Mathematique Informatique et Genome

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[1] Golik, W., Dameron, O., Bugeon, J., Fatet, A., Hue, I., Hurtaud, C., Reichstadt, M., Salaün, M.-C., Vernet, J., Joret, L., Papazian, F., Nédellec, C. and Bail, P.-Y. (2012). Atol: The multi-species livestock trait ontology. In Metadata and Semantics Research (MTSR-2012), (J. Dodero, M. Palomo-Duarte, and P. Karampiperis, ed.), 289-300, Communications in Computer and Information Science. Springer Berlin Heidelberg. [ DOI | http ]
[2] Mäder, U. and Nicolas, P. (2012). Systems Biology of Bacteria. (C. Harwood and A. Wipat, ed.), volume 39 of Methods in Microbiology, chapter 6 - Array-based approaches to bacterial transcriptome analysis, 151-182.
[3] Papazian, F., Bossy, R. and Nédellec, C. (July, 2012). Alvisae: a collaborative web text annotation editor for knowledge acquisition. In Proceedings of the Sixth Linguistic Annotation Workshop (LAW-2012), 149-152, Jeju, Republic of Korea. Association for Computational Linguistics. [ http ]
[4] Zinovyev, A., Fourquet, S., Tournier, L., Calzone, L. and Barillot, E. (2012). Cell death and life in cancer: mathematical modeling of cell fate decisions. In Advances in Systems Biology, 261-274, Adv. Exp. Med. Biol. Springer New York.
[5] Aichaoui, L., Jules, M., Le Chat, L., Aymerich, S., Fromion, V. and Goelzer, A. (2012). Basylica : a tool for automatic processing of a bacterial live cell array. Bioinformatics. 28(20) 2705-6.
[6] Aguileta, G., Lengelle, J., Chiapello, H., Giraud, T., Viaud, M., Fournier, E., Rodolphe, F., Marthey, S., Ducasse, A., Gendrault-Jacquemard, A., Poulain, J., Wincker, P. and Gout, L. (2012). Genes under positive selection in a model plant pathogenic fungus, botrytis. Infection Genetics and Evolution. 12 987-996.
[7] Amari, M., Laguerre, S., Vuillemin, M., Robert, H., Loux, V., Klopp, C., Morel, S., Gabriel, B., Remaud-Siméon, M., Gabriel, V., Moulis, C. and Fontagné-Faucher, C. (2012). Genome Sequence of Weissella confusa LBAE C39-2, Isolated from a Wheat Sourdough. Journal of Bacteriology. 194 (6) 1608-1609. [ DOI | http ]
[8] Barbier, P., Houel, A., Loux, V., Poulain, J., Bernardet, J.-F., Touchon, M. and Duchaud, E. (June, 2012). Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water. Journal of Bacteriology. 194 (11) 3024-3025. [ DOI | http ]
[9] Bossy, R., Jourde, J., Manine, A. P., Veber, P., Alphonse, E., van de Guchte, M., Bessieres, P. and Nedellec, C. (2012). BioNLP Shared Task - The Bacteria Track. BMC Bioinformatics. 13 (Suppl 11) S3+. [ DOI | http ]
[10] Buescher, J. M., Liebermeister, W., Jules, M., Uhr, M., Muntel, J., Botella, E., Hessling, B., Kleijn, R. J., Le Chat, L., Lecointe, F., Mäder, U., Nicolas, P., Piersma, S., Rügheimer, F., Becher, D., Bessières, P., Bidnenko, E., Denham, E. L., Dervyn, E., Devine, K. M., Doherty, G., Drulhe, S., Felicori, L., Fogg, M. J., Goelzer, A., Hansen, A., Harwood, C. R., Hecker, M., Hubner, S., Hultschig, C., Jarmer, H., Klipp, E., Leduc, A., Lewis, P., Molina, F., Noirot, P., Peres, S., Pigeonneau, N., Pohl, S., Rasmussen, S., Rinn, B., Schaffer, M., Schnidder, J., Schwikowski, B., Dijl, J. M. V., Veiga, P., Walsh, S., Wilkinson, A. J., Stelling, J., Aymerich, S. and Sauer, U. (2012). Global network reorganization during dynamic adaptations of bacillus subtilis metabolism. Science. 335 (6072) 1099-1103. [ DOI | http ]
[11] Celton, M., Goelzer, A., Camarasa, C., Fromion, V. and Dequin, S. (2012b). A constraint based model analysis of the metabolic consequences of increased NADPH oxidation in saccharomyces cerevisiae. Metabolic Engineering. 14(4) 366-379.
