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M Zytnicki, C Gaspin, S de Givry, and T Schiex. Bound arc consistency for
 
M Zytnicki, C Gaspin, S de Givry, and T Schiex. Bound arc consistency for
weighted csps. _Journal of Artificial Intelligence Research_, 35, 2009.
+
weighted csps. Journal of Artificial Intelligence Research, 35, 2009.
  
 
Matthieu Vignes and Florence Forbes. Gene clustering via integrated markov
 
Matthieu Vignes and Florence Forbes. Gene clustering via integrated markov
models combining individual and pairwise features. _IEEE/ACM Transactions on
+
models combining individual and pairwise features. IEEE/ACM Transactions on
Computational Biology and Bioinformatics_, 6(2):260-270, apr 2009.
+
Computational Biology and Bioinformatics, 6(2):260-270, apr 2009.
  
G Verfaillie and T Schiex. _Constraint Satisfaction Problems_, chapter 6,
+
G Verfaillie and T Schiex. Constraint Satisfaction Problems, chapter 6,
 
pages 265-320. Number ISBN 978-1-84821-116-2. ISTE-Wiley, 2009.
 
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
 
M Sanchez, D Allouche, S de Givry, and T Schiex. Algorithme des poupées russes
exploitant une décomposition arborescente. In Yves Deville, editor, _Actes des
+
exploitant une décomposition arborescente. In Yves Deville, editor, Actes des
Cinquièmes Journées Francophones de Programmation par Contraintes_, Orléans,
+
Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans,
 
2009.
 
2009.
  
 
M Sanchez, D Allouche, S de Givry, and T Schiex. Russian doll search with tree
 
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.
+
decomposition. In Proc. of IJCAI'09, Pasadena (CA), USA, 2009.
  
 
J Gouzy, S Carrere, and T Schiex. Framedp: sensitive peptide detection on
 
J Gouzy, S Carrere, and T Schiex. Framedp: sensitive peptide detection on
noisy matured sequences. _Bioinformatics_, Jan 2009.
+
noisy matured sequences. Bioinformatics, Jan 2009.
  
 
A Favier, S de Givry, and P Jégou. Comptage de solutions en exploitant la
 
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
+
structure du graphe de contraintes. In Yves Deville, editor, Actes des
Cinquièmes Journées Francophones de Programmation par Contraintes_, Orléans,
+
Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans,
 
2009.
 
2009.
  
 
A Favier, S de Givry, and P Jégou. Exploiting problem structure for solution
 
A Favier, S de Givry, and P Jégou. Exploiting problem structure for solution
counting. In _CP_, 2009.
+
counting. In CP, 2009.
  
 
T Faraut, S de Givry, C Hitte, Y Lahlib-Mansais, M Morisson, D Milan, T
 
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
 
Schiex, B Servin, A Vignal, F Galibert, and M Yerle. Contributions of
radiation hybrids to genome mapping in domestic animals. _Cytogenetic and
+
radiation hybrids to genome mapping in domestic animals. Cytogenetic and
Genome Research_, A paraître, 2009.
+
Genome Research, A paraître, 2009.
  
 
Juliette Blanchet and Matthieu Vignes. A model-based approach to gene
 
Juliette Blanchet and Matthieu Vignes. A model-based approach to gene
 
clustering with missing observation reconstruction in a markov random field
 
clustering with missing observation reconstruction in a markov random field
framework. _Journal of Computational Biology_, 16(3):475-486, mar 2009.
+
framework. Journal of Computational Biology, 16(3):475-486, mar 2009.
  
A Kozomara. _Prédiction de gènes d'ARN dans les séquences génomiques_. PhD
+
A Kozomara. Prédiction de gènes d'ARN dans les séquences génomiques. PhD
 
thesis, Université Paul Sabatier, Toulouse, Toulouse, France, Juin 2009.
 
thesis, Université Paul Sabatier, Toulouse, Toulouse, France, Juin 2009.
  
