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Publications avant 2014

Journaux

Allouche, D., Andre, I., Barbe, S., Davies, J., De Givry, S., Katsirelos, G., O'Sullivan, B., Prestwich, S., Schiex, T., Traore, S. (2014). Computational protein design as an optimization problem. Artificial Intelligence, 212, 59-79. DOI : 10.1016/j.artint.2014.03.005 http://prodinra.inra.fr/record/262300

Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., Alberti, A., Aury, J.-M., Louis, A., Dehais, P., Bardou, P., Montfort, J., Klopp, C., Cabau, C., Gaspin, C., Thorgaard, G. H., Boussaha, M., Quillet, E., Guyomard, R., Galiana, D., Bobe, J., Volff, J.-N., Genet, C., Wincker, P., Jaillon, O., Roest Crollius, H., Guiguen, Y. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications, 5, 1-10. DOI : 10.1038/ncomms4657 http://prodinra.inra.fr/record/258629

Champion, M., Cierco-Ayrolles, C., Gadat, S., Vignes, M. (2014). Sparse regression and support recovery with L2L2-Boosting algorithms. Journal of Statistical Planning and Inference. DOI : 10.1016/j.jspi.2014.07.006 http://prodinra.inra.fr/record/267781

Choulet, F., Alberti, A., Theil, S., Glover, N. M., Barbe, V., Daron, J., Pingault, L., Sourdille, P., Couloux, A., Paux, E., Leroy, P., Mangenot, S., Guilhot, N., Le Gouis, J., Balfourier, F., Alaux, M., Jamilloux, V., Julie, P., Durand, C., Bellec, A., Gaspin, C., Šafář, J., Doležel, J., Rogers, J., Vandepoele, K., Aury, J.-M., Mayer, K., Berges, H., Quesneville, H., Wincker, P., Feuillet, C. (2014). Structural and Functional Partitioning of Bread Wheat Chromosome 3B. Science, 345 (6194 ), online. DOI : 10.1126/science.1249721 http://prodinra.inra.fr/record/265119

Leroux, D., Rahmani, A., Jasson, S., Ventelon, M., Louis, F., Moreau, L., Mangin, B. (2014). Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 127 (4), 921-933. DOI : 10.1007/s00122-014-2267-1
http://prodinra.inra.fr/record/262344

Ogier, J.-C., Pages, S., Bisch, G., Chiapello, H., Médigue, C., Rouy, Z., Teyssier, C., Vincent, S., Tailliez, P., Givaudan, A., Gaudriault, S. (2014). Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii. Genome Biology and Evolution, 6. DOI : 10.1093/gbe/evu119
http://prodinra.inra.fr/record/262449

Sallet, E., Gouzy, J., Schiex, T. (2014). EuGene-PP: a next generation automated annotation pipeline for prokaryotic genomes. Bioinformatics (Oxford, England). DOI : 10.1093/bioinformatics/btu366 http://prodinra.inra.fr/record/262304

Villa-Vialaneix, N. (Auteur de correspondance), Vignes, M., Viguerie, N., San Cristobal, M. (2014). Inferring networks from multiple samples with consensus LASSO. Quality Technology & Quantitative Management, 11 (1), 39-60. http://prodinra.inra.fr/record/257034  

Zytnicki, M., Akhunov, E., Quesneville, H. (2014). Tedna: a transposable element de novo assembler. Bioinformatics, (on-line), 1-3. DOI : 10.1093/bioinformatics/btu365 http://prodinra.inra.fr/record/269361

Chapitres de livre

Coste, F., Nédellec, C., Schiex, T., Vert, J.-P. (2014). Bioinformatique. In: Panorama de l'Intelligence Artificielle. Vol 3 : L'intelligence artificielle : frontières et applications. Toulouse, FRA : Cepadues Editions. http://prodinra.inra.fr/record/262303

Schiex, T., De Givry, S., Cooper, M. (2014). Réseaux de contraintes valués. In: Panorama de l'intelligence artificielle. Vol 2 : Algorithmes pour l'intelligence artificielle. FRA : Cepaduès Editions. http://prodinra.inra.fr/record/262302  

Actes de conférences

Bacchus, F., Davies, J., Tsimpoukelli, M., Katsirelos, G. (2014). Relaxation search: a simple way of managing optional clauses. Presented at AAAI 2014 - 28th AAAI Conference, Québec, CAN (2014-07-27 - 2014-07-31).
http://prodinra.inra.fr/record/263230

Bessiere, C., Hebrard, E., Katsirelos, G., Kiziltan, Z., Picard-Cantin, E., Quimper, C.-G., Walsh, T. (2014). The balance constraint family. Presented at CP 2014 - 20th International Conference on Principles and Practice of Constraint Programming, Lyon, FRA (2014-09-08 - 2014-09-12).
http://prodinra.inra.fr/record/263231

de Givry, S., Hurley, B., Allouche, D., Katsirelos, G., O'Sullivan, B., Schiex, T. (2014). An experimental evaluation of CP/AI/OR solvers for optimization in graphical models. Presented at Congrès ROADEF'2014, Bordeaux, FRA (2014-02-26 - 2014-02-28). http://prodinra.inra.fr/record/266023

de Givry, S., Lee, J. H., Leung, K., Shum, Y. (2014). Solving a judge assignment problem using conjunctions of global cost functions. Presented at 20th International Conference on Principles and Practice of Constraint Programming - CP2014, Lyon, FRA (2014-09-08 - 2014-09-12). http://prodinra.inra.fr/record/266026

Schiex, T., Bessière, C., De Givry, S., Nguyên, T. H. H. (2014). Maintaining Virtual Arc Consistency Dynamically During Search. Presented at International Conference on Tools with Artifical Intelligence, Limassol (2014-11-10 - 2014-11-12).
http://prodinra.inra.fr/record/271604

Picheny, V., Vandel, J., Vignes, M., Villa-Vialaneix, N. (2014). Reconstruction quality of a biological network when its constituting elements are partially observed. 17th International Conference on Artificial Intelligence and Statistics, Reykjavik, ISL (2014-04-22 - 2014-04-25). http://prodinra.inra.fr/record/258178

2013

Journaux

Akplogan, M., De Givry, S., Metivier, J.-P., Quesnel, G., Joannon, A., Garcia, F. (2013). Solving the crop allocation problem using hard and soft constraints. RAIRO Recherche Opérationnelle, 47 (2), 151-172. DOI : 10.1051/ro/2013032 http://prodinra.inra.fr/record/208958

Bardol, N., Ventelon, M., Mangin, B., Jasson, S., Loywick, V., Couton, F., Derue, C., Blanchard, P., Charcosset, A., Moreau, L. (2013). Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism. Theoretical and Applied Genetics, 126 (11), 2717 - 2736. DOI : 10.1007/s00122-013-2167-9
http://prodinra.inra.fr/record/221836

Cadic, E., Coque, M., Vear, F., Grezes-Besset, B., Pauquet, J., Piquemal, J., Lippi, Y., Blanchard, P., Romestant, M., Pouilly, N., Rengel, D., Gouzy, J., Langlade, N., Mangin, B., Vincourt, P. (2013). Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.). Theoretical and Applied Genetics, 126 (5), 1337-1356. DOI : 10.1007/s00122-013-2056-2
http://prodinra.inra.fr/record/257135

Campo, S., Peris-Peris, C., Siré, C., Moreno, A. B., Donaire, L., Zytnicki, M., Notredame, C., Llave, C., San Segundo, B. (Auteur de correspondance) (2013). Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. New Phytologist, 199 (1), 212-27. DOI : 10.1111/nph.12292 http://prodinra.inra.fr/record/259842

