Publications

• Google scolar, Citeseer Documents, Citations, DBLP, Coauthors, CSB, ACM guide, ACM DL.

• Computer science, = Biology,= Bioinformatics

2012

• Filtrage de fonctions de coût globales décomposables
  D. Allouche, C. Bessiere, P. Boizumault, S. de Givry, P. Gutierrez, S. Loudni, JP. Métivier, T. Schiex
  JFPC'12, Toulouse, France.
• Decomposing Global Cost Functions
  D. Allouche, C. Bessiere, P. Boizumault, S. de Givry, P. Gutierrez, S. Loudni, JP. Métivier, T. Schiex
  AAAI'12, Toronto, Canada.
• Detecting Long Tandem Duplications in Genomic Sequences
  E. Audemard, T. Schiex, T. Faraut
  BMC Bioinformatics, 13:83. doi:10.1186/1471-2105-13-83.
• From Hosts to Symbionts: Integrated Gene Prediction for Prokaryotic Genomes using EuGene
  Erika Sallet, Jérôme Gouzy, Brice Roux, Delphine Capela, Laurant Sauviac, Claude Bruand, Pascal Gamas, Thomas Schiex
  Plant and Animal Genome XX, Invited talk, 2012.

2011

• Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis
  Matthieu Vignes, Jimmy Vandel, David Allouche, Nidal Ramadan-Alban, Christine Cierco-Ayrolles, Thomas Schiex, Brigitte Mangin, Simon de Givry
  PLOS One.
• The Medicago genome provides insight into the evolution of rhizobial symbioses
  Nevin D. Young, F. Debellé et al.
  Nature (2011).
• Decomposing Global Cost Functions
  D. Allouche, C. Bessiere, P. Boizumault, S. de Givry, P. Gutierrez, S. Loudni, JP. Métivier, T. Schiex
  Soft'11, Perugia, Italy.
• Integrated Gene Prediction for Prokaryotic Genomes using EuGene
  Erika SALLET, Jérôme GOUZY, Brice ROUX, Delphine CAPELA, Laurent SAUVIAC, Claude BRUAND, Pascal GAMAS and Thomas SCHIEX
  JOBIM'11, Institut Pasteur, Paris, France.
• Pairwise decomposition for combinatorial optimization in graphical models
  A. Favier, S. de Givry, A. Legarra, T. Schiex.
  IJCAI'11, Barcelona, Spain.
• Décomposition par paire pour l'optimisation combinatoire dans les modèles graphiques
  A. Favier, S. de Givry, A. Legarra, T. Schiex.
  JFPC'2011, Lyon, France.
• The genome of Theobroma cacao
  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 & Claire Lanaud.
  Nature Genetics, doi:10.1038/ng.736.

2010

• Towards Parallel Non Serial Dynamic Programming for Weighted CSP
  D. Allouche, S. de Givry, T. Schiex.
  Proc. of CP'2010. St-Andrews (Scotland). pp 53-60 . September 2010.
• Détection de régions génomiques homologues par un algorithme de flots avec coûts.
  E. Audemard, T.Faraut, T. Schiex.
  Actes de ROADEF'2010. Toulouse, France, Février 2010.
• Soft Arc Consistency Revisited
  MC. Cooper, S. de Givry, M. Sanchez, T. Schiex, M. Zytnicki, T. Werner
  Artificial Intelligence, 2010.
• Le cadre PFU, un modèle et des algorithmes génériques pour la décision séquentielle incluant incertitudes, faisabilités et utilités
  C. Pralet, G. Verfaillie, T. Schiex
  TSI. Technique et science informatique, 2010, vol. 29, no1, pp. 85-114