 
Lionel Dupuy, Matthieu Vignes, Blair McKenzie, and Philip White. Meristematic
 
Lionel Dupuy, Matthieu Vignes, Blair McKenzie, and Philip White. Meristematic
waves, a new approach to model root architecture dynamics. In _Proceedings of
+
waves, a new approach to model root architecture dynamics. In Proceedings of
the 10th JOBIM_, Nantes, June 2009.
+
the 10th JOBIM, Nantes, June 2009.
  
 
<h1>2008</h1>
 
<h1>2008</h1>
  
M Zytnicki. _Localisation d'ARN non-codants par réseaux de contraintes
+
M Zytnicki. Localisation d'ARN non-codants par réseaux de contraintes
pondérées_. PhD thesis, Université Paul Sabatier, Toulouse, 2008.
+
pondérées. PhD thesis, Université Paul Sabatier, Toulouse, 2008.
  
 
M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA
 
M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA
motif localization. _Constraints_, 13(1):91-109, 2008.
+
motif localization. Constraints, 13(1):91-109, 2008.
  
 
M Sanchez, S de Givry, and T Schiex. Mendelian error detection in complex
 
M Sanchez, S de Givry, and T Schiex. Mendelian error detection in complex
pedigrees using weighted constraint satisfaction techniques. _Constraints_,
+
pedigrees using weighted constraint satisfaction techniques. Constraints,
 
13(1):130-154, 2008.
 
13(1):130-154, 2008.
  
 
Céline Noirot, Christine Gaspin, Thomas Schiex, and Jérôme Gouzy. LeARN: a
 
Céline Noirot, Christine Gaspin, Thomas Schiex, and Jérôme Gouzy. LeARN: a
platform for detecting, clustering and annotating non-coding RNAs. _BMC
+
platform for detecting, clustering and annotating non-coding RNAs. BMC
Bioinformatics_, 9:21, 2008.
+
Bioinformatics, 9:21, 2008.
  
 
Brigitte Mangin, Pauline Garnier-Gere, and Christine Cierco-Ayrolles. The
 
Brigitte Mangin, Pauline Garnier-Gere, and Christine Cierco-Ayrolles. The
 
estimator of the optimal measure of allelic association: Mean, variance and
 
estimator of the optimal measure of allelic association: Mean, variance and
probability distribution when the sample size tends to infinity. _Statistical
+
probability distribution when the sample size tends to infinity. Statistical
Applications in Genetics and Molecular Biology_, 7(1), 2008.
+
Applications in Genetics and Molecular Biology, 7(1), 2008.
  
 
J Larrosa, F Heras, and S de Givry. A logical approach to efficient max-sat
 
J Larrosa, F Heras, and S de Givry. A logical approach to efficient max-sat
solving. _Artificial Intelligence_, 172(2-3), 2008.
+
solving. Artificial Intelligence, 172(2-3), 2008.
  
 
F Heras, J Larrosa, S de Givry, and T Schiex. 2006 and 2007 max-sat
 
F Heras, J Larrosa, S de Givry, and T Schiex. 2006 and 2007 max-sat
evaluations: Contributed instances. _Journal of Satisfiability, Boolean
+
evaluations: Contributed instances. Journal of Satisfiability, Boolean
Modeling and Computation_, 4:239-250, 2008.
+
Modeling and Computation, 4:239-250, 2008.
  
 
S Foissac, J Gouzy, S Rombauts, C Mathé, J Amselem, L Sterk, Y van de Peer, P
 
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
 
Rouzé, and T Schiex. Genome annotation in plants and fungi: Eugène as a model
platform. _Current Bioinformatics_, 3(2):87-97, 5 2008.
+
platform. Current Bioinformatics, 3(2):87-97, 5 2008.
  
 
Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc
 
Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc
 
Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, and
 
Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, and
 
David Allouche. Biomaj: a flexible framework for databanks synchronization and
 
David Allouche. Biomaj: a flexible framework for databanks synchronization and
processing. _Bioinformatics_, 24(16):1823-5, Aug 2008.
+
processing. Bioinformatics, 24(16):1823-5, Aug 2008.
  
