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), (G. P. Nhre, A. G. Ninoche, and C. Geourjon, ed.), 15-23, Lyon, France.
[4] Cussens, J. and Nedellec, C. (2005). Proceedings of the Learning Language in Logic ICML joint workshop and the Challenge task, Extracting Relations from Biomedical Texts, http://www.cs.york.ac.uk/aig/lll/lll05/. Springer Verlag, Bonn, Germany.
[5] Fromion, V. and Scorletti, G. (2005). Connecting incremental Lyapunov stability with the linearizations Lyapunov stability. In Proc. IEEE Conf. on Decision and Control, pages??, Seville, Spain. publisher??
[6] Hoebeke, M., Chiapello, H., Gibrat, J.-F., Nhres, P. B. and Garnier, J. (2005). Annotation and databases: status and prospects. In Database Annotation in Molecular Biology: Principles and Practice, (A. Lesk, ed.). John Wiley & Sons, London.
[7] Litrico, X. and Fromion, V. (2005). Design of structured multivariable controllers for irrigation canals. In Proc. IEEE Conf. on Decision and Control, pages??, Seville, Spain. publisher??
[8] Martin, J., Gibrat, J.-F. and Rodolphe, F. (2005a). Hmm for local protein structure. In Proceedings of Applied Stochastic Models and Data Analysis, (J. Janssen and P. Lenca, ed.), Brest, France.
[9] Nedellec, C. and Nazarenko, A. (2005). Ontology and Information Extraction: A Necessary Symbiosis. (B. M. P. Buitelaar, P. Cimiano, ed.). Volume 123 Frontiers in Artificial Intelligence and Application. IOS Press.
[10] Poirriez, V., Marin, A., Andonov, R. and Gibrat, J.-F. (april, 2005). Frost: revisited and distributed. In HICOMB Online Proceedings, Fourth IEEE International Workshop on High Performance Computational Biology, Denver.
[11] Robin, S., Rodolphe, F. and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press, English version of ADN, mots et modèles, BELIN 2003.
[12] Reinert, G., Schbath, S. and Waterman, M. (2005). Applied Combinatorics on Words. volume 105 of Encyclopedia of Mathematics and its Applications, chapter Statistics on Words with Applications to Biological Sequences. Cambridge University Press.
[13] Taly, J.-F., Marin, A., Martin, J. and Gibrat, J.-F. (2005). Définition de mesures décrivant l'environnement local des acides aminés pour une application à l'évaluation de modèles structuraux. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), (G. P. Nhre, A. G. Ninoche, and C. Geourjon, ed.), 359-369, Lyon, France.
[14] Chiapello, H., Bourgait, I., Sourivong, F., Heuclin, G., Gendrault-Jacquemard, A., Petit, M. and El Karoui, M. (2005b). Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics. 6 171.
[15] Chaillou, S. N., Nhs, M.-C. C.-V., Cornet, M., Crutz-LeCoq, A.-M., Dudez, A.-M., Martin, V. N., Beaufils, S., Nhre, E. D.-R., Bossy, R., Loux, V. and Zagorec, M. (2005). The complete genome sequence of the meat-borne lactic acid bacterium lactobacillus sakei23k. Nature Biotechnology. 23 (12) 1527 - 1533.
[16] Dinh, M., Scorletti, G., Fromion, V. and Magaroto, E. (2005). Parameter dependent H control by finite dimensional LMI optimization: application to trade-off dependent control. Int. J. Robust and Nonlinear Control. 15 383-406.
[17] Gitton, C., Meyrand, M., Wang, J., Caron, C., Trubuil, A., Guillot, A. and Mistou, M.-Y. (2005). Proteomic signature of lactococcus lactis ncdo763 cultivated in milk. Appl Environ Microbiol. 71 7152-7163.
[18] Gusto, G. and Schbath, S. (2005). FADO: a statistical method to detect favored or avoided distances between motif occurrences using the hawkes' model. Statistical Applications in Genetics and Molecular Biology. 4 0. Article 24.
[19] Hennequet-Antier, C., Chiapello, H., Piot, K., Degrelle, S., Hue, I., Renard, J., Rodolphe, F. and Robin, S. (2005). Anovarray: a set of sas macros for the analysis of variance of gene expression data. BMC Bioinformatics. 6 150.
[20] Litrico, X., Fromion, V., Baume, J.-P. and Rijo, M. (2005). Experimental validation of a methodology to control irrigation canals based on Saint-Venant equations. Journal of Control Engineering Practice. 13/11 1425-1437.
[21] Martin, J., Gibrat, J.-F. and Rodolphe, F. (2005b). How to choose the optimal hidden markov model for protein secondary structure prediction. IEEE Intelligent Systems. 60 (6) 19-25.
[22] Martin, J., Letellier, G., Marin, A., Taly, J.-F., de Brevern, A. and Gibrat, J.-F. (2005c). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol. 5 17.
[23] Sen, T., Jernigan, R., Garnier, J. and Kloczkowski, A. (2005). GOR V server for protein secondary structure prediction. Bioinformatics. 21 2787-2788. [ http ]
[24] Wang, J., Caron, C., He, X., Carpentier, A., Mistou, M.-Y., Gitton, C., Henry, C. and Guillot, A. (2005). A system for integrative and post-planned analysis of 2-de/ms centered proteomics data. Journal of Integrative Bioinformatics. 2 3-17.

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