2009

• Combinatorial optimization in graphical models
  R. Dechter, S. de Givry, R. Marinescu, T. Schiex
  Tutorial at IJCAI'09, Pasadena (CA), USA.
• FrameDP: sensitive peptide detection on noisy matured sequences
  J. Gouzy, S. Carrère, T. Schiex
  Bioinformatics 2009 25(5):670-671; doi:10.1093/bioinformatics/btp024
• TagSNP selection using Weighted CSP and Russian Doll Search with Tree Decomposition
  D Allouche, S de Givry, M Sanchez, and T Schiex
  CP-09 workshop on Constraint Based Methods for Bioinformatics, Lisbon, Portugal, 2009.
• Russian Doll Search with Tree Decomposition
  M. Sanchez, D. Allouche, S. de Givry, T. Schiex
  Proc. of IJCAI'09. 2009. Pasadena (CA). USA.
• Poupées russes et décomposition arborescente
  M. Sanchez, D. Allouche, S. de Givry, T. Schiex
  Actes de JFPC 2009, Nantes,
• TagSNP selection using Weighted CSP and Russian Doll Search with Tree Decomposition
  D. Allouche, S. de Givry, M. Sanchez, T. Schiex
  In the Proc. of the Workshop on Constraint Based Methods for Bioinformatics, Lisbon, Portugal.
• Bound arc consistency for weighted CSPs
  M. Zytnicki, C. Gaspin, S. de Givry, T. Schiex.
  JAIR,Volume 35, pages 593-621, 2009.
• Contributions of Radiation Hybrids to Genome Mapping in domestic animals
  T. Faraut, S. de Givry, C. Hitte, Y. Lahlib-Mansais, M. Morisson, D. Milan, T. Schiex, B. Servin, A. Vignal, F. Galibert, M. Yerle.
  Cytogenetic and Genome Research 2009; 126:21-33 (DOI:10.1159/000245904).

2008

• 2006 and 2007 Max-SAT evaluations: Contributed instances.
  F. Heras, J. Larrosa, S. de Givry, T. Schiex.
  Journal of Satisfiability, Boolean Modeling and Computation. IOS Press. Vol. 4. p. 239-250.
• Russian Doll Search with Tree Decomposition.
  M. Sanchez, D. Allouche, S. de Givry, T. Schiex.
  Soft'08 Workshop attached to CP'08 conference, Sydnay, Australia.
• Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
  P. Abad, J. Gouzy, JM. Aury, P. Castagnone-Sereno, E. 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, P. Wincker
  Nature Biotechnology 26, 909-915, July 2008.
• Genome Annotation in Plants and Fungi: EuGène as a Model Platform.
  S. Foissac, J. Gouzy, S. Rombauts, C. Mathé, J. Amselem, L. Sterk, Y. van de Peer, P. Rouzé, T. Schiex.
  Current Bioinformatics, Volume 3, Number 2, p. 87-97, May 2008
• Virtual Arc Consistency for Weighted CSP.
  M. Cooper, S. de Givry, M. Sanchez, T. Schiex and M. Zytnicki.
  Proc. of AAAI'2008. Chicago, USA.
• Arc cohérence virtuelle pour CSP pondérés.
  M. Cooper, S. de Givry, M. Sanchez, T. Schiex and M. Zytnicki.
  Actes de JFPCI'2008. Nantes, France.
• LeARN: a platform for detecting, clustering and annotating non-coding RNAs.
  C. Noirot, C. Gaspin, T. Schiex, J. Gouzy .
  BMC Bioinformatics 2008, 9:21.
• Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques.
  M. Sanchez, S. de Givry, T. Schiex.
  Constraints, 13(1), 2008.
• DARN! A weighted constraint solver for RNA motif localization.
  M. Zytnicki, C. Gaspin, T. Schiex.
  Constraints, 13(1), 2008. A short version was also accepted for a long communication in JOBIM'2007

2007

• Optimal soft arc consistency.
  M. Cooper, S. de Givry and T. Schiex.
  Proc. of IJCAI'2007. Hyderabad, India.
• A comparative genome approach to marker ordering.
  T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte c and T. Schiex.
  . Bioinformatics 23(2). p e50-e56. 2007. Final version of the ECCB paper.
• An algebraic graphical model for decision with uncertainties, feasibilities, and utilities.
  C. Pralet, G. Verfaillie, T. Schiex.
  Journal of Artificial Intelligence Research, Volume 29, pages 421-489.
• Un cadre graphique et algébrique pour les problèmes de décision incluant incertitudes, faisabilités et utilités.
  C. Pralet, G. Verfaillie, T. Schiex.
  Revue d'Intelligence Artificielle, vol. 21, no.3/2007
• Algorithmes et complexités génériques pour différents cadres de décision séquentielle dans l'incertain.
  C. Pralet, T. Schiex, G. Verfaillie.
  Revue d'Intelligence Artificielle, To appear in 2007
• High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.
  A. Prasad , T. Schiex , S. McKay , B. Murdoch , Z. Wang , J.E Womack , P. Stothard and S.S Moore.
  BMC Genomics, 2007, 8:310 doi:10.1186/1471-2164-8-310.
• Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.
  S. Aubourg, ML. Martin-Magniette, V. Brunaud, L. Taconnat, F. Bitton, S. Balzergue, P. E Jullien, M. Ingouff, V. Thareau, T. Schiex, A. Lecharny and JP. Renou
  BMC Genomics 2007, 8:401.

