Mathematique Informatique et Genome

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[1] Bossy, R., Jourde, J., Bessières, P., van de Guchte, M. and Nédellec, C. (2011a). BioNLP Shared Task 2011 - Bacteria Biotope. In Proceeding of BioNLP Shared Task 2011 Workshop, 56-64, Portland, Oregon (USA). Communication orale.
[2] Bossy, R., Jourde, J., Bessières, P., Van de Guchte, M. and Nédellec, C. (2011b). Bionlp shared tasks 2011 - bacteria biotope. In BioNLP workshop associ ACL, Portland, Etats-Unis. [ .pdf ]
[3] Chaves, M. and Tournier, L. (2011). Predicting the asymptotic dynamics of large biological networks by interconnections of Boolean modules. Proceedings of 50th IEEE Conference on Decision and Control, Orlando, FL,USA.
[4] Golik, W., Warnier, P. and Nédellec, C. (2011). Corpus-based extension of termino-ontology by linguistic analysis: a use case in biomedical event extraction. In Ontology and Lexicon: new insights. Workshop TIA 2011 : 9th International Conference on Terminology and Artificial Intelligence, Paris, France.
[5] de Hillerin, S., Scorletti, G. and Fromion, V. (2011a). Convex conditions for model reduction of linear parameter varying systems. In Proc. IEEE Conf. on Decision and Control and European Control Conference, 3410-3415, Orlando, USA. IEEE.
[6] de Hillerin, S., Scorletti, G. and Fromion, V. (Dec., 2011b). Reduced-complexity controllers for LPV systems: Towards incremental synthesis. In Proc. IEEE Conf. on Decision and Control and European Control Conference, 3404-3409, Orlando, USA. IEEE.
[7] Jourde, J., Manine, A.-P., Veber, P., Fort, K., Bossy, R., Alphonse, E. and Bessières, P. (2011). Shared task 2011 - Bacteria Gene Interactions and Renaming. In Proceeding of BioNLP Shared Task 2011 Workshop, 65-73, Portland, Oregon (USA). Communication orale.
[8] Koskas, M., Grasseau, G., Birmelé, E., Schbath, S. and Robin, S. (2011). Nemo: Fast count of network motifs. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), (E. Barillot, C. Froidevaux, and E. Rocha, ed.), 53-60, Paris, France.
[9] Kim, J.-D., Pyysalo, S., Ohta, T., Bossy, R., Nguyen, N. and Tsujii, J. (2011). Shared task 2011 - Overview of BioNLP. In Proceeding of BioNLP Shared Task 2011 Workshop, 1-6, Portland, Oregon (USA). Communication à un congrès.
[10] Meslem, N. and Fromion, V. (Dec., 2011). Lyapunov function for irreversible linear metabolic pathways with allosteric and genetic regulation. In Proc. IEEE Conf. on Decision and Control and European Control Conference, 5182-5187, Orlando, USA. IEEE.
[11] Ratkovic, Z., Golik, W., Warnier, P., Veber, P. and Nédellec, C. (2011). BioNLP 2011 Task Bacteria Biotope - The Alvis system. In Proceeding of BioNLP Shared Task 2011 Workshop, 102-111, Portland, Oregon (USA). Communication à un congrès.
[12] Schbath, S. and Hoebeke, M. (2011). Advances in genomic sequence analysis and pattern discovery. (L. Elnitski, O. Piontkivska, and L. Welch, ed.), chapter R'MES: a tool to find motifs with a significantly unexpected frequency in biological sequences. Science, Engineering, and Biology Informatics, vol. 7. World Scientific.
[13] Warnier, P. and Nédellec, C. (2011). Sentence filtering for bionlp: Searching for renaming acts. In BioNLP workshop associ ACL, Portland, Etats-Unis. [ .pdf ]
[14] Ambroset, C., Petit, M., Brion, C., Sanchez, I., Delobel, P., Guérin, C., Chiapello, H., Nicolas, P., Bigey, F., Dequin, S. and Blondin, B. (2011). Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. G3. 1 263-281.
[15] Delorme, C., Bartholini, C., Luraschi, M., Pons, N., Loux, V., Almeida, M., Guedon, E., Gibrat, J. F. and Renault, P. (2011b). Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232. Journal of Bacteriology. 193 (19) 5581-5582. [ DOI | http ]
[16] Dominguez-Escobar, J., Chastanet, A., Crevenna, A.-H., Fromion, V., Wedlich-Söldner, R. and Carballido-López, R. (2011). Processive movement of mreb-associated cell wall biosynthetic complexes in bacteria. Science. 333(6039) 225-8.