 
MC Cooper, S de Givry, M Sanchez, T Schiex, and M Zytnicki. Cohérence d'arc
 
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
+
virtuelle pour csp pondérés. In Actes des Quatrièmes Journées Francophones de
Programmation par Contraintes_, Nantes, 2008.
+
Programmation par Contraintes, Nantes, 2008.
  
 
MC Cooper, S de Givry, M Sanchez, T Schiex, and M Zytnicki. Virtual arc
 
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.
+
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
 
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
 
Verfaillie, and M Zytnicki. Max-csp competition 2007: toolbar/toulbar2 solver
 
brief description. In C; Roussel O van Dongen, MRC; Lecoutre, editor,
 
brief description. In C; Roussel O van Dongen, MRC; Lecoutre, editor,
_Proceedings of the Second International CSP Solver Competition_, pages 19-21,
+
Proceedings of the Second International CSP Solver Competition, pages 19-21,
 
2008.
 
2008.
  
 
S Bérard, C Chauve, and C Paul. A more efficient algorithm for perfect sorting
 
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.
+
by reversals. Information Processing Letters, 106(3):90-95, 4 2008.
  
 
Pierre Abad, Jérôme Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne
 
Pierre Abad, Jérôme Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne
Ligne 112 : Ligne 112 :
 
Quesneville, Marie-Noëlle Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach,
 
Quesneville, Marie-Noëlle Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach,
 
and Patrick Wincker. Genome sequence of the metazoan plant-parasitic nematode
 
and Patrick Wincker. Genome sequence of the metazoan plant-parasitic nematode
meloidogyne incognita. _Nat Biotechnol_, 26(8):909-15, Aug 2008.
+
meloidogyne incognita. Nat Biotechnol, 26(8):909-15, Aug 2008.
  
 
<h1>2007</h1>
 
<h1>2007</h1>
  
 
M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA
 
M Zytnicki, C Gaspin, and T Schiex. DARN! a soft constraint solver for RNA
motif localization. In _Proc. of JOBIM'2007_, Marseille, France, 2007.
+
motif localization. In Proc. of JOBIM'2007, Marseille, France, 2007.
  
 
Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang,
 
Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang,
 
James E Womack, Paul Stothard, and Stephen S Moore. High resolution radiation
 
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
 
hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome
sequence assembly. _BMC Genomics_, 8:310, 2007.
+
sequence assembly. BMC Genomics, 8:310, 2007.
  
 
C Pralet, T Schiex, and G Verfaillie. Algorithmes et complexités génériques
 
C Pralet, T Schiex, and G Verfaillie. Algorithmes et complexités génériques
pour différents cadres de décision séquentielle dans l'incertain. _Revue
+
pour différents cadres de décision séquentielle dans l'incertain. Revue
d'Intelligence Artificielle_, 21:459-488, 2007.
+
d'Intelligence Artificielle, 21:459-488, 2007.
  
 
C Pralet, G Verfaillie, and T Schiex. Un cadre graphique et algébrique pour
 
C Pralet, G Verfaillie, and T Schiex. Un cadre graphique et algébrique pour
 
les problèmes de décision incluant incertitudes, faisabilités et utilités.
 
les problèmes de décision incluant incertitudes, faisabilités et utilités.
_Revue d'Intelligence Artificielle_, 21(3), 2007.
+
Revue d'Intelligence Artificielle, 21(3), 2007.
  
 
C Pralet, G Verfaillie, and T Schiex. An algebraic graphical model for
 
C Pralet, G Verfaillie, and T Schiex. An algebraic graphical model for
decision with uncertainties, feasibilities, and utilities. _Journal of
+
decision with uncertainties, feasibilities, and utilities. Journal of
Artificial Intelligence Research_, 29:421-489, 2007.
+
Artificial Intelligence Research, 29:421-489, 2007.
  
 
Elisa Marques, Simon de Givry, Paul Stothard, Brenda Murdoch, Zhiquan Wang,
 
Elisa Marques, Simon de Givry, Paul Stothard, Brenda Murdoch, Zhiquan Wang,
 
James Womack, and Stephen S Moore. A high resolution radiation hybrid map of
 
James Womack, and Stephen S Moore. A high resolution radiation hybrid map of
 
bovine chromosome 14 identifies scaffold rearrangement in the latest bovine
 
bovine chromosome 14 identifies scaffold rearrangement in the latest bovine
assembly. _BMC Genomics_, 8:254, 2007.
+
assembly. BMC Genomics, 8:254, 2007.
  