2006

• Soft constraints chapter in the "Handbook of Constraint Programming.
  P. Meseguer, F. Rossi and T. Schiex.
  Elsevier. ISBN: 0-444-52726-5. 2006
• Soft constraint solving (PPT format)
  Javier Larrosa and Thomas Schiex.
  CP'2006 tutorial, a PDF version is available here.
• Decomposition of multi-operators queries on semiring-based graphical models.
  C. Pralet, T. Schiex, G. Verfaillie.
  Proc. of CP'2006. Nantes, France, USA.
• From influence diagrams to multioperator cluster DAGs.
  C. Pralet, T. Schiex, G. Verfaillie.
  Proc. of UAI'2006. Boston (MA), USA.
• Problèmes de satisfaction de contraintes.
  G. Verfaillie, T. Schiex.
  Concepts et méthodes pour l'aide à  la décision. Eds. D. Bouyssou, D. Dubois, M. Pirolot, H. Prade, Hermès, ISBN 2-7462-1289-7, 2006.
• Exploiting Tree Decomposition and Soft Local Consistency in Weighted CSP.
  S. de Givry, T. Schiex, G. Verfaillie.
  Proc. of AAAI'2006. Boston (MA), USA.
• Déomposition arborescente et cohérence locale souple dans les CSP pondérés.
  S. de Givry, T. Schiex, G. Verfaillie.
  Acte de JFPC'2006. France.
• Decision with uncertainties, feasibilities and utilities: towards a unified algebraic framework
  C. Pralet, G. Verfaillie and T. Schiex.
  Proc. of ECAI'2006. Trento, Italy.
• Décision avec incertitudes, faisabilités et utilités: vers un cadre algébrique unifié.
  C. Pralet, G. Verfaillie and T. Schiex.
  Actes des JFPDA'2006. France.
• Une nouvelle architecture de calcul pour résoudre des diagrammes d'influence.
  C. Pralet, T. Schiex and G. Verfaillie.
  Actes des JFPDA'2006. France.
• A new local consistency for weighted CSP dedicated to long domains
  M. Zytnicki, C. Gaspin, T. Schiex.
  Proc. of SAC''2006. Dijon, France.
• The quest for the best arc consistent closure in weighted CSP.
  M. Cooper, S. de Givry and T. Schiex.
  Proc. of Soft'06. In the framework of CP'2006, Nantes, France.
• Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes.
  Steven B. Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérà´me 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
  PNAS, Oct. 2006, vol. 103, no. 40, 14959-14964.
• Combining constraint network processing and pattern matching to describe and locate structured motifs in genomic sequences.
  P. Thébault, S. de Givry, T. Schiex, C. Gaspin.
  Bioinformatics, vol. 22, N. 17 p. 2074-2080. 2006. Preprint.
• A comparative genome approach to marker ordering.
  T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte c and T. Schiex.
  in the proc. of ECCB'2006 (Eilat, Israel).