[17] Devillers, H., Chiapello, H., Schbath, S. and El Karoui, M. (2011). Robustness assessment of whole bacterial genome segmentations. Journal of Computational Biology. 18 1155-1165. [ DOI ]
[18] Delorme, C., Guedon, E., Pons, N., Cruaud, C., Couloux, A., Loux, V., Chiapello, H., Poyart, C., Gautier, C., Sanchez, N., Almeida, M., Kennedy, S. P., Ehrlich, S. D., Gibrat, J. F., Wincker, P. and Renault, P. (2011a). Complete Genome Sequence of the Clinical Streptococcus salivarius Strain CCHSS3. Journal of Bacteriology. 193 (18) 5041-5042. [ DOI | http ]
[19] Dalmasso, M., Nicolas, P., Falentin, H., Valence, F., Tanskanen, J., Jatila, H., Salusjärvi, T. and Thierry, A. (2011). Multilocus sequence typing of Propionibacterium freudenreichii. International Journal of Food Microbiology. 145 113-120. [ DOI ]
[20] Derozier, S., Samson, F., Tamby, J.-P., Guichard, C., Brunaud, V., Grevet, P., Leple, J.-C., Lecharny, A. and Aubourg, S. (2011). Exploration of plant genomes in the FLAGdb++ environment. Plant Methods. 7:8 . [ DOI ]
[21] Escobar, M., Nicolas, P., Sangar, F., Laurent-Chabalier, S., Clair, P., Joubert, D., Jay, P. and Legraverend, C. (2011). Intestinal epithelial stem cells do not protect their genome by asymmetric chromosome segregation. Nature Communications. 2 e258. [ DOI ]
[22] Fleuchot, B., Gitton, C., Guillot, A., Vidic, J., Nicolas, P., Besset, C., Fontaine, L., Hols, P., Leblond-Bourget, N., Monnet, V. and Gardan, R. (2011). Rgg proteins associated with internalized small hydrophobic peptides: a new quorum-sensing mechanism in streptococci. Molecular Microbiology. 80(4) 1102-1119. [ DOI ]
[23] Guedon, E., Delorme, C., Pons, N., Cruaud, C., Loux, V., Couloux, A., Gautier, C., Sanchez, N., Layec, S., Galleron, N., Almeida, M., van de Guchte, M., Kennedy, S. P., Ehrlich, S. D., Gibrat, J.-F., Wincker, P. and Renault, P. (2011). Complete Genome Sequence of the Commensal Streptococcus salivarius Strain JIM8777. Journal of Bacteriology. 193 (18) 5024. [ DOI | http ]
[24] Goelzer, A., Fromion, V. and Scorletti, G. (2011). Cell design in bacteria as a convex optimization problem. Automatica. 47(6) 1210-1218. [ DOI ]
[25] Goelzer, A. and Fromion, V. (2011). Bacterial growth rate reflects a bottleneck in resource allocation. BBA general Subjects. 1810(10) 978-988. [ DOI ]
[26] Hébert, A., Forquin-Gomez, M.-P., Roux, A., Aubert, J., Junot, C., Loux, V., Heilier, J.-F., Bonnarme, P., Beckerich, J.-M. and Landaud, S. (2011). Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Applied Microbiology and Biotechnology. 91 (5) 1409-1423. [ DOI | http ]
[27] Lacroix, T., Loux, V., Gibrat, J.-F., Gendrault, A. and Chiapello, H. (2011). CompaGB: An open framework for genome browsers comparison. BMC Research Notes. 4 133.
[28] Marchadier, E., Carballido-López, R., Brinster, S., fabret, C., Mervelet, P., Bessières, P., Noirot-Gros, M.-F., Fromion, V. and Noirot, P. (2011). An expanded protein-protein interaction network in bacillus subtilis reveals a group of hubs: Exploration by an integrative approach. proteomics. 11(15) 2981-91.
[29] Mäder, U., Nicolas, P., Richard, H., Bessières, P. and Aymerich, S. (2011). Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Current Opinion in Biotechnology. 22 32-41. [ DOI ]
[30] Roudier, F., Ahmed, I., Bérard, C., Sarazin, A., Mary-Huard, T., Cortijo, S., Bouyer, D., Caillieux, E., Duvernois-Berthet, E., Al-Shikhley, I., Giraut, L., Després, B., Drevensek, S., Barneche, F., Dèrozier, S., Brunaud, V., Aubourg, S., Schnittger, A., Bowler, C., Martin-Magniette, M. L., Robin, S., Caboche, M. and Colot, V. (2011). Integrative epigenomic mapping defines four main chromatin states in arabidopsisembo open. The EMBO Journal.  . [ DOI ]
[31] Szczepankowska, A. K., Prestel, E., Mariadassou, M., Bardowski, J. K. and Bidnenko, E. (2011). Phylogenetic and complementation analysis of a single-stranded dna binding protein family from lactococcal phages indicates a non-bacterial origin. PLoS One. 6 (11) e26942. [ http ]
[32] Stefanov, V., Robin, S. and Schbath, S. (2011). Occurrence of structured motifs in random sequences: Arbitrary number of boxes. Discrete Applied mathematics. 159 826-831. [ DOI ]
[33] Schbath, S. (2011). Statistiques de motifs. Gazette des mathématiciens. 130 60-65.
[34] Touchon, M., Barbier, P., Bernardet, J.-F., Loux, V., Vacherie, B., Barbe, V., Rocha, E. P. C. and Duchaud, E. (2011). Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Applied and Environmental Microbiology. AEM.05625-11v1. [ DOI | http ]
[35] Touzain, F., Petit, M.-A., Schbath, S. and El Karoui, M. (2011). DNA motifs that sculpt the bacterial chromosome. Nature Reviews Microbiology. 9 15-26. [ DOI ]
[36] Tai, C.-H., Sam, V., Gibrat, J.-F., Garnier, J., Munson, P.-J. and Lee, B. (2011). Protein domain assignment from the recurrence of locally similar structures. Proteins. 79 853-866. [ DOI ]

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