 
T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T
 
T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T
Schiex. A comparative genome approach to marker ordering. _Bioinformatics_,
+
Schiex. A comparative genome approach to marker ordering. Bioinformatics,
 
23(2):e50-6, Jan 2007.
 
23(2):e50-6, Jan 2007.
  
MC Cooper, S de Givry, and T Schiex. Optimal soft arc consistency. In _Proc.
+
MC Cooper, S de Givry, and T Schiex. Optimal soft arc consistency. In Proc.
of IJCAI-07_, pages 68-73, Hyderabad, India, 2007.
+
of IJCAI-07, pages 68-73, Hyderabad, India, 2007.
  
 
Judith Burstin, Pascal Marget, Myriam Huart, Annie Moessner, Brigitte Mangin,
 
Judith Burstin, Pascal Marget, Myriam Huart, Annie Moessner, Brigitte Mangin,
Ligne 152 : Ligne 152 :
 
Developmental genes have pleiotropic effects on plant morphology and source
 
Developmental genes have pleiotropic effects on plant morphology and source
 
capacity, eventually impacting on seed protein content and productivity in
 
capacity, eventually impacting on seed protein content and productivity in
pea. _Plant Physiology_, 144(2):768-781, jun 2007.
+
pea. Plant Physiology, 144(2):768-781, jun 2007.
  
 
S Boitard and P Loisel. Probability distribution of haplotype frequencies
 
S Boitard and P Loisel. Probability distribution of haplotype frequencies
 
under the two-locus Wright-Fisher model by diffusion approximation.
 
under the two-locus Wright-Fisher model by diffusion approximation.
_Theoretical Population Biology_, 71(3):380-391, 2007.
+
Theoretical Population Biology, 71(3):380-391, 2007.
  
 
Sandrine Boisset, Thomas Geissmann, Eric Huntzinger, Pierre Fechter, Nadia
 
Sandrine Boisset, Thomas Geissmann, Eric Huntzinger, Pierre Fechter, Nadia
Ligne 163 : Ligne 163 :
 
Romby. Staphylococcus aureus RNAIII coordinately represses the synthesis of
 
Romby. Staphylococcus aureus RNAIII coordinately represses the synthesis of
 
virulence factors and the transcription regulator Rot by an antisense
 
virulence factors and the transcription regulator Rot by an antisense
mechanism. _Genes Dev_, 21(11):1353-66, Jun 2007.
+
mechanism. Genes Dev, 21(11):1353-66, Jun 2007.
  
 
S Bérard, A Bergeron, C Chauve, and C Paul. Perfect sorting by reversal is not
 
S Bérard, A Bergeron, C Chauve, and C Paul. Perfect sorting by reversal is not
always difficult. _IEEE/ACM Transactions on Computational Biology and
+
always difficult. IEEE/ACM Transactions on Computational Biology and
Bioinformatics_, 4(1):4-16, 2007.
+
Bioinformatics, 4(1):4-16, 2007.
  
 
Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine
 
Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine
Ligne 173 : Ligne 173 :
 
Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, and Jean-Pierre
 
Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, and Jean-Pierre
 
Renou. Analysis of CATMA transcriptome data identifies hundreds of novel
 
Renou. Analysis of CATMA transcriptome data identifies hundreds of novel
functional genes and improves gene models in the Arabidopsis genome. _BMC
+
functional genes and improves gene models in the Arabidopsis genome. BMC
Genomics_, 8:401, 2007.
+
Genomics, 8:401, 2007.
  
 
<h1>2006</h1>
 
<h1>2006</h1>
  
 
M Zytnicki, C Gaspin, and T Schiex. A new local consistency for weighted CSP
 
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
+
dedicated to long domains. In Proceedings of the 2006 ACM Symposium on
Applied Computing_, pages 394-398, Dijon, France, 2006.
+
Applied Computing, pages 394-398, Dijon, France, 2006.
  