Dunner, S. (Auteur de correspondance), Sevane, N., Garcia, D., Levéziel, H., Williams, J. L., Mangin, B., Valentini, A., GeMQual Consortium (2013). Genes involved in muscle lipid composition in 15 European Bos taurus breeds. Animal Genetics, 44 (5), 493-501. DOI : 10.1111/age.12044
http://prodinra.inra.fr/record/209514

Dunner, S. (Auteur de correspondance), Sevane, N., Garcia, D., Cortés, O., Valentini, A., Williams, J., Mangin, B., Canon, J., Levéziel, H., GeMQual Consortium (2013). Association of genes involved in carcass and meat quality traits in 15 European bovine breeds. Livestock Science, 154 (1-3), 34-44. DOI : 10.1016/j.livsci.2013.02.020
http://prodinra.inra.fr/record/194353

Norais, C., Moisan, A., Gaspin, C., Clouet-d'Orval, B. (2013). Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biology, 10 (5), 659 - 670. DOI : 10.4161/rna.23927 http://prodinra.inra.fr/record/208600

Sallet, E., Roux, B., Sauviac, L., Jardinaud, M.-F., Carrere, S., Faraut, T., De Carvalho-Niebel, F., Gouzy, J., Gamas, P., Capela, D., Bruand, C., Schiex, T. (Auteur de correspondance) (2013). Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011. DNA Research, 20 (4), 339-353. DOI : 10.1093/dnares/dst014 http://prodinra.inra.fr/record/213929

Traore, S., Allouche, D., Andre, I., De Givry, S., Katsirelos, G., Schiex, T., Barbe, S. (2013). A new framework for computational protein design through cost function network optimization. Bioinformatics, 29 (17), 2129-2136. DOI : 10.1093/bioinformatics/btt374 http://prodinra.inra.fr/record/209477  

Chapitres d'ouvrage

Allouche, D., Cierco-Ayrolles, C., De Givry, S., Guillermin, G., Mangin, B., Schiex, T., Vandel, J., Vignes, M. (2013). A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics. In: Alberto de la Fuente, dir., Gene network inference, verification of methods for systems genetics data (p. 9-32). Germany : Editions Springer. DOI : 10.1007/978-3-642-45161-4 http://prodinra.inra.fr/record/259107

Actes de conférence

Bessiere, C., Carbonnel, C., Hebrard, E., Katsirelos, G., Walsh, T. (2013). Detecting and exploiting subproblem tractability. In: IJCAI'13 Proceedings of the Twenty-Third international joint conference on Artificial Intelligence (p. 468-474). Presented at IJCAI 2013 - 23rd International Joint Conference on Artificial Inteligence, Pekin, CHN (2013-08-03 - 2013-08-09).
http://prodinra.inra.fr/record/263216

Bessière, C., Coletta, R., Hebrard, E., Katsirelos, G., Lazaar, N., Narodytska, N., Quimper, C.-G., Walsh, T. (2013). Constraint acquisition via partial queries. Presented at IJCAI 2013 - 23rd International Joint Conference on Artificial Inteligence, Pékin, CHN (2013-08-03 - 2013-08-09).
http://prodinra.inra.fr/record/263217

Chiapello, H., Mallet, L., Guerin, C., Aguileta , G., Rodolphe, F., Gendrault, A., Kreplak, J., Amselem, J., Ortega-Abboud, E., Lebrun, M.-H., Tharreau, D., Fournier, E. (2013). Genome evolution of fungal pathogens from the Magnaporthe oryzae/grisea clade. Presented at 27th Fungal Genetics Conference - Asilomar Conference Grounds,, Asilomar, USA (2013-03-12 - 2013-03-17). http://prodinra.inra.fr/record/207881

de Givry, S., Prestwich, S., O'Sullivan, B. (2013). Dead-end elimination for weighted CSP . In: Principles and Practice of Constraint Programming (p. 263-272). Lecture Notes in Computer Science. Presented at 19th International Conference, Constraint Programming 2013, Uppsala, SWE (2013-09-16 - 2013-09-20). Berlin, DEU : Springer Verlag. DOI : 10.1007/978-3-642-40627-0_22 http://prodinra.inra.fr/record/259125

Katsirelos, G., Sabharwal, A., Samulowitz, H., Simon, L. (2013). Resolution and parallelizability: barriers to the effficient parallelization of SAT solvers. In: Twenty-Seventh AAAI Conference on Artificial Intelligence. Presented at AAAI 2013 - 27th AAAI Conference, Bellevue, USA (2013-07-14 - 2013-07-18).
http://prodinra.inra.fr/record/263218

Nguyên, T. H. H., Bessiere, C., Schiex, T. (2013). Cohérence d'arc virtuelle dynamique. In: Actes des Neuvièmes Journées Francophones de Programmation par Contraintes (p. 249-258). Presented at JFPC 2013 - Neuvièmes Journées Francophones de Programmation par Contraintes, Aix-en -Provence, FRA (2013-06-12 - 2013-06-14). http://prodinra.inra.fr/record/263528

Nguyên, T. H. H., Schiex, T., Bessiere, C. (2013). Dynamic virtual arc consistency. In: Proceedings of the 28th Annual ACM Symposium on Applied Computing (p. 98-103). Presented at 28th Annual ACM Symposium on Applied Computing, Coimbra, PRT (2013-03-18 - 2013-03-22). New York, USA : ACM - Association for Computing Machinery. DOI : 10.1145/2480362.2480384 http://prodinra.inra.fr/record/177820

2012

Journaux

Audemard, E. (Auteur de correspondance), Schiex, T., Faraut, T. (Auteur de correspondance) (2012). Detecting long tandem duplications in genomic sequences. BMC Bioinformatics, 13, online (may), Non paginé. DOI : 10.1186/1471-2105-13-83 Facteur d'impact (2 ans) : 3.024 Notoriété à 2 ans : Excellente (math.comput.biol.) http://prodinra.inra.fr/record/194932

Bink, M., Schiex, T. (2012). EU COST Action TD0801: statistical challenges on the 1000 euro genome sequences in plants. In EMBnet journal, 17 (Suppl. B). Presented at SeqAhead Scientific Meeting (COST Action BM1006), Bruxelles, BEL (2011-11-07 - 2011-11-09). DOI : 10.14806/ej.17.B.280 http://prodinra.inra.fr/record/177812   Dupuy, L. X., Vignes, M. (2012). An algorithm for the simulation of the growth of root systems on deformable domains. Journal of Theoretical Biology, 310, 164 - 174. DOI : 10.1016/j.jtbi.2012.06.025 Facteur d'impact (2 ans) : 2.351 Notoriété à 2 ans : Correcte (biology ; math.comput.biol.) http://prodinra.inra.fr/record/213247

Fresard, L., Leroux, S., Dehais, P., Servin, B., Gilbert, H., Bouchez, O., Klopp, C., Cabau, C., Vignoles, F., Feve, K., Ricros, A., Gourichon, D., Diot, C., Richard, S., Leterrier, C., Beaumont, C., Vignal, A., Minvielle, F., Pitel, F. (2012). Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail. BMC Genomics, 13, online (october), Non paginé. DOI : 10.1186/1471-2164-13-551
Facteur d'impact (2 ans) : 4.397
Notoriété à 2 ans : Excellente (biotechnol.appl.microbiol. ; genet.hered.)
http://prodinra.inra.fr/record/171046

Lariepe, A., Mangin, B., Jasson, S., Combes, V., Dumas, F., Jamin, P., Lariagon, C., Jolivot, D., Madur, D., Fievet, J., Gallais, A., Dubreuil, P., Charcosset, A., Moreau, L. (2012). The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics, 190 (2), 795-811. DOI : 10.1534/genetics.111.133447
Facteur d'impact (2 ans) : 4.389
Notoriété à 2 ans : Excellente (genet.hered.)
http://prodinra.inra.fr/record/178161

