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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

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

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

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

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

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

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.    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.  

Actes de conférences

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).   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).

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).



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

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


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

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

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  

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

Actes de conférence


N Billotte, F-C Baurens, B Cochard, B Courtois, H de Franqueville, A Flori, C Louise, A-M Risterucci, M Ruiz, P Amblard, B Nouy, T Durand-Gasselin, A D'Hont, B Mangin, and C Lanaud. Multi-parent qtl/gene mapping, novel field trial systems and intra-gene markers: a key method for marker-assisted selection in oil palm (elaeis guineensis jacq.). Actes of the Plant & Animal Genomes XVIIII Conference, Janvier 2012.

E Cadic, P Debaeke, N Langlade, B Grèzes-Besset, J Pauquet, M Coque, T André, S Chatre, P Casadebaig, B Mangin, and P Vincourt. Phenotyping the response of sunflower (helianthus annuus l.) to drought scenarios in multi-environmental trials for the purpose of association genetics. Actes of the Plant & Animal Genomes XVIIII Conference, january 2012.

S Mezmouk, P Dubreuil, L Decousset, S Praud, and B Mangin. Applying the new ld measures, that correct the bias due to structure and relatedness, to maize panels. Actes of the Plant & Animal Genomes XVIIII Conference, 2012.


M Akplogan, J Dury, S de Givry, G Quesnel, A Joannon, A Reynaud, J-E Bergez, and F Garcia. A weighted csp approach for solving spatio-temporal planning problem in farming systems. In Proc. of the Soft'2011 workshop, pages 1-15, Perugia, Italy, 2011.

D Allouche, C Bessiere, P Boizumault, S de Givry, P Gutierrez, S Loudni, JP Métivier, and T Schiex. Decomposing global cost functions. In Proc. of the Soft'2011 workshop, Perugia, Italie, Septembre 2011.

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.

MJ Cros, A de Monte, J Mariette, P Bardou, B Grenier-Boley, D Gautheret, H Touzet, and C Gaspin. an integrated environment for the prediction, annotation and analysis of ncrna. RNA, 17(11), 2011.

A Favier, S de Givry, and P Jégou. Solution counting for csp and sat with large tree-width. Control Systems and Computers, (2):4-13, 2011.

A Favier, S de Givry, A Legarra, and T Schiex. Pairwise decomposition for combinatorial optimization in graphical models. In Proc. of IJCAI'11, pages 2126-2132, 2011.

A Favier, S de Givry, A Legarra, and T Schiex. Décomposition par paire pour l'optimisation combinatoire dans les modèles graphiques. In Proc. of JFPC'2011, Lyon, France, 2011.

S de Givry. Optimisation combinatoire dans les réseaux de fonctions de coût. Habilitation à dirigé des recherches, UPS, Toulouse, 2011.

A Larièpe, B Mangin, S Jasson, V Combes, F Dumas, P Jamin, C Lariagon, D Jolivot, D Madur, JB Fiévet, A Gallais, P Dubreuil, A Charcosset, and L Moreau. The genetic basis of heterosis: Multiparental qtl mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (zea mays l.). Genetics, aop November, 2011.

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.

Sofiane Mezmouk, Pierre Dubreuil, Mickaël Bosio, Laurent Décousset, Alain Charcosset, Sébastien Praud, and Brigitte Mangin. Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Theoretical and Applied Genetics, 122:1149-1160, 2011.

K Phok, A Moisan, D Rinaldi, N Brucato, AJ Carpousis, C Gaspin, and B Clouet-d'Orval. Identification of crispr and riboswitch related rnas among novel noncoding rnas of the euryarchaeon pyrococcus abyssi. BMC Genomics, Jun 13;12:312, 2011.

E Sallet, J Gouzy, B Roux, D Capela, L Sauviac, C Bruand, P Gamas, and T Schiex. Integrated gene prediction for prokaryotic genomes using eugene. In Proc. of JOBIM'2011, Institut Pasteur, Paris, France, 2011.

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.


C. Cierco-Ayrolles, S. Dejean, A. Legarra, H. Gilbert, T. Druet, F. Ytournel, D. Estivals, and B. Oumouhou, N. & Mangin. Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of qtl location in animal pedigree? Genetics Selection Evolution, 42(1):38, October 2010.

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.

M Beaume, D Hernandez, L Farinelli, C Deluen, P Linder, C Gaspin, P Romby, J Schrenzel, and P Francois. Cartography of methicillin-resistant (S. aureus) transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One, May 20;5(5):e1072, 2010.

N Billotte, MF Jourjon, N Marseillac, A Berger, A Flori, H Asmady, B Adon, R Singh, B Nouy, F Potier, SC Cheah, W Rohde, E Ritter, B Courtois, A Charrier, and B Mangin. Qtl detection by multi-parent linkage mapping in oil palm (elaeis guineensis jacq.). Theoretical and Applied Genetics, 120:1673-1687, 2010.