 
P Thébault, S de Givry, T Schiex, and C Gaspin. Searching rna motifs and their
 
P Thébault, S de Givry, T Schiex, and C Gaspin. Searching rna motifs and their
intermolecular contacts with constraint networks. _Bioinformatics_,
+
intermolecular contacts with constraint networks. Bioinformatics,
 
22(17):2074-80, Sep 2006.
 
22(17):2074-80, Sep 2006.
  
 
C Pralet, G Verfaillie, and T Schiex. Decision with uncertainties,
 
C Pralet, G Verfaillie, and T Schiex. Decision with uncertainties,
feasibilities and utilities: towards a unified algebraic framework. In _Proc.
+
feasibilities and utilities: towards a unified algebraic framework. In Proc.
of ECAI'2006_, Trento, Italy, 2006.
+
of ECAI'2006, Trento, Italy, 2006.
  
 
C Pralet, T Schiex, and G Verfaillie. From influence diagrams to multioperator
 
C Pralet, T Schiex, and G Verfaillie. From influence diagrams to multioperator
cluster dags. In _Proc. of UAI'2006_, Boston (MA), USA, 2006.
+
cluster dags. In Proc. of UAI'2006, Boston (MA), USA, 2006.
  
C Pralet. _Un cadre générique pour représenter et résoudre des problèmes de
+
C Pralet. Un cadre générique pour représenter et résoudre des problèmes de
décision séquentiels avec incertitudes, faisabilités et utilités_. PhD thesis,
+
décision séquentiels avec incertitudes, faisabilités et utilités. PhD thesis,
 
Ecole Nationale Superieure de l'Aéronautique et de l'Espace, Toulouse,
 
Ecole Nationale Superieure de l'Aéronautique et de l'Espace, Toulouse,
 
Toulouse, France, 2006.
 
Toulouse, France, 2006.
  
 
C Pralet, T Schiex, and G Verfaillie. Decomposition of multi-operators queries
 
C Pralet, T Schiex, and G Verfaillie. Decomposition of multi-operators queries
on semiring-based graphical models. In _Proc. of CP'2006_, Nantes, France,
+
on semiring-based graphical models. In Proc. of CP'2006, Nantes, France,
 
2006.
 
2006.
  
P Meseguer, F Rossi, and T Schiex. _Soft Constraints_, chapter 9, pages
+
P Meseguer, F Rossi, and T Schiex. Soft Constraints, chapter 9, pages
 
281-328. Elsevier, 2006.
 
281-328. Elsevier, 2006.
  
A Lucas and S Jasson. Using amap and ctc packages for huge clustering. _R
+
A Lucas and S Jasson. Using amap and ctc packages for huge clustering. R
News_, 5(6):58-60, 2006.
+
News, 5(6):58-60, 2006.
  
G Verfaillie and T Schiex. _Problemes de satisfaction de contraintes_, volume
+
G Verfaillie and T Schiex. Problemes de satisfaction de contraintes, volume
1 of _ Traite IC2, serie Informatique et Systemes d'Information_, chapter 6,
+
1 of Traite IC2, serie Informatique et Systemes d'Information, chapter 6,
 
pages 287-344. Hermes Sciences, 2006.
 
pages 287-344. Hermes Sciences, 2006.
  
 
S de Givry and L Jeannin. A unified framework for partial and hybrid search
 
S de Givry and L Jeannin. A unified framework for partial and hybrid search
methods in constraint programming. _Computer & Operations Research_,
+
methods in constraint programming. Computer & Operations Research,
 
33(10):2805-2833, 2006.
 
33(10):2805-2833, 2006.
  
 
T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T
 
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
+
Schiex. A comparative genome approach to marker ordering. In Actes de
JOBIM'06_, page 11, Bordeaux, France, 2006.
+
JOBIM'06, page 11, Bordeaux, France, 2006.
  
 
T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, and T
 
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
+
Schiex. A comparative genome approach to marker ordering. In Proc. of
ECCB'2006_, 2006.
+
ECCB'2006, 2006.
  