Mangin, B. (Auteur de correspondance), Siberchicot, A., Nicolas, S., Doligez, A., This, P., Cierco-Ayrolles, C. (2012). Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity, 108 (3), 285-291. DOI : 10.1038/hdy.2011.73
Facteur d'impact (2 ans) : 4.11
Notoriété à 2 ans : Excellente (ecology ; genet.hered.)
http://prodinra.inra.fr/record/49275

Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata , D., Aoki, K., Egholm, M., Knight , J., Bogden, R., Li, C., Shuang, Y., Xu, X., Pan, S., Cheng, S., Liu, X., Ren, Y., Wang, J., Albiero, A., Dal Pero, F., Todesco, S., Van Eck, J., Buels, R. M., Bombarely, A., Gosselin, J. R., Huang, M., Leto , J., Menda, N., Strickler, S., Mao, L., Gao, S., Tecle, I. Y., York, T., Zheng, Y., Vrebalov, J. T., Lee, J., Zhong, S., Mueller, L. A., Stiekema, W. J., Ribeca, P., Alioto, T., Yang, W., Huang , S., Du, Y., Zhang, Z., Gao, J., Guo, Y., Wang, X., Li , Y., He, J., Li, C., Cheng, Z., Zuo, J., Ren, J., Zhao, J., Yan, L., Jiang, H., Wang , B., Li, H., Li , Z., Fu, F., Chen, B., Han, B., Feng, Q., Fan, D., Wang, Y., Ling, H., Xue, Y., Ware, D., McCombie, W. R., Lippmamn, Z. B., Chia, J.-M., Jiang, K., Pastermak, S., Gelley, L., Kramer, M., Anderson, L. K., Chang, S.-B., Royer, S., Shearer, L. A., Stack, S. M., Rose, J. K. C., Xu, Y., Eannetta , N., Matas, A. J., McQuinn, R., Tanksley, S. D., Camara, F., Guigo, R., Rombauts, S., Fawcett, J., Van de Peer, Y., Zamir, D., Liang, C., Spannagl, M., Gundlach, H., Bruggmann , R., Mayer, K., Jia, Z., Zhang, J., Ye, Z., Bishop, G. J., Butcher, S., Lopez-Cobollo, R., Buchan, D., Filippis, I., Abbot, J., Dixit, R., Singh, M., Singh, A., Pal, J. K., Pandit, A., Singh, P. K., Mahato, A. K., Dogra, V., Gaikwad, K., Sharma, T. R., Mohapatra, T., Singh , N. K., Causse, M., Rothan, C., Schiex, T., Noirot, C., Bellec, A., Klopp, C., Delalande, C., Berges, H., Mariette, J., Frasse, P., Vautrin, S., Zouine, M., Latche, A., Rousseau, C., Regad, F., Pech, J.-C., Philippot, M., Bouzayen, M., Pericard, P., Osorio, S., Del Carmen, A. F., Monforte, A., Granell, A., Fernandez-Munoz, R., Conte, M., Lichtenstein, G., Carrari, F., De Bellis, G., Fuligni, F., Peano, C., Grandillo, S., Termolino, P., Pietrella, M., Fantini, E., Falcone, G., Fiore, A., Giuliano, G., Lopez, L., Facella, P., Perrotta, G., Daddiego, L., Bryan, G., Orozco , M., Pastor , X., Torrents, D., Van Schriek, K. N. V. M. G. M., Feron, R. M. C., Van Oeveren, J., De Heer, P., DaPonte, L., Jacobs-Oomen, S., Cariaso, M., Prins, M., Van Ejik, M. J. T., Janssen, A., Van Haaren, M. J. J., Jo, S.-H., Kim, J., kwon, S.-Y., Kim, S., Koo, D.-H., Lee, S., Hur , C.-G., Clouser, C., Rico, A., Hallab, A., Gebhardt, C., Klee, K., Joecker, A., Warfsmann, J., Gobel, U., Kawamura, S., Yano, K., Sherman, J. D., Fukuoka, H., Negoro, S., Bhutty, S., Chowdhury , P., Chattopadhyay, D., Datema, E., Smit, S., Schijlen , E. W. M., Van de Belt, J., Van Haarst, J. C., Peters, S. A., Van Staveren , M. J., Henkens, M. H. C., Mooyman , P. J., Hesselink, T., Van Ham, R. C. H. J., Jiang, G., Driege, M., Choi, D., Kang , B.-C., Kim, B. D., Park, M., Kim, S., Yeil, S.-I., Lee, Y.-H., Choi, Y.-D., Li, G., Gao, J., Liu, Y., Huang, S., Fernandez Pedrosa, V., Collado, C., Zuniga, S., Wang, G., Cade, R., Dietrich, R. A., Rogers, J., Knapp, S., Fei, Z., White , R. A., Thannhauser, T. W., Giovannoni, J. J., Botella, M. A., Gilbert, L., Gonzalez, R., Goicoechea, J. L., Yu , Y., Kudrna, D., Collura, K., Wissotski, M., Wing, R., Schoof, H., Meyer, B. C., Gurazada, A. B., Green, P. J., Mathur, S., Vyas, S., Solanke, A. U., Kumar , R., Gupta, V., Sharma, A. K., Khurana, P., Khurana, J. P., Tyagi , A. K., Dalmay , T., Mohorianu, I., Walts, B., Chamala , S., Barbazuk, W. B., Li, J., Guo, H., Lee , T.-H., Wang , Y., Zhang, D., Paterson, A. H., Wang, X., Tang, H., Barone, A., Chiusano, M. L., Ercolano, M. R., D'Agostino, N., Di Filippo, M., Traini, A., Sanseverino, W., Frusciante, L., Seymour, G. B., Elharam, M., Fu, Y., Hua , A., Kenton, S., Lewis, J., Lin, S., Najar, F., Lai, H., Qin, B., Qu, C., Shi, R., White, D., White, J., Xing, Y., Yang, K., Yi, J., Yao, Z., Shou, L., Roe, B. A., Vezzi, A., D'Angelo, M., Zimbello, R., Schiavon, R., Caniato, E., Rigobello, C., Campagna, D., Vitulo, N., Valle, G., Nelson, D. R., De Paoli, E., Szinay, D., de Jong, H. H., Bai, Y., Visser, R. G., Lankhorst, R. M. K., Beasley, H., McLaren, K., Nicholson, C., Riddle, C., Gianese, G. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400), 635-641. DOI : 10.1038/nature11119 Facteur d'impact (2 ans) : 38.597 Notoriété à 2 ans : Exceptionnelle (multidiscip.sci.) http://prodinra.inra.fr/record/174085

Schiex, T. (Auteur de correspondance) (2012). Le séquençage du génome humain. Bibliothèque Tangente, 104-109. http://prodinra.inra.fr/record/177818

Vandel, J., Mangin, B., Vignes, M., Leroux, D., Loudet, O., Magniette, M.-L., De Givry, S. (2012). Inférence de réseaux de régulation de gènes au travers de scores étendus dans les réseaux bayésiens. Revue d'Intelligence Artificielle, 26 (6), 679-708. DOI : 10.3166/ria.26.679-708 http://prodinra.inra.fr/record/189870

