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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 Vignes and F 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.

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

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.

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

A Favier, S de Givry, and P Jégou. Exploiting problem structure for solution counting. In CP, 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, A paraître, 2009.

J Blanchet and M 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.

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

L Dupuy, M Vignes, B McKenzie, and P White. Meristematic waves, a new approach to model root architecture dynamics. In Proceedings of the 10th JOBIM, Nantes, June 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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