 
S de Givry, T Schiex, and G Verfaillie. Décomposition arborescente et
 
S de Givry, T Schiex, and G Verfaillie. Décomposition arborescente et
cohérence locale souple dans les csp pondérés. In _Actes des Deuxièmes
+
cohérence locale souple dans les csp pondérés. In Actes des Deuxièmes
Journées Francophones de Programmation par Contraintes_, Nîmes, 2006.
+
Journées Francophones de Programmation par Contraintes, Nîmes, 2006.
  
 
S de Givry, T Schiex, and T Verfaillie. Exploiting tree decomposition and soft
 
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,
+
local consistency in weighted CSP. In Proc. of AAAI'2006, Boston (MA), USA,
 
2006.
 
2006.
  
Ligne 239 : Ligne 239 :
 
Town, Satoshi Tabata, Yves Van de Peer, and Nevin D Young. Legume genome
 
Town, Satoshi Tabata, Yves Van de Peer, and Nevin D Young. Legume genome
 
evolution viewed through the medicago truncatula and lotus japonicus genomes.
 
evolution viewed through the medicago truncatula and lotus japonicus genomes.
_Proc Natl Acad Sci U S A_, 103(40):14959-64, Oct 2006.
+
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
 
S Bérard, F Nicolas, J Buard, O Gascuel, and E Rivals. Fast and specific
 
alignment method for minisatellite maps applied to human y chromosome
 
alignment method for minisatellite maps applied to human y chromosome
minisatellite msy1. _Evolutionary Bioinformatics Online_, 2:327-344, 2006.
+
minisatellite msy1. Evolutionary Bioinformatics Online, 2:327-344, 2006.
  
 
S Boitard, J Abdallah, H de Rochambeau, C Cierco-Ayrolles, and B Mangin.
 
S Boitard, J Abdallah, H de Rochambeau, C Cierco-Ayrolles, and B Mangin.
Linkage disequilibrium interval mapping of quantitative trait loci. _BMC
+
Linkage disequilibrium interval mapping of quantitative trait loci. BMC
Genomics_, 7:54, 2006.
+
Genomics, 7:54, 2006.
  
 
<h1>2005</h1>
 
<h1>2005</h1>
Ligne 253 : Ligne 253 :
 
MH Renalier, N Joseph, C Gaspin, P Thebault, and A Mougin. The Cm56 tRNA
 
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
 
modification in archaea is catalyzed either by a specific 2'-O-methylase, or a
C/D sRNP. _RNA_, 11(7):1051-63, 2005.
+
C/D sRNP. RNA, 11(7):1051-63, 2005.
  
 
S Genin, M Salanoubat, J Gouzy, A Moisan, T Schiex, S Cunnac, M Lavie, C
 
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
 
Zischek, P Barberis, and C Boucher. The Ralstonia solanacearum complete genome
sequence: outputs and prospects. In _Bacterial wilt disease and the Ralstonia
+
sequence: outputs and prospects. In Bacterial wilt disease and the Ralstonia
solanacearum species complex_, pages 335-342. American Phytopathological
+
solanacearum species complex, pages 335-342. American Phytopathological
 
Society (APS Press), St. Paul, USA, 2005.
 
Society (APS Press), St. Paul, USA, 2005.
  
 
M Zytnicki, F Heras, S de Givry, and L Larrosa. Cohérence d'arc existentielle:
 
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
+
un pas de plus vers la cohérence d'arc complète. In Actes des Premières
Journées Francophones de Programmation par Contraintes_, pages 139-148, Lens,
+
Journées Francophones de Programmation par Contraintes, pages 139-148, Lens,
 
France, 2005.
 
France, 2005.
  
 
MF Jourjon, S Jasson, J Marcel, B Ngom, and B Mangin. MCQTL: multi-allelic qtl
 
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.
+
mapping in multi-cross design. Bioinformatics, 21(1):128-30, 2005.
  
 
Sylvain Foissac and Thomas Schiex. Integrating alternative splicing detection
 
Sylvain Foissac and Thomas Schiex. Integrating alternative splicing detection
into gene prediction. _BMC Bioinformatics_, 6:25, 2005.
+
into gene prediction. BMC Bioinformatics, 6:25, 2005.
  
