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<h1>2009</h1>
  
 +
M Zytnicki, C Gaspin, S de Givry, and T Schiex. Bound arc consistency for
 +
weighted csps. _Journal of Artificial Intelligence Research_, 35, 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.
 +
 +
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.
 +
 +
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.
 +
 +
A Kozomara. _Prédiction de gènes d'ARN dans les séquences génomiques_. PhD
 +
thesis, Université Paul Sabatier, Toulouse, Toulouse, France, Juin 2009.
 +
 +
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.
 +
 +
<h1>2008</h1>
 +
 +
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.
 +
 +
Céline Noirot, Christine Gaspin, Thomas Schiex, and Jérôme Gouzy. LeARN: a
 +
platform for detecting, clustering and annotating non-coding RNAs. _BMC
 +
Bioinformatics_, 9:21, 2008.
 +
 +
Brigitte Mangin, Pauline Garnier-Gere, and Christine 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.
 +
 +
Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc
 +
Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, and
 +
David 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.
 +
 +
Pierre Abad, Jérôme Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne
 +
G J Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch, Véronique Anthouard,
 +
François Artiguenave, Vivian C Blok, Marie-Cécile Caillaud, Pedro M Coutinho,
 +
Corinne Dasilva, Francesca De Luca, Florence Deau, Magali Esquibet, Timothé
 +
Flutre, Jared V Goldstone, Noureddine Hamamouch, Tarek Hewezi, Olivier
 +
Jaillon, Claire Jubin, Paola Leonetti, Marc Magliano, Tom R Maier, Gabriel V
 +
Markov, Paul McVeigh, Graziano Pesole, Julie Poulain, Marc Robinson-Rechavi,
 +
Erika Sallet, Béatrice Ségurens, Delphine Steinbach, Tom Tytgat, Edgardo
 +
Ugarte, Cyril van Ghelder, Pasqua Veronico, Thomas J Baum, Mark Blaxter,
 +
Teresa Bleve-Zacheo, Eric L Davis, Jonathan J Ewbank, Bruno Favery, Eric
 +
Grenier, Bernard Henrissat, John T Jones, Vincent Laudet, Aaron G Maule, Hadi
 +
Quesneville, Marie-Noëlle Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach,
 +
and Patrick Wincker. Genome sequence of the metazoan plant-parasitic nematode
 +
meloidogyne incognita. _Nat Biotechnol_, 26(8):909-15, Aug 2008.
 +
 +
<h1>2007</h1>
 +
 +
M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA
 +
motif localization. In _Proc. of JOBIM'2007_, Marseille, France, 2007.
 +
 +
Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang,
 +
James E Womack, Paul Stothard, and Stephen S 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.
 +
 +
Elisa Marques, Simon de Givry, Paul Stothard, Brenda Murdoch, Zhiquan Wang,
 +
James Womack, and Stephen S 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.
 +
 +
Judith Burstin, Pascal Marget, Myriam Huart, Annie Moessner, Brigitte Mangin,
 +
Christiane Duchene, Bruno Desprez, Nathalie Munier-Jolain, and Gerard 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.
 +
 +
Sandrine Boisset, Thomas Geissmann, Eric Huntzinger, Pierre Fechter, Nadia
 +
Bendridi, Maria Possedko, Clément Chevalier, Anne Catherine Helfer, Yvonne
 +
Benito, Alain Jacquier, Christine Gaspin, François Vandenesch, and Pascale
 +
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.
 +
 +
Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine
 +
Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E Jullien, Mathieu
 +
Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, and Jean-Pierre
 +
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.
 +
 +
<h1>2006</h1>
 +
 +
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.
 +
 +
Steven B Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung,
 +
Jérôme Gouzy, Xiaohong Wang, Joann Mudge, Jayprakash Vasdewani, Thomas Schiex,
 +
Manuel Spannagl, Erin Monaghan, Christine Nicholson, Sean J Humphray, Heiko
 +
Schoof, Klaus F X Mayer, Jane Rogers, Francis Quétier, Giles E Oldroyd,
 +
Frédéric Debellé, Douglas R Cook, Ernest F Retzel, Bruce A Roe, Christopher D
 +
Town, Satoshi Tabata, Yves Van de Peer, and Nevin D 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.
 +
 +
<h1>2005</h1>
 +
 +
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.
 +
 +
Sylvain Foissac and Thomas 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.
 +
 +
Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas
 +
Schiex. Carthagene: multipopulation integrated genetic and radiation hybrid
 +
mapping. _Bioinformatics_, 21(8):1703-4, Apr 2005.
 +
 +
Béatrice Clouet-d'Orval, Christine Gaspin, and Annie 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.