Actes de conférences

Akplogan, M., dury, J., De Givry, S., Quesnel, G., Joannon, A., Garcia, F. (2012). Résolution du problème d’allocation de culture par satisfaction de contraintes pondérées. Presented at Journées Francophones de Programmation par Contraintes , Toulouse, FRA (2012-05-22 - 2012-05-24). http://prodinra.inra.fr/record/226487   Allouche, D., Bessière, C., Boizumault, P., De Givry, S., Gutierrez, P., Loudni, S., Métivier, J.-P., Schiex, T. (2012). Filtering decomposable global cost functions. In: Proceedings of the Twenty-Sixth AAAI Conference on Artificial Intelligence. Presented at Twenty-Sixth Conference on Artificial Intelligence, Toronto, CAN (2012-07-22 - 2012-07-26). Menlo Park, USA : AAAI - Association for the Advancement of Artificial Intelligence. http://prodinra.inra.fr/record/259129

Allouche, D., Traore, S., Andre, I., De Givry, S., Katsirelos, G., Barbe, S., Schiex, T. (2012). Computational protein design as a cost function network optimization problem. In: Principles and Practice of Constraint Programming - 18th International Conference CP 2012 (p. 840-849). Lecture Notes in Computer Science. Presented at CP 2012 - 18th International Conference on Principles and Practice of Constraint Programming , Québec, CAN (2012-10-08 - 2012-10-12). DOI : 10.1007/978-3-642-33558-7_60 http://prodinra.inra.fr/record/177811

Allouche, D., Bessiere, C., Boizumault, P., De Givry, S., Gutierrez, P., Loudni, S., Metivier, J.-P., Schiex, T. (2012). Filtrage de fonctions de coût globales décomposables. In: Actes des Huitièmes Journées Francophones de Programmation par Contraintes (p. 15-24). Presented at Huitièmes Journées Francophones de Programmation par Contraintes (JFPC), Toulouse, FRA (2012-05-22 - 2012-05-24). http://prodinra.inra.fr/record/262305

Katsirelos, G., Narodytska, N., Walsh, T. (2012). The SeqBin constraint revisited. In: Principles and Pratice of Constraint Programming (p. 332-347). Lecture Notes in Computer Science, 0302-9743. Presented at CP 2012 - 18th International Conference on Principles and Practice of Constraint Programming , Québec, CAN (2012-10-08 - 2012-10-12). DOI : 10.1007/978-3-642-33558-7_26 http://prodinra.inra.fr/record/263226

Katsirelos, G., Simon, L. (2012). Learning polynomials over GF(2) in a SAT solver . Presented at SAT 2012 - 15th International Conference on Theory and Applications of Satisfiability Testing, Trente, ITA (2012-06-17 - 2012-06-20). http://prodinra.inra.fr/record/263229

Katsirelos, G., Simon, L. (2012). Eigenvector centrality in industrial SAT instances. In: Principles and Practice of Constraint Programming (p. 348-356). Lecture Notes in Computer Science, 0302-9743. Presented at CP 2012 - 18th International Conference on Principles and Practice of Constraint Programming , Québec, CAN (2012-10-08 - 2012-10-12). DOI : 10.1007/978-3-642-33558-7_27 http://prodinra.inra.fr/record/263227

Vandel, J., Mangin, B., De Givry, S. (2012). New local move operators for Bayesian networks structure learning . In: Proceedings of the Sixth European Workshop on Probabilistic Graphical Models (p. 339-346). Presented at The Sixth European Workshop on Probabilistic Graphical Models, Granada, ESP (2012-09-19 - 2012-09-21). http://prodinra.inra.fr/record/259127

2011

Journaux

Xavier Argout, Jerome Salse, Jean-Marc Aury, Mark J Guiltinan, Gaetan Droc, Jerome Gouzy, Mathilde Allegre, Cristian Chaparro, Thierry Legavre, Siela N Maximova, Michael Abrouk, Florent Murat, Olivier Fouet, Julie Poulain, Manuel Ruiz, Yolande Roguet, Maguy Rodier-Goud, Jose Fernandes Barbosa-Neto, Francois Sabot, Dave Kudrna, Jetty Siva S Ammiraju, Stephan C Schuster, John E Carlson, Erika Sallet, Thomas Schiex, Anne Dievart, Melissa Kramer, Laura Gelley, Zi Shi, Aurélie Bérard, Christopher Viot, Michel Boccara, Ange Marie Risterucci, Valentin Guignon, Xavier Sabau, Michael J Axtell, Zhaorong Ma, Yufan Zhang, Spencer Brown, Mickael Bourge, Wolfgang Golser, Xiang Song, Didier Clement, Ronan Rivallan, Mathias Tahi, Joseph Moroh Akaza, Bertrand Pitollat, Karina Gramacho, Angélique D'Hont, Dominique Brunel, Diogenes Infante, Ismael Kebe, Pierre Costet, Rod Wing, W Richard McCombie, Emmanuel Guiderdoni, Francis Quetier, Olivier Panaud, Patrick Wincker, Stephanie Bocs, and Claire Lanaud. The genome of theobroma cacao. Nat Genet, 43(2):101-8, Feb 2011.

Cros, M.-J., de Monte, A., Mariette, J., Bardou, P., Grenier-Boley, B., Gautheret, D., Touzet, H. (Auteur de correspondance), Gaspin, C. (Auteur de correspondance) (2011). RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA, 17 (11), 1947-1956. DOI : 10.1261/rna.2844911 Facteur d'impact (2 ans) : 5.095 Notoriété à 2 ans : Excellente (biochem.mol.biol.) http://prodinra.inra.fr/record/176684

Favier, A., De Givry, S. (Auteur de correspondance), Jégou, P. (2011). Solution counting for CSP and SAT with large tree-width. Control Systems and Computers, Vol. 2, 4-13. http://prodinra.inra.fr/record/166643

Mezmouk, S., Dubreuil, P., Bosio, M., Decousset, L., Charcosset, A., Praud, S., Mangin, B. (2011). Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Theoretical and Applied Genetics (122), 1149-1160. DOI : 10.1007/s00122-010-1519-y Facteur d'impact (2 ans) : 3.297 Notoriété à 2 ans : Exceptionnelle (horticulture) http://prodinra.inra.fr/record/177938

B Mangin, A Siberchicot, S Nicolas, A Doligez, P This, and C Cierco-Ayrolles. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity, aop August, 2011.

Phok, K., Moisan, A., Rinaldi, D., Brucato, N., Carpousis, A. J., Gaspin, C., Clouet-d'Orval, B., Brucato, N., Carpousis, A. J., Gaspin, C., Clouet-d'Orval, B. (2011). Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. BMC Genomics, 12. DOI : 10.1186/1471-2164-12-312 Facteur d'impact (2 ans) : 4.073 Notoriété à 2 ans : Excellente (biotechnol.appl.microbiol. ; genet.hered.) http://prodinra.inra.fr/record/164604

Vignes, M. (Auteur de correspondance), Blanchet, J., Leroux, D., Forbes, F. (2011). SpaCEM(3), a software for biological module detection when data is incomplete, high dimensional and dependent. Bioinformatics, 27 (6), 881-882. DOI : 10.1093/bioinformatics/btr034 Facteur d'impact (2 ans) : 5.468 Notoriété à 2 ans : Exceptionnelle (math.comput.biol.) http://prodinra.inra.fr/record/165180   Vignes, M. (Auteur de correspondance), Vandel, J., Allouche, D., Ramadan-Alban, N., Cierco-Ayrolles, C., Schiex, T., Mangin, B., De Givry, S. (2011). Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis. Plos One, 6 (12), 1-15. DOI : 10.1371/journal.pone.0029165 Facteur d'impact (2 ans) : 4.092 Notoriété à 2 ans : Excellente (biology) http://prodinra.inra.fr/record/164166