 
S de Givry, M Zytnicki, F Heras, and J Larrosa. Existential arc consistency:
 
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-
+
getting closer to full arc consistency in weighted CSPs. In Proc. of IJCAI-
05_, pages 84-89, Edinburgh, Scotland, 2005.
+
05, pages 84-89, Edinburgh, Scotland, 2005.
  
 
Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas
 
Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas
 
Schiex. Carthagene: multipopulation integrated genetic and radiation hybrid
 
Schiex. Carthagene: multipopulation integrated genetic and radiation hybrid
mapping. _Bioinformatics_, 21(8):1703-4, Apr 2005.
+
mapping. Bioinformatics, 21(8):1703-4, Apr 2005.
  
 
Béatrice Clouet-d'Orval, Christine Gaspin, and Annie Mougin. Two different
 
Béatrice Clouet-d'Orval, Christine Gaspin, and Annie Mougin. Two different
 
mechanisms for tRNA ribose methylation in Archaea: a short survey.
 
mechanisms for tRNA ribose methylation in Archaea: a short survey.
_Biochimie_, 87(9-10):889-95, Sep-Oct 2005.
+
Biochimie, 87(9-10):889-95, Sep-Oct 2005.
  
C Gaspin and P Thébault. Identification d'ARN non codants. _Biofutur_,
+
C Gaspin and P Thébault. Identification d'ARN non codants. Biofutur,
 
251:33-36, 2005.
 
251:33-36, 2005.
  
S Boitard. _Cartographie de gènes à caractères quantitatifs par déséquilibre
+
S Boitard. Cartographie de gènes à caractères quantitatifs par déséquilibre
de liaison_. PhD thesis, Université Paul Sabatier, Toulouse III, 2005.
+
de liaison. PhD thesis, Université Paul Sabatier, Toulouse III, 2005.
  
 
S Boitard. Computation of the haplotype frequency distribution under the two-
 
S Boitard. Computation of the haplotype frequency distribution under the two-
locus wright-fisher model. a diffusion approximation method. In _Proc. of
+
locus wright-fisher model. a diffusion approximation method. In Proc. of
 
European mathematical genetics meeting in annals of human genetics 69(6) ,p.
 
European mathematical genetics meeting in annals of human genetics 69(6) ,p.
765_, pages 764-774, Le Kremlin-Bicêtre, France, 2005.
+
765, pages 764-774, Le Kremlin-Bicêtre, France, 2005.
  
 
S Bérard, A Bergeron, C Chauve, and C Paul. Perfect sorting by reversal is not
 
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
+
always difficult. In Proc. of the 5th Workshop on Algorithms in
Bioinformatics (WABI'05)_, number 3692 in LNCS, pages 228-238, 2005.
+
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
 
S Bérard, L Tichit, and C Herrmann. Simct, a tool to visualize ontology based
relationships. In _Actes des Journées Ouvertes Biologie Informatique
+
relationships. In Actes des Journées Ouvertes Biologie Informatique
Mathématiques (JOBIM'05)_, pages 447-457, Lyon, 2005.
+
Mathématiques (JOBIM'05), pages 447-457, Lyon, 2005.
  
 
S Aubourg, V Brunaud, C Bruyere, M Cock, R Cooke, A Cottet, A Couloux, P
 
S Aubourg, V Brunaud, C Bruyere, M Cock, R Cooke, A Cottet, A Couloux, P
Ligne 311 : Ligne 311 :
 
M Tognolli, M Caboche, and A Lecharny. GeneFarm, structural and functional
 
M Tognolli, M Caboche, and A Lecharny. GeneFarm, structural and functional
 
annotation of Arabidopsis gene and protein families by a network of experts.
 
annotation of Arabidopsis gene and protein families by a network of experts.
_Nucleic Acids Res_, 33(Database issue):D641-6, 2005.
+
Nucleic Acids Res, 33(Database issue):D641-6, 2005.

Version du 11 septembre 2009 à 15:15

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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