2005

• CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping
  S. de Givry, M. Bouchez, P. Chabrier, D. Milan, et T. Schiex.
  Bioinformatics, 21(8): 1703-1704 (2005).
• Integrating alternative splicing detection into gene prediction.
  S. Foissac, T. Schiex.
  BMC Bioinformatics 2005, 6:25 (Feb 2005).
• Combining constraint processing and pattern matching to describe and locate structured motifs in genomic sequences,
  Patricia Thébault, Simon de Givry, Thomas Schiex, and Christine Gaspin
  Fifth IJCAI-05 Workshop on Modelling and Solving Problems with Constraints, Edindurgh, Scotland, 2005.
• Soft Constraint Processing, (a PowerPoint file :-()
  J. Larrosa,P. Meseguer and T. Schiex
  IJCAI 2005 Tutorial. A PDF version is available here.
• Soft Constraint Processing (Teaching document, 34 pages),
  T. Schiex
  First International Summer School on Constraint Programming. You can get the associated slides here.
• Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques,
  S. de Givry, I. Palhiere, Z. Vitezica, and T. Schiex
  ICLP-05 workshop on Constraint Based Methods for Bioinformatics, Sitges, Spain, 2005.
• A new local consistency for weighted CSP applied to ncRNA detection.,
  Christine Gaspin, Simon de Givry, Thomas Schiex, Patricia Thébault, and Matthias Zytnicki.
  ICLP-05 workshop on Constraint Based Methods for Bioinformatics, Sitges, Spain, 2005.
• Combining tree decomposition and local consistency in Max-CSPs.,
  Simon de Givry, Thomas Schiex, and Gérard Verfaillie
  7th International CP-05 Workshop on Preferences and Soft Constraints, Sitges,Spain, 2005
• Bound arc consistency for weighted CSPs.,
  Christine Gaspin, Thomas Schiex and Matthias Zytnicki.
  7th International CP-05 Workshop on Preferences and Soft Constraints, Sitges,Spain, 2005
• Composite graphical models for reasoning about uncertainties, feasibilities, and utilities.,
  Cedric Pralet, Gerard Verfaillie, and Thomas Schiex
  7th International CP-05 Workshop on Preferences and Soft Constraints, Sitges,Spain, 2005

2004

• Arc consistency for soft constraints,
  Martin Cooper, Thomas Schiex
  Artificial Intelligence, Volume 154 (1-2), Avril 2004, 199-227.
  A preliminary version is available here.
• Solving weighted CSP by maintaining arc consistency,
  Javier Larrosa,Thomas Schiex
  Artificial Intelligence, Volume 159 (1-2), Novembre 2004, 1-26.
• Teaching support on CSP and optimisation: Partie 1, Part 2, Part 3, Part 4, Part 5,
  T. Schiex, 2004.
• Soft Constraint Processing, (a PowerPoint file :-()
  J. Larrosa,P. Meseguer and T. Schiex
  ECAI 2004 Tutorial. A PDF version is available here.

2003

• In the quest of the best form of local consistency for Weighted CSP,
  J. Larrosa and T. Schiex
  Proc. of IJCAI'03, Acapulco (Mexico), August 2003.
• Solving Max-SAT as weighted CSP,
  Simon de Givry, J. Larrosa,P. Meseguer and T. Schiex
  Proc. of CP'2003, Cork (Ireland), October 2003.
• FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy maturated eukaryotic sequences.
  T. Schiex, J. Gouzy, A. Moisan, Y. de Oliveira
  Nucleic Acid Res., vol. 31, n. 13, 2003
• EuGene'Hom: a generic similarity-based gene finder using multiple homologuous sequences.
  S. Foissac, P. Bardou, A. Moisan, MJ. Cros, T. Schiex.
  Nucleic Acid Res., vol. 31, n. 13, 2003
• Rearranged gene order between pig and human in a QTL region on SSC7
  O. Demeure, C. Renard, M. Yerle, T. Faraut, J. Riquet, A. Robic, T. Schiex, A. Rink, D. Milan
  Mammalian Genome, Vol (14), 2003.
• Application des techniques du voyageur de commerce à  la production de cartes génétiques
  P. Chabrier, C. Gaspin, S. de Givry, T. Schiex.
  Proc. of ROADEF-03, pages 74-76, Avignon, France, 2003.