Young, N. D. (Auteur de correspondance), Debellé, F., Oldroyd, G. E. D., Geurts, R., Cannon, S., Udvardi, M. K., Benedito, V. A., Mayer, K. F. X., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R., Meyers, B. C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A. K., Murray, J. D., Naoumkina, M. A., Rosen, B., Silverstein, K. A. T., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J. J., Dudez, A.-M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., Gonzalez, A. J., Green, P. J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D.-H., Jing, Y., Jöcker, A., Kenton, S. M., Kim, D.-J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S. L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E. L., Mun, J.-H., Najar, F. Z., Nicholson, C., Noirot, C., O'Bleness, M., Paule, C. R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A., Sherrier, D. J., Shi, R., Sims, S., Singer, S. R., Sinharov, S., Sterck, L., Viollet, A., Wang, B.-B., Wang , K., Wang, M., Wang, X., Warfsmann, J., Weissenbach, J., White, D. D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Denarié, J., Dixon, R. A., Mary, G. D., Schwartz, D. C., Rogers, J., Quétier, F., Town, C. D., Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480 (7378), 520-524. DOI : 10.1038/nature10625 Facteur d'impact (2 ans) : 36.28 Notoriété à 2 ans : Exceptionnelle (multidiscip.sci.) http://prodinra.inra.fr/record/164615

Chapitres de livre

Caldelari, I., Fechter, P., Lioliou, E., Romilly, C., Chevalier, C., Gaspin, C., Romby, P. (2011). A current overview of regulatory RNAs in Staphylococcus aureus. In: A. Marchfelder, W. Hess, Regulatory RNAs in prokaryotes (p. 51-75). Vienne, AUT : Springer. DOI : 10.1007/978-3-7091-0218-3_3 http://prodinra.inra.fr/record/260243

Actes de conférences

Davies, J., Katsirelos, G., Narodytska, N., Walsh, T. (2011). Complexity of and algorithms for Borda manipulation. In: Proceedings of the twenty-fifth AAAI Conference on Artificial Intelligence. Presented at Twenty-fifth Conference on Artificial Intelligence, AAAI 2011, Association for the Advancement of Artificial Intelligence, San Francisco, California, USA (2011-11-04 - 2011-11-06). Menlo Park, USA : AAAI - Association for the Advancement of Artificial Intelligence. http://prodinra.inra.fr/record/164609   Favier, A., De Givry, S., Legarra Albizu, A., Schiex, T. (2011). Décomposition par paire pour l'optimisation combinatoire dans les modèles graphiques. Presented at JFPC 2011 - Septièmes Journées Francophones de Programmation par Contraintes, Lyon, FRA. http://prodinra.inra.fr/record/164657   Favier, A., De Givry, S., Legarra Albizu, A., Schiex, T. (2011). Pairwise decomposition for combinatorial optimization in graphical models. Presented at IJCAI 2011 - Twenty-second International Joint Conference on Artificial Intelligence, Barcelona, ESP. http://prodinra.inra.fr/record/164653

Sallet, E., Gouzy, J., Roux, B., Capela, D., Sauviac, L., Bruand, C., Gamas, P., Schiex, T. (2011). Integrated gene prediction for prokaryotic genomes using EuGene. Presented at JOBIM 2011 - 12e édition du Colloque - Journées Ouvertes en Biologie, Informatique et Mathématiques, Paris, FRA (2011-06-28 - 2011-07-01). http://prodinra.inra.fr/record/164650

J Vandel and S de Givry. A new local move operator for reconstructing gene regulatory networks. In CP-11 workshop on Constraint Based Methods for Bioinformatics, pages 67-72, Perugia, Italy, 2011.

Matthieu Vignes, Juliette Blanchet, Damien Leroux, and Florence Forbes. Spacem3, a software for biological module detection when data is incomplete, high dimensional and dependent. Bioinformatics, 27(6):881-882, mar 2011.

M Vignes, J Vandel, D Allouche, N Ramadan-Alban, C Cierco-Ayrolles, T Schiex, B Mangin, and S de Givry. Gene regulatory network reconstruction using bayesian networks, the dantzig selector, the lasso and their meta-analysis. PLoS ONE, 6(12):e29165, 2011.

Nevin D Young, Frédéric Debellé, Giles E D Oldroyd, Rene Geurts, Steven B Cannon, Michael K Udvardi, Vagner A Benedito, Klaus F X Mayer, Jérôme Gouzy, Heiko Schoof, Yves Van de Peer, Sebastian Proost, Douglas R Cook, Blake C Meyers, Manuel Spannagl, Foo Cheung, Stéphane De Mita, Vivek Krishnakumar, Heidrun Gundlach, Shiguo Zhou, Joann Mudge, Arvind K Bharti, Jeremy D Murray, Marina A Naoumkina, Benjamin Rosen, Kevin A T Silverstein, Haibao Tang, Stephane Rombauts, Patrick X Zhao, Peng Zhou, Valérie Barbe, Philippe Bardou, Michael Bechner, Arnaud Bellec, Anne Berger, Hélène Bergès, Shelby Bidwell, Ton Bisseling, Nathalie Choisne, Arnaud Couloux, Roxanne Denny, Shweta Deshpande, Xinbin Dai, Jeff J Doyle, Anne-Marie Dudez, Andrew D Farmer, Stéphanie Fouteau, Carolien Franken, Chrystel Gibelin, John Gish, Steven Goldstein, Alvaro J González, Pamela J Green, Asis Hallab, Marijke Hartog, Axin Hua, Sean J Humphray, Dong-Hoon Jeong, Yi Jing, Anika Jöcker, Steve M Kenton, Dong-Jin Kim, Kathrin Klee, Hongshing Lai, Chunting Lang, Shaoping Lin, Simone L Macmil, Ghislaine Magdelenat, Lucy Matthews, Jamison McCorrison, Erin L Monaghan, Jeong-Hwan Mun, Fares Z Najar, Christine Nicholson, Céline Noirot, Majesta O'Bleness, Charles R Paule, Julie Poulain, Florent Prion, Baifang Qin, Chunmei Qu, Ernest F Retzel, Claire Riddle, Erika Sallet, Sylvie Samain, Nicolas Samson, Iryna Sanders, Olivier Saurat, Claude Scarpelli, Thomas Schiex, Béatrice Segurens, Andrew J Severin, D Janine Sherrier, Ruihua Shi, Sarah Sims, Susan R Singer, Senjuti Sinharoy, Lieven Sterck, Agnès Viollet, Bing-Bing Wang, Keqin Wang, Mingyi Wang, Xiaohong Wang, Jens Warfsmann, Jean Weissenbach, Doug D White, Jim D White, Graham B Wiley, Patrick Wincker, Yanbo Xing, Limei Yang, Ziyun Yao, Fu Ying, Jixian Zhai, Liping Zhou, Antoine Zuber, Jean Dénarié, Richard A Dixon, Gregory D May, David C Schwartz, Jane Rogers, Francis Quétier, Christopher D Town, and Bruce A Roe. The medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480(7378):520-4, Dec 2011.