Simon Boitard, Brigitte Mangin, and Jean-Marc Azaïs. Asymptotic distribution of the "orthogonal" quantitative transmission disequilibrium test in a structured population: Exact formula. Statistical Application in Genetics and Molecular Biology, 9(1):11, 2010.

MC Cooper, S de Givry, M Sanchez, T Schiex, M Zytnicki, and T Werner. Soft arc consistency revisited. Artificial Intelligence, 2010.

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.

A Favier, J-M Elsen, S de Givry, and A Legarra. Optimal haplotype reconstruction in half-sib families. In ICLP-10 workshop on Constraint Based Methods for Bioinformatics, Edinburgh, UK, 2010.

A Favier, J-M Elsen, S de Givry, and A Legarra. Exact haplotype reconstruction in half-sib families with dense marker maps. In 9th World Congress on Genetics Applied to Livestock Production (WCGALP-10), Leipzig, Germany, 2010.

C Gaspin, JF Rami, and B Lescure. Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function. BMC Plant Biology, Dec 20;10:283, 2010.

S Leroux, K Feve, F Vignoles, O Bouchez, C Klopp, C Noirot, D Gourichon, S Richard, C Leterrier, C Beaumont, F Minvielle, A Vignal, and F Pitel. Non PCR-amplified transcripts and AFLP(R)(R) fragments as reduced representations of the quail genome for 454 titanium sequencing. BMC Research Note, 3:214, 2010.

P Meseguer, F Rossi, and T Schiex. Constraint-based approaches to preference modelling and reasoning. Constraints, Special issue., 2010.

Sofiane Mezmouk, Laurent Décousset, Mikaël Bosio, Alain Charcosset, Sébastien Praud, Pierre Dubreuil, and Brigitte Mangin. Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Actes of 52nd Annual Maize Genetics Conference, mars 2010.

Sofiane Mezmouk, Laurent Décousset, Jérémy Derory, Morgan Renault, Brigitte Mangin, Marie-Hélène Tixier, Mickaël Bosio, Christophe Tatout, Pierre Dubreuil, and Sébastien Praud. Association mapping in maize (zea mays) at biogemma. Actes of Plant & Animal Genomes XVIII Conference, january 2010.

S Nicolas, J-P Peros, P This, T Lacombe, L Le Cunff, M Boursiquot, A Dereeper, R Bacilieri, V Laucou, M Di Vecchi Staraz, A Walker, P Cousins, A Siberchicot, C Cierco-Ayrolles, B Mangin, R Eibach, and A Doligez. Genetic structure and linkage disequilibrium in four vitis species. in Actes of the 10th International Conference on Grapevine Breeding and Genetics, Geneva, USA, August 2010, 2010.

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

Cédric Pralet, Gérard Verfaillie, and Thomas Schiex. Le cadre pfu, un modèle et des algorithmes génériques pour la décision séquentielle incluant incertitudes, faisabilités et utilités. Techniques et Science Informatique, 29(1):85-114, 2010.

Abdelaziz Rahmani, Sylvain Jasson, Florence Louis, Marjolaine Ventelon-Debout, Laurence Moreau, and Brigitte Mangin. Introducing the use of the linkage desiquilibrium for qtl mapping by mcqtl. Actes of the Plant & Animal Genomes XVIII Conference, january 2010. Démontration et Poster.

B Servin, S de Givry, and Faraut T. Modelling radiation hybrid maps uncertainty and application to the validation of whole genome assemblies. In 9th World Congress on Genetics Applied to Livestock Production (WCGALP-10), Leipzig, Germany, 2010.

B Servin, S de Givry, and T Faraut. Statistical confidence measures for genome maps: application to the validation of genome assemblies. Bioinformatics, 26(24):3035-3042, 2010.

Lena Tasse, Juliette Bercovici, Sandra Pizzut-Serin, Patrick Robe, Julien Tap, Christophe Klopp, Brandi L Cantarel, Pedro M Coutinho, Bernard Henrissat, Marion Leclerc, Joël Doré, Pierre Monsan, Magali Remaud-Simeon, and Gabrielle Potocki-Veronese. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res, 20(11):1605-12, Nov 2010.

D Allouche, S de Givry, and T Schiex. Toulbar2, an open source exact cost function network solver. Technical report, INRA, 2010. Contributors: M. Sanchez (SP), S. Bouveret (F), H. Fargier (F), F. Heras (SP), P. Jégou (F), J. Larrosa (SP), K. L. Leung (CN), S. N'diaye (F), E. Rollon (SP), C. Terrioux (F), G. Verfaillie (F), M. Zytnicki.

Jimmy Vandel, Simon de Givry, Brigitte Mangin, and Matthieu Vignes. Reconstruction de réseaux de régulations de gènes à l'aide de données génomiques et de données génétiques. in Actes de CAP'10, Clermont-Ferrand, Juin 2010, 2010.

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.


Lionel Dupuy, Matthieu Vignes, Blair McKenzie, and Philip White. Meristematic waves, a new approach to model root architecture dynamics. In Proceedings of the 10th JOBIM, Nantes, June 2009.