2002

• Intelligence Artificielle et Informatique Théorique (in french)
  J-M. Alliot et T. Schiex
  Ed. CEPADUES, ISBN: 2-85-428-324-4. 1993. The 2nd edition, 2002, includes new authors P. Brisset and F. Garcia and new chapters on CAML and reinforcement learning.
• Genome sequence of the plant pathogen Ralstonia solanacearum
  M. Salanoubat, S. Genin, F. Artiguenave, J. Gouzy, S. Mangenot, M. Arlat, A. Billault, P. Brottier, J. C. Camus, L. Cattolico, M. Chandler, N. Choisne, C. Claudel-Renard, S. Cunnac, N. Demange, C. Gaspin, M. Lavie, A. Moisan, C. Robert, W. Saurin, T. Schiex, P. Siguier, P. Thébault, M. Whalen, P. Wincker, M. Levy, J. Weissenbach & C. A. Boucher Nature, 415, 497-502 (2002).
• Current methods of gene prediction, their strengths and weaknesses
  C. Mathé, MF. Sagot, T. Schiex and P. Rouzé.
  Nucleic Acid Res., Vol 30, No. 19. Nov. 2002.
• Exploring root symbiotic programs in the model legume medicago truncatula using EST analysis.
  EP. Journet, D. van Tuinen, J. Gouzy, H. Crespeau, V. Carreau, MJ. Farmer, A. Niebel, T. Schiex, O. Jaillon, O. Chatagnier, L. Godiard, F. Micheli, D. Kahn, V. Gianinazzi-Pearson, P. Gamas
  Nucleic Acid Res., 2002.
• Integration of Genetic and Radiation Hybrid Maps of the Pig : the Second Generation IMpRH Maps.
  Denis Milan , Thomas Schiex, Martine Yerle , Anette Rink , Craig Beattie , Rachel Hawken , Larry Schook , Hiroshi Yasue , Merete Fredholm , Gary Rohrer
  Plant, Animal & Microbe Genomes X Conference, January 12-16, 2002. San Diego, CA.
• Une comparaison des cohérences d'arc dans les Max-CSP (in french),
  T. Schiex
  Actes de JNPC'2002. Nice, Mai 2002.
• Constraint and preferences: the interplay of preferences and algorithms,
  T. Schiex and M. Cooper
  Proc. of the "AAAI workshop on preferences in AI and CP", Edmonton (Canada), August 2002.

2001

• Boosting EM for Radiation Hybrid and Genetic Mapping
  Thomas Schiex, Patrick Chabrier, Martin Bouchez and Denis Milan
  In the proceedings of WABI'2001 (First Workshop on Algorithms in Bioinformatics), LNCS 2149. Aug. 2001.
• EuGène: An Eucaryotic Gene Finder that combines several sources of evidence.
  T. Schiex, A. Moisan and P. Rouzé.
  Computational Biology, Eds. O. Gascuel and M-F. Sagot, LNCS 2066, pp. 111-125, 2001.
• Gene Finding integrating external evidence.
  T. Schiex, C. Mathé, A. Moisan and P. Rouzé.
  Proc. of WABI 2001, First Workshop on Algorithms in Bioinformatics. LNCS 2149. Denmark, August 28-31, 2001 (extended abstract).
• CP 2001 tutorial on soft constraints: models, algorithms, and applications.
  Pedro Meseguer, Francesca Rossi, Thomas Schiex.
  Part 1: models, Part 2: algorithms,Part 1: applications.

2000

• Arc consistency for Soft Constraints
  T. Schiex
  Proc. of CP'2000. Singapour, September 2000.
• EuGène: An Eucaryotic Gene Finder that combines several sources of evidence.
  T. Schiex, A. Moisan and P. Rouzé.
  Proc. of JOBIM'2000 - Journées Ouvertes Biologie Informatique Mathématiques. Montpellier, 2000.
• Recherche des génes et des erreurs de séquenà§age dans les génomes bactériens GC-riches.
  T. Schiex, P. Thébault, D. Kahn.
  Proc. of JOBIM'2000 (Journées Ouvertes Biologie Informatique Mathématiques). Montpellier, 2000.
• CarthaGene: A Maximum Likelihood Multiple Population Genetic/Radiated Hybrid Mapping Software
  Patrick Chabrier, Christine Gaspin, Thomas Schiex
  Abstract in PAG-VIII. 2000.
• Demonstration of CarthaGene, a genetic/radiated hybric mapping software Software
  Thomas Schiex, Patrick Chabrier, Christine Gaspin
  Abstract in PAG-VIII. 2000.
• Cohérence d'arc pour contraintes molles (in french)
  T. Schiex
  Proc of JNPC'2000. Marseille, Juin 2000.
• Réseaux de contraintes valués: invited talk. Paper (in french), slides (in french)
  T. Schiex
  Actes de JNPC'2000. Marseille, Juin 2000.
• Réseaux de contraintes
  T. Schiex.
  This synthetic document has been written for my "Habilitation à  diriger les recherches". April 2000.

1999

• Maintaining Reversible DAC for Max-CSP
  J. Larrosa, P. Meseguer, T. Schiex
  Artificial Intelligence Journal, Vol 107,(1). pages 149-163. January 1999.
• Radio Link Frequency Assignment.
  Bertrand Cabon, Simon de Givry, Lionel Lobjois, Thomas Schiex, Joost P. Warners. Constraints 4(1): 79-89 (1999)
• EuGène: A Simple yet Effective Gene Finder for Eucaryotic Organisms (Arabidopsis thaliana)