2010

Journaux

Beaume, M., Hernandez, D., Farinelli, L., Deluen, C., Linder, P., Gaspin, C., Romby, P., Schrenzel, J., Francois, P. (2010). Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. Plos One, 5 (5), e10725. DOI : 10.1371/journal.pone.0010725 Facteur d'impact (2 ans) : 4.411 Notoriété à 2 ans : Excellente (biology) http://prodinra.inra.fr/record/260244

Billotte, N., Jourjon, M.-F., Marseillac, N., Berger, A., Flori, A., Asmady, H., Adon, B., Singh, R., Nouy, B., Potier, F., Cheah, S. C., Rohde, W., Ritter, E., Courtois, B., Charrier, A., Mangin, B. (2010). QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 120 (8), 1673-1687. DOI : 10.1007/s00122-010-1284-y http://prodinra.inra.fr/record/262520

Boitard, S., Mangin, B., Azaïs, J.-M. (2010). Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula. Statistical Applications in Genetics and Molecular Biology, 9, online (1), Non paginé. DOI : 10.2202/1544-6115.1521 Facteur d'impact (2 ans) : 1.842 Notoriété à 2 ans : Excellente (stat.probab.) http://prodinra.inra.fr/record/47775

Cierco-Ayrolles, C. (Auteur de correspondance), Dejean, C., Legarra Albizu, A., Gilbert, H., Druet, T., Ytournel, F., Estivals, D., Oumouhou, N., Mangin, B. (2010). Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?. Genetics Selection Evolution, 42, online (october), Non paginé. DOI : 10.1186/1297-9686-42-38 Facteur d'impact (2 ans) : 1.484 Notoriété à 2 ans : Excellente (agric.,dairy anim.sci.) http://prodinra.inra.fr/record/39007

Cooper, M. C., De Givry, S., Sanchez, M., Schiex, T., Zytnicki, M., Werner, T. (2010). Soft arc consistency revisited. Artificial Intelligence (174), 449-478. DOI : 10.1016/j.artint.2010.02.001 http://prodinra.inra.fr/record/187837

Lionel Dupuy, Matthieu Vignes, Blair McKenzie, and Philip White. The dynamics of root meristem distribution in the soil. Plant Cell and Environment, 33(3):358-369, mar 2010.

Gaspin, C., Rami, J.-F., Lescure, B. (2010). Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function. BMC Plant Biology, 10. DOI : 10.1186/1471-2229-10-283 Facteur d'impact (2 ans) : 4.085 Notoriété à 2 ans : Excellente (plant sci.) http://prodinra.inra.fr/record/221181

Meseguer, P., Rossi, F. (Auteur de correspondance), Schiex, T. (2010). Introduction to the special issue on constraint-based approaches to preference modelling and reasoning. Constraints, 15 (4), 453-455. DOI : 10.1007/s10601-010-9096-x Facteur d'impact (2 ans) : 1.41 Notoriété à 2 ans : Correcte (comput.sci.,artif.intell. ; comput.sci.,theory methods) http://prodinra.inra.fr/record/263531

Pralet, C., Verfaillie, G., Schiex, T. (Auteur de correspondance) (2010). Le cadre PFU, un modèle et des algorithmes génériques pour la décision séquentielle incluant incertitudes, faisabilités et utilités. Technique et Science Informatiques, 29 (1), 85-114. DOI : 10.3166/tsi.29.85-114 http://prodinra.inra.fr/record/262310

Servin, B. (Auteur de correspondance), De Givry, S., Faraut, T. (2010). Statistical confidence measures for genome maps: application to the validation of genome assemblies. Bioinformatics, 26 (24), 3035–3042. DOI : 10.1093/bioinformatics/btq598 Facteur d'impact (2 ans) : 4.877 Notoriété à 2 ans : Exceptionnelle (math.comput.biol.) http://prodinra.inra.fr/record/41884

Livres

C Pralet, T Schiex, and T Verfaillie. Sequential Decision-Making Problems: Representation and Solution. ISTE-Wiley, 2010.

Actes de conférences

David Allouche, Simon de Givry, and Thomas Schiex. Towards parallel non serial dynamic programming for weighted csp. In Proc. CP'2010, number 6307 in LNCS, pages 53-60, St-Andrews, UK, 2010. Springer.

E Audemard, T Faraut, and T Schiex. Détection de régions génomiques homologues par un algorithme de flot avec coûts. In ROADEF'2010, Toulouse, FEV 2010.

Vandel, J., De Givry, S., Mangin, B., Vignes, M. (2010). Reconstruction de réseau de régulation de gène à l’aide de données génomiques et de données génétiques. In: Proceedings of the CAp'2010. Presented at Conférence d'Apprentissage Automatique (CAP 2010), Clermont Ferrand, FRA (2010-05-17 - 2010-05-19). http://prodinra.inra.fr/record/266027

Jimmy Vandel, Brigitte Mangin, Matthieu Vignes, and Simon de Givry. Extended bayesian scores for reconstructing gene regulatory networks. in Actes of ECCS, WGM, Lisbonne, Portugal, Septembre 2010, 2010.

2009

Journaux

Blanchet, J., Vignes, M. (2009). A model-based approach to gene clustering with missing observation reconstruction in a Markov random field framework . Journal of Computational Biology, 16 (3), 475-486. DOI : 10.1089/cmb.2008.0078 Facteur d'impact (2 ans) : 1.694 Notoriété à 2 ans : Excellente (stat.probab.) http://prodinra.inra.fr/record/189894

Faraut, T., De Givry, S., Hitte, C., Lahbib Mansais, Y., Morisson, M., Milan, D., Schiex, T., Servin, B., Vignal, A., Galibert, F., Yerle, M. (2009). Contribution of radiation hybrids to genome mapping in domestic animals. Cytogenetic and Genome Research, 126 (1-2), 21-33. DOI : 10.1159/000245904 http://prodinra.inra.fr/record/5437

Geissmann, T., Chevalier, C., Cros, M.-J., Boisset, S., Fechter, P., Noirot, C., Schrenzel, J., François, P., Vandenesh, F., Gaspin, C., Romby, P. (2009). A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Research, 37 (21), 7239-7257. DOI : doi:10.1093/nar/gkp668 Facteur d'impact (2 ans) : 7.479 Notoriété à 2 ans : Excellente (biochem.mol.biol.) http://prodinra.inra.fr/record/257210

Gouzy, J., Carrere, S., Schiex, T. (2009). FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics, 25 (5), 670-671. DOI : 10.1093/bioinformatics/btp024 Facteur d'impact (2 ans) : 4.877 Notoriété à 2 ans : Exceptionnelle (math.comput.biol.) http://prodinra.inra.fr/record/40318

Vignes, M., Forbes, F. (2009). Gene clustering via integrated Markov models combining individual and pairwise features. IEEE/ACM transactions on computational biology and bioinformatics, 6 (2), 260-270. DOI : 10.1109/TCBB.2007.70248 Facteur d'impact (2 ans) : 2.246 Notoriété à 2 ans : Excellente (comput.sci.,interdiscip.appl. ; math.,interdiscip.appl. ; stat.probab.) http://prodinra.inra.fr/record/189889

Zytnicki, M., Gaspin, C., De Givry, S., Schiex, T. (2009). Bounds arc consistency for weighted CSPs. Journal of Artificial Intelligence Research, 35, 593-621. DOI : 10.1613/jair.2797 http://prodinra.inra.fr/record/187831

Chapitres de livre

C Gaspin. Traduction du chapitre 20, chapter Analyse des génomes et biologie des systèmes, pages 545-567. Pearson Education France, 6 edition, 2009.

K Phok, A Moisan, MJ Cros, C Gaspin, and B Clouet d'Orval. Identification and characterisation of new non-coding RNA in Pyrococcus abyssi. In Regulatory RNA in Prokaryotes, Berlin, 2009.

G Verfaillie and T Schiex. Constraint Satisfaction Problems, chapter 6, pages 265-320. Number ISBN 978-1-84821-116-2. ISTE-Wiley, 2009.