[12] Cousin, S., Ma, L., Creno, S., Clermont, D., Loux, V., Bizet, C. and Bouchier, C. (2012). Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T, Isolated from a Chicken Crop. Journal of Bacteriology. 194 (21) 5973. [ DOI | http ]
[13] Celton, M., Sanchez, I., Goelzer, A., Fromion, V., Camarasa, C. and Dequin, S. (2012a). A comparative transcriptomic, fluxomic and metabolomic analysis of the reponse of saccharomyces cerevisiae to increases in NADPH oxidation. Bioinformatics. 13(1) 317.
[14] Dalmasso, M., Aubert, J., Even, S., Falentin, H., Maillard, M.-B., Parayre, S., Loux, V., Tanskanen, J. and Thierry, A. (June, 2012). Propionibacterium freudenreichii accumulates intracellular glycogen and trehalose in conditions mimicking cheese ripening in the cold. Applied and Environmental Microbiology. 22 -. [ DOI | http ]
[15] Delauné, A., Dubrac, S., Blanchet, C., Poupel, O., Mäder, U., Hiron, A., Leduc, A., Fitting, C., Nicolas, P., Cavaillon, J.-M., Adib-Conquy, M. and Msadek, T. (Oct, 2012). The walkr system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response. Infect Immun. 80 (10) 3438-3453. [ DOI | http ]
[16] Durand, S., Gilet, L., Bessières, P., Nicolas, P. and Condon, C. (Mar, 2012). Three essential ribonucleases-rnase y, j1, and iii-control the abundance of a majority of bacillus subtilis mrnas. PLoS Genet. 8 (3) e1002520. [ DOI | http ]
[17] Devillers, H. and Schbath, S. (2012). Separating significant matches from spurious matches in dna sequences. Journal of Computational Biology. 19 1-12. [ DOI ]
[18] Fayyaz, A., Launay, G., Schbath, S., Gibrat, J.-F. and Rodolphe, F. (2012). Statistical significance of threading scores. Journal of Computational Biology. 19 1-18. [ DOI ]
[19] Grépinet, O., Boumart, Z., Virlogeux-Payant, I., Loux, V., Chiapello, H., Gendrault, A., Gibrat, J.-F., Chemaly, M. and Velge, P. (May, 2012b). Genome Sequence of the Persistent Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209. Journal of Bacteriology. 194 (9) 2385-2386. [ DOI | http ]
[20] Grépinet, O., Rossignol, A., Loux, V., Chiapello, H., Gendrault, A., Gibrat, J.-F., Velge, P. and Virlogeux-Payant, I. (May, 2012a). Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5. Journal of Bacteriology. 194 (9) 2387-2388. [ DOI | http ]
[21] Huillet, E., Tempelaars, M.-H., André-Leroux, G., Pagakrong, W., Bridoux, L., Makhzami, S., Panbangred, W., Martin-Verstraete, I., Abee, T. and Lereclus, D. (2012). PlcRa, a new quorum-sensing regulator from Bacillus cereus, plays a role in oxidative stress responses and cysteine metabolism in stationary phase. Plos One. 7 (12) . PMID = 23239999.