Version du 11 septembre 2009 à 15:10

2009

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

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.

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.

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

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.

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.

Céline Noirot, Christine Gaspin, Thomas Schiex, and Jérôme Gouzy. LeARN: a platform for detecting, clustering and annotating non-coding RNAs. _BMC Bioinformatics_, 9:21, 2008.

Brigitte Mangin, Pauline Garnier-Gere, and Christine 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.

Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, and David 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.

Pierre Abad, Jérôme Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne G J Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch, Véronique Anthouard, François Artiguenave, Vivian C Blok, Marie-Cécile Caillaud, Pedro M Coutinho, Corinne Dasilva, Francesca De Luca, Florence Deau, Magali Esquibet, Timothé Flutre, Jared V Goldstone, Noureddine Hamamouch, Tarek Hewezi, Olivier Jaillon, Claire Jubin, Paola Leonetti, Marc Magliano, Tom R Maier, Gabriel V Markov, Paul McVeigh, Graziano Pesole, Julie Poulain, Marc Robinson-Rechavi, Erika Sallet, Béatrice Ségurens, Delphine Steinbach, Tom Tytgat, Edgardo Ugarte, Cyril van Ghelder, Pasqua Veronico, Thomas J Baum, Mark Blaxter, Teresa Bleve-Zacheo, Eric L Davis, Jonathan J Ewbank, Bruno Favery, Eric Grenier, Bernard Henrissat, John T Jones, Vincent Laudet, Aaron G Maule, Hadi Quesneville, Marie-Noëlle Rosso, Thomas Schiex, Geert Smant, Jean 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.

Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang, James E Womack, Paul Stothard, and Stephen S 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.

Elisa Marques, Simon de Givry, Paul Stothard, Brenda Murdoch, Zhiquan Wang, James Womack, and Stephen S 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.

Judith Burstin, Pascal Marget, Myriam Huart, Annie Moessner, Brigitte Mangin, Christiane Duchene, Bruno Desprez, Nathalie Munier-Jolain, and Gerard 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.

Sandrine Boisset, Thomas Geissmann, Eric Huntzinger, Pierre Fechter, Nadia Bendridi, Maria Possedko, Clément Chevalier, Anne Catherine Helfer, Yvonne Benito, Alain Jacquier, Christine Gaspin, François Vandenesch, and Pascale 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.

Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, and Jean-Pierre 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.

Steven B Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérôme Gouzy, Xiaohong Wang, Joann Mudge, Jayprakash Vasdewani, Thomas Schiex, Manuel Spannagl, Erin Monaghan, Christine Nicholson, Sean J Humphray, Heiko Schoof, Klaus F X Mayer, Jane Rogers, Francis Quétier, Giles E Oldroyd, Frédéric Debellé, Douglas R Cook, Ernest F Retzel, Bruce A Roe, Christopher D Town, Satoshi Tabata, Yves Van de Peer, and Nevin D 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.

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.

Sylvain Foissac and Thomas 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.

Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas Schiex. Carthagene: multipopulation integrated genetic and radiation hybrid mapping. _Bioinformatics_, 21(8):1703-4, Apr 2005.

Béatrice Clouet-d'Orval, Christine Gaspin, and Annie 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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