Actes de conférences

Dupuy, L., Vignes, M. (2009). Simplified root architectural models using continuous deformable domains. Presented at PMA '09 Proceedings of the 2009 Plant Growth Modeling, Simulation, Visualization, and Applications , Pékin, Chine (2009-11-09 - 2009-11-13). Washington, USA : IEEE Computer Society. DOI : 10.1109/PMA.2009.23 http://prodinra.inra.fr/record/189892

Dechter, R., Marinescu, R., Schiex, T., De Givry, S. (2009). Combinatorial optimization for graphical models. Presented at IJCAI 2009 - International Joint Conference on Artificial Intelligence, Pasadena, USA (2009-07-11 - 2009-07-17). http://prodinra.inra.fr/record/262313

Favier, A., De Givry, S., Jegou, P. (2009). Exploiting problem structure for solution counting. In: Principles and Practice of Constraint Programming - CP 2009 (p. 335-343). Lecture Notes in Computer Science , 5732. Presented at 15th International Conference on Principles and Practice of Constraint Programming, Lisbonne, PRT (2009-09-20 - 2009-09-24). DEU : Springer: Berlin Heidelberg. DOI : 10.1007/978-3-642-04244-7_27 http://prodinra.inra.fr/record/187830

A Favier, S de Givry, and P Jégou. Comptage de solutions en exploitant la structure du graphe de contraintes. In Yves Deville, editor, Actes des Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, 2009.

Sanchez, M., Allouche, D., De Givry, S., Schiex, T. (2009). Algorithme des Poupées Russes exploitant une décomposition arborescente. In: Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, juin 2009 (p. 15-25). Presented at Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, juin 2009, FRA (2009-06-02). http://prodinra.inra.fr/record/245980

Sanchez, M., Allouche, D., De Givry, S., Schiex, T. (2009). Russian doll search with tree decomposition. In: Proceedings of the 21st International Joint Conference on Artificial Intelligence, Pasadena, California, USA, July 11-17, 2009 (p. 603-608). Presented at 21st International Joint Conference on Artificial Intelligence, Pasadena, USA (2009-07-11 - 2009-07-17). San Fransisco, USA : Morgan Kaufmann. http://prodinra.inra.fr/record/187829

Saint-Pierre A., Brigitte Mangin, and Maria Martinez. Bivariate linkage analysis for mapping quantitative trait loci in pedigrees: Comparison of methods and assessment of the test statistics distributions in the nemo study. ANNALS OF HUMAN GENETICS, 73(Part 6):58, European Mathematical Genetics Meeting, Munich, GERMANY, MAY 14-15, 2009, WILEY-BLACKWELL PUBLISHING, INC, COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA, English, 2009.

Schiex T. Combinatorial optimization for pedigree analysis using graphical models. Invited talk at the 2nd channel conference of the International Biometry Society, apr 2009.

2008

M Zytnicki. Localisation d'ARN non-codants par réseaux de contraintes pondérées. PhD thesis, Université Paul Sabatier, Toulouse, 2008.

M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA motif localization. Constraints, 13(1):91-109, 2008.

M Sanchez, S de Givry, and T Schiex. Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques. Constraints, 13(1):130-154, 2008.

C Noirot, C Gaspin, T Schiex, and J Gouzy. LeARN: a platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics, 9:21, 2008.

B Mangin, P Garnier-Gere, and C Cierco-Ayrolles. The estimator of the optimal measure of allelic association: Mean, variance and probability distribution when the sample size tends to infinity. Statistical Applications in Genetics and Molecular Biology, 7(1), 2008.

J Larrosa, F Heras, and S de Givry. A logical approach to efficient max-sat solving. Artificial Intelligence, 172(2-3), 2008.

F Heras, J Larrosa, S de Givry, and T Schiex. 2006 and 2007 max-sat evaluations: Contributed instances. Journal of Satisfiability, Boolean Modeling and Computation, 4:239-250, 2008.

S Foissac, J Gouzy, S Rombauts, C Mathé, J Amselem, L Sterk, Y van de Peer, P Rouzé, and T Schiex. Genome annotation in plants and fungi: Eugène as a model platform. Current Bioinformatics, 3(2):87-97, 5 2008.

O Filangi, Y Beausse, A Assi, L Legrand, JM Larré, V Martin, O Collin, C Caron, H Leroy, and D Allouche. Biomaj: a flexible framework for databanks synchronization and processing. Bioinformatics, 24(16):1823-5, Aug 2008.

MC Cooper, S de Givry, M Sanchez, T Schiex, and M Zytnicki. Cohérence d'arc virtuelle pour csp pondérés. In Actes des Quatrièmes Journées Francophones de Programmation par Contraintes, Nantes, 2008.

MC Cooper, S de Givry, M Sanchez, T Schiex, and M Zytnicki. Virtual arc consistency for weighted csp. In Proc. of AAAI'2008, Chicago, USA, 2008.

S Bouveret, S de Givry, F Heras, J Larrosa, E Rollon, M Sanchez, T Schiex, G Verfaillie, and M Zytnicki. Max-csp competition 2007: toolbar/toulbar2 solver brief description. In C; Roussel O van Dongen, MRC; Lecoutre, editor, Proceedings of the Second International CSP Solver Competition, pages 19-21, 2008.

S Bérard, C Chauve, and C Paul. A more efficient algorithm for perfect sorting by reversals. Information Processing Letters, 106(3):90-95, 4 2008.

P Abad, J Gouzy, JM Aury, P Castagnone-Sereno, EGJ Danchin, E Deleury, L Perfus-Barbeoch, V Anthouard, F Artiguenave, VC Blok, MC Caillaud, PM Coutinho, C Dasilva, F De Luca, F Deau, M Esquibet, T Flutre, JV Goldstone, N Hamamouch, T Hewezi, O Jaillon, C Jubin, P Leonetti, M Magliano, TR Maier, GV Markov, P McVeigh, G Pesole, J Poulain, M Robinson-Rechavi, E Sallet, B Ségurens, D Steinbach, T Tytgat, E Ugarte, C van Ghelder, P Veronico, TJ Baum, M Blaxter, T Bleve-Zacheo, EL Davis, JJ Ewbank, B Favery, E Grenier, B Henrissat, JT Jones, V Laudet, AG Maule, H Quesneville, MN Rosso, T Schiex, G Smant, J Weissenbach, and Patrick Wincker. Genome sequence of the metazoan plant-parasitic nematode meloidogyne incognita. Nat Biotechnol, 26(8):909-15, Aug 2008.

2007

M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA motif localization. In Proc. of JOBIM'2007, Marseille, France, 2007.

A Prasad, T Schiex, S McKay, B Murdoch, Z Wang, JE Womack, P Stothard, and SS Moore. High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly. BMC Genomics, 8:310, 2007.

C Pralet, T Schiex, and G Verfaillie. Algorithmes et complexités génériques pour différents cadres de décision séquentielle dans l'incertain. Revue d'Intelligence Artificielle, 21:459-488, 2007.

C Pralet, G Verfaillie, and T Schiex. Un cadre graphique et algébrique pour les problèmes de décision incluant incertitudes, faisabilités et utilités. Revue d'Intelligence Artificielle, 21(3), 2007.

C Pralet, G Verfaillie, and T Schiex. An algebraic graphical model for decision with uncertainties, feasibilities, and utilities. Journal of Artificial Intelligence Research, 29:421-489, 2007.

E Marques, S de Givry, P Stothard, B Murdoch, Z Wang, J Womack, and SS Moore. A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly. BMC Genomics, 8:254, 2007.

T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T Schiex. A comparative genome approach to marker ordering. Bioinformatics, 23(2):e50-6, Jan 2007.

MC Cooper, S de Givry, and T Schiex. Optimal soft arc consistency. In Proc. of IJCAI-07, pages 68-73, Hyderabad, India, 2007.

J Burstin, P Marget, M Huart, A Moessner, B Mangin, C Duchene, B Desprez, N Munier-Jolain, and G Duc. Developmental genes have pleiotropic effects on plant morphology and source capacity, eventually impacting on seed protein content and productivity in pea. Plant Physiology, 144(2):768-781, jun 2007.

S Boitard and P Loisel. Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation. Theoretical Population Biology, 71(3):380-391, 2007.