[22] Irlinger, F., Loux, V., Bento, P., Gibrat, J.-F., Straub, C., Bonnarme, P., Landaud, S. and Monnet, C. (2012). Genome Sequence of Staphylococcus equorum subsp. equorum Mu2, Isolated from a French Smear-Ripened Cheese. Journal of Bacteriology. 194 (18) 5141-5142. [ DOI | http ]
[23] Laguerre, S., Amari, M., Vuillemin, M., Robert, H., Loux, V., Klopp, C., Morel, S., Gabriel, B., Remaud-Siméon, M., Gabriel, V., Moulis, C. and Fontagné-Faucher, C. (Mar., 2012). Genome Sequences of Three Leuconostoc citreum Strains, LBAE C10, LBAE C11, and LBAE E16, Isolated from Wheat Sourdoughs. Journal of Bacteriology. 194 (6) 1610-1611. [ DOI | http ]
[24] Loux, V., Meslier, V. and Renault, P. (2012). Genome sequence of lactococcus raffinolactis strain 4877, isolated from natural dairy starter culture. Journal of Bacteriology. 194 (22) 6364. [ DOI | http ]
[25] Launay, G., Sanz, G., Pajot, E. and Gibrat, J.-F. (2012b). Modeling of mammalian olfactory receptors and docking of odorants. Biophys Rev. 4 255-269. [ DOI ]
[26] Launay, G., Teletchea, S., Wade, F., Pajot-Augy, E., Gibrat, J.-F. and Sanz, G. (2012a). Automatic modeling of mammalian olfactory receptors and docking of odorants. Protein Eng Des Sel. 25 377-86.
[27] Mariadassou, M., Bar-Hen, A. and Kishino, H. (2012). Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference. Syst. Biol. 61 (2) 337-345. [ DOI | http ]
[28] Monnet, C., Loux, V., Bento, P., Gibrat, J.-F., Straub, C., Bonnarme, P., Landaud, S. and Irlinger, F. (2012). Genome sequence of corynebacterium casei ucma 3821, isolated from a smear-ripened cheese. Journal of Bacteriology. 194(3) 738-739.
[29] Meslier, V., Loux, V. and Renault, P. (2012). Genome sequence of leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. Journal of Bacteriology. 194 (23) 6637. [ DOI | http ]
[30] Nicolas, P., Mäder, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M., Aymerich, S., Becher, D., Bisicchia, P., Botella, E., Delumeau, O., Doherty, G., Denham, E. L., Fogg, M. J., Fromion, V., Goelzer, A., Hansen, A., Härtig, E., Harwood, C. R., Homuth, G., Jarmer, H., Jules, M., Klipp, E., Chat, L. L., g ois Lecointe, F., Lewis, P., Liebermeister, W., March, A., Mars, R. A. T., Nannapaneni, P., Noone, D., Pohl, S., Rinn, B., Rügheimer, F., Sappa, P. K., Samson, F., Schaffer, M., Schwikowski, B., Steil, L., Stülke, J., Wiegert, T., Devine, K. M., Wilkinson, A. J., van Dijl, J. M., Hecker, M., Völker, U., Bessières, P. and Noirot, P. (2012). Condition-dependent transcriptome reveals high-level regulatory architecture in bacillus subtilis. Science. 335 (6072) 1103-1106. [ DOI | http ]
[31] Ratkovic, Z., Golik, W. and Warnier, P. (2012). Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach. BMC Bioinformatics. 13 (Suppl 11) S8+. [ DOI | http ]
[32] Rochat, T., Nicolas, P., Delumeau, O., Rabatinová, A., Korelusová, J., Leduc, A., Bessières, P., Dervyn, E., Krásny, L. and Noirot, P. (Oct, 2012). Genome-wide identification of genes directly regulated by the pleiotropic transcription factor spx in bacillus subtilis. Nucleic Acids Res. 40 (19) 9571-9583. [ DOI | http ]
[33] Schbath, S., Martin, V., Zytnicki, M., Fayolle, J., Loux, V. and Gibrat, J.-F. (2012). Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. Journal of Computational Biology. 19 796-813. [ DOI ]
[34] Samson, F., Shrager, R., Tai, C.-H., Sam, V., Lee, B.-K., Munson, P., Gibrat, J.-F. and Garnier, J. (2012). Domire: a web server for identifying structural domains and their neighbors in proteins. Bioinformatics. 28 (7) 1040-1041. [ DOI ]
[35] Weiss, S., Samson, F., Navarro, D. and Casaregola, S. (2012). Yeastip: a database for identification and phylogeny of saccharomycotina yeasts. FEMS Yeast Res.  -. [ DOI ]
[36] Zweers, J., Nicolas, P., Wiegert, T., van Dijl, J.-M. and Denham, E. (2012). Definition of the sigma(w) regulon of bacillus subtilis in the absence of stress. PLoS One. 7 (11) e48471. [ DOI | http ]

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