A Kozomara. Prédiction de gènes d'ARN dans les séquences génomiques. PhD thesis, Université Paul Sabatier, Toulouse, Toulouse, France, Juin 2009.

D Allouche, S de Givry, M Sanchez, and T Schiex. Tagsnp selection using weighted csp and russian doll search with tree decomposition. In CP-09 workshop on Constraint Based Methods for Bioinformatics, 2009.

P Bardou, MJ Cros, C Gaspin, D Gautheret, JM Larré, B Grenier-Boley, J Mariette, A de Monte, and H Touzet. RNAspace non-coding RNA annotation web platform. In JOBIM, Nantes, 2009.

Juliette Blanchet and Matthieu Vignes. 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, mar 2009.

Pierrot Casel, François Moreews, Sandrine Lagarrigue, and Christophe Klopp. sigreannot: an oligo-set re-annotation pipeline based on similarities with the ensembl transcripts and unigene clusters. BMC Proc, 3 Suppl 4:S3, 2009.

MJ Cros. Développement d'une plateforme web avec cheerypy. In PYCON, Paris, 2009.

R Dechter, S de Givry, R Marinescu, and T Schiex. Combinatorial optimization for graphical models. In Selected tutorial at IJCAI'2009., Pasadena (CA), USA., 2009.

Lionel Dupuy and Matthieu Vignes. Simplified root architectural models using continuous deformable domains. In Plant Growth Modeling, Simulation, Visualization and Applications (PMA), 2009 Third International Symposium on, pages 142-148. IEEE Computer Society, nov 2009.

T Faraut, S de Givry, C Hitte, Y Lahlib-Mansais, M Morisson, D Milan, T Schiex, B Servin, A Vignal, F Galibert, and M Yerle. Contributions of radiation hybrids to genome mapping in domestic animals. Cytogenetic and Genome Research, 126:21-33, 2009.

A Favier, S de Givry, and P Jégou. Exploiting problem structure for solution counting. In Proc. of CP'2009, LNCS, Lisbon, Portugal, 2009.

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.

Elodie Fleury, Arnaud Huvet, Christophe Lelong, Julien de Lorgeril, Viviane Boulo, Yannick Gueguen, Evelyne Bachère, Arnaud Tanguy, Dario Moraga, Caroline Fabioux, Penelope Lindeque, Jenny Shaw, Richard Reinhardt, Patrick Prunet, Grace Davey, Sylvie Lapègue, Christopher Sauvage, Charlotte Corporeau, Jeanne Moal, Frederick Gavory, Patrick Wincker, François Moreews, Christophe Klopp, Michel Mathieu, Pierre Boudry, and Pascal Favrel. Generation and analysis of a 29,745 unique expressed sequence tags from the pacific oyster (crassostrea gigas) assembled into a publicly accessible database: the gigasdatabase. BMC Genomics, 10:341, 2009.

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

T Geissmann, C Chevalier, MJ Cros, S Boisset, P Fechter, C Noirot, J Schrenzel, P François, F Vandenesch, C Gaspin, and P Romby. A search for small noncoding RNAs in staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Research, 2009.

J Gouzy, S Carrere, and T Schiex. Framedp: sensitive peptide detection on noisy matured sequences. Bioinformatics, Jan 2009.

Florence Jaffrezic, Jakob Hedegaard, Magali Sancristobal, Christophe Klopp, and Dirk-Jan de Koning. The eadgene and sabre post-analyses workshop. BMC Proc, 3 Suppl 4:I1, 2009.

B Mangin. Une contribution de génoplante en bioinformatique. In Les 10 ans de GÉNOPLANTE, Paris, apr 2009.

Pieter B T Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack A M Leunissen, Martien A M Groenen, and Christophe Klopp. Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. BMC Proc, 3 Suppl 4:S1, 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.

Aude Saint-Pierre, 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, Month = NOV, Note = European Mathematical Genetics Meeting, Munich, GERMANY, MAY 14-15, 2009, Publisher = WILEY-BLACKWELL PUBLISHING, INC, Address = COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA, Type = Meeting Abstract, Language = English, 2009.

M Sanchez, D Allouche, S de Givry, and T Schiex. Russian doll search with tree decomposition. In Proc. of IJCAI'09, Pasadena (CA), USA, 2009.

M Sanchez, D Allouche, S de Givry, and T Schiex. Algorithme des poupées russes exploitant une décomposition arborescente. In Yves Deville, editor, Actes des Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, 2009.

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

J Vandel and S de Givry. Inférence de réseaux de régulation de gènes à partir de données d'expression et de polymorphisme. In JOBIM-09 workshop sur Modèles graphiques probabilistes pour l'intégration de données hétérogènes et la découverte de modèles causaux en biologie, Nantes, France, 2009.

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

Matthieu Vignes and Florence Forbes. Gene clustering via integrated markov models combining individual and pairwise features. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(2):260-270, apr 2009.

M Zytnicki, C Gaspin, S de Givry, and T Schiex. Bound arc consistency for weighted csps. Journal of Artificial Intelligence Research, 35, 2009.


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.


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.


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.


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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