S Boisset, T Geissmann, E Huntzinger, P Fechter, N Bendridi, M Possedko, Ct Chevalier, ACe Helfer, Y Benito, A Jacquier, C Gaspin, F Vandenesch, and P Romby. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev, 21(11):1353-66, Jun 2007.

S Bérard, A Bergeron, C Chauve, and C Paul. Perfect sorting by reversal is not always difficult. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(1):4-16, 2007.

S Aubourg, ML Martin-Magniette, V Brunaud, L Taconnat, F Bitton, S Balzergue, P E Jullien, M Ingouff, V Thareau, T Schiex, An Lecharny, and JP Renou. Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics, 8:401, 2007.

2006

M Zytnicki, C Gaspin, and T Schiex. A new local consistency for weighted CSP dedicated to long domains. In Proceedings of the 2006 ACM Symposium on Applied Computing, pages 394-398, Dijon, France, 2006.

P Thébault, S de Givry, T Schiex, and C Gaspin. Searching rna motifs and their intermolecular contacts with constraint networks. Bioinformatics, 22(17):2074-80, Sep 2006.

C Pralet, G Verfaillie, and T Schiex. Decision with uncertainties, feasibilities and utilities: towards a unified algebraic framework. In Proc. of ECAI'2006, Trento, Italy, 2006.

C Pralet, T Schiex, and G Verfaillie. From influence diagrams to multioperator cluster dags. In Proc. of UAI'2006, Boston (MA), USA, 2006.

C Pralet. Un cadre générique pour représenter et résoudre des problèmes de décision séquentiels avec incertitudes, faisabilités et utilités. PhD thesis, Ecole Nationale Superieure de l'Aéronautique et de l'Espace, Toulouse, Toulouse, France, 2006.

C Pralet, T Schiex, and G Verfaillie. Decomposition of multi-operators queries on semiring-based graphical models. In Proc. of CP'2006, Nantes, France, 2006.

P Meseguer, F Rossi, and T Schiex. Soft Constraints, chapter 9, pages 281-328. Elsevier, 2006.

A Lucas and S Jasson. Using amap and ctc packages for huge clustering. R News, 5(6):58-60, 2006.

G Verfaillie and T Schiex. Problemes de satisfaction de contraintes, volume 1 of Traite IC2, serie Informatique et Systemes d'Information, chapter 6, pages 287-344. Hermes Sciences, 2006.

S de Givry and L Jeannin. A unified framework for partial and hybrid search methods in constraint programming. Computer & Operations Research, 33(10):2805-2833, 2006.

T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T Schiex. A comparative genome approach to marker ordering. In Actes de JOBIM'06, page 11, Bordeaux, France, 2006.

T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T Schiex. A comparative genome approach to marker ordering. In Proc. of ECCB'2006, 2006.

S de Givry, T Schiex, and G Verfaillie. Décomposition arborescente et cohérence locale souple dans les csp pondérés. In Actes des Deuxièmes Journées Francophones de Programmation par Contraintes, Nîmes, 2006.

S de Givry, T Schiex, and T Verfaillie. Exploiting tree decomposition and soft local consistency in weighted CSP. In Proc. of AAAI'2006, Boston (MA), USA, 2006.

SB Cannon, L Sterck, S Rombauts, S Sato, F Cheung, J Gouzy, X Wang, J Mudge, J Vasdewani, T Schiex, M Spannagl, E Monaghan, C Nicholson, SJ Humphray, H Schoof, KFX Mayer, J Rogers, F Quétier, GE Oldroyd, F Debellé, DR Cook, EF Retzel, BA Roe, CD Town, S Tabata, Y Van de Peer, and ND Young. Legume genome evolution viewed through the medicago truncatula and lotus japonicus genomes. Proc Natl Acad Sci U S A, 103(40):14959-64, Oct 2006.

S Bérard, F Nicolas, J Buard, O Gascuel, and E Rivals. Fast and specific alignment method for minisatellite maps applied to human y chromosome minisatellite msy1. Evolutionary Bioinformatics Online, 2:327-344, 2006.

S Boitard, J Abdallah, H de Rochambeau, C Cierco-Ayrolles, and B Mangin. Linkage disequilibrium interval mapping of quantitative trait loci. BMC Genomics, 7:54, 2006.

G Blanc, A Charcosset, B Mangin, A Gallais, and L Moreau. Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize. TAG, 113:206-224, 2006.

2005

MH Renalier, N Joseph, C Gaspin, P Thebault, and A Mougin. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA, 11(7):1051-63, 2005.

S Genin, M Salanoubat, J Gouzy, A Moisan, T Schiex, S Cunnac, M Lavie, C Zischek, P Barberis, and C Boucher. The Ralstonia solanacearum complete genome sequence: outputs and prospects. In Bacterial wilt disease and the Ralstonia solanacearum species complex, pages 335-342. American Phytopathological Society (APS Press), St. Paul, USA, 2005.

M Zytnicki, F Heras, S de Givry, and L Larrosa. Cohérence d'arc existentielle: un pas de plus vers la cohérence d'arc complète. In Actes des Premières Journées Francophones de Programmation par Contraintes, pages 139-148, Lens, France, 2005.

MF Jourjon, S Jasson, J Marcel, B Ngom, and B Mangin. MCQTL: multi-allelic qtl mapping in multi-cross design. Bioinformatics, 21(1):128-30, 2005.

S Foissac and T Schiex. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics, 6:25, 2005.

S de Givry, M Zytnicki, F Heras, and J Larrosa. Existential arc consistency: getting closer to full arc consistency in weighted CSPs. In Proc. of IJCAI- 05, pages 84-89, Edinburgh, Scotland, 2005.

S de Givry, M Bouchez, P Chabrier, D Milan, and T Schiex. Carthagene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics, 21(8):1703-4, Apr 2005.

B Clouet-d'Orval, C Gaspin, and A Mougin. Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Biochimie, 87(9-10):889-95, Sep-Oct 2005.

C Gaspin and P Thébault. Identification d'ARN non codants. Biofutur, 251:33-36, 2005.

S Boitard. Cartographie de gènes à caractères quantitatifs par déséquilibre de liaison. PhD thesis, Université Paul Sabatier, Toulouse III, 2005.

S Boitard. Computation of the haplotype frequency distribution under the two- locus wright-fisher model. a diffusion approximation method. In Proc. of European mathematical genetics meeting in annals of human genetics 69(6) ,p. 765, pages 764-774, Le Kremlin-Bicêtre, France, 2005.

S Bérard, A Bergeron, C Chauve, and C Paul. Perfect sorting by reversal is not always difficult. In Proc. of the 5th Workshop on Algorithms in Bioinformatics (WABI'05), number 3692 in LNCS, pages 228-238, 2005.

S Bérard, L Tichit, and C Herrmann. Simct, a tool to visualize ontology based relationships. In Actes des Journées Ouvertes Biologie Informatique Mathématiques (JOBIM'05), pages 447-457, Lyon, 2005.

S Aubourg, V Brunaud, C Bruyere, M Cock, R Cooke, A Cottet, A Couloux, P Dehais, G Deleage, A Duclert, M Echeverria, A Eschbach, D Falconet, G Filippi, C Gaspin, C Geourjon, JM Grienenberger, G Houlne, E Jamet, F Lechauve, O Leleu, P Leroy, R Mache, C Meyer, H Nedjari, I Negrutiu, V Orsini, E Peyretaillade, C Pommier, J Raes, JL Risler, S Riviere, S Rombauts, P Rouze, M Schneider, P Schwob, I Small, G Soumayet-Kampetenga, D Stankovski, C Toffano, M Tognolli, M Caboche, and A Lecharny. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res, 33(Database issue):D641-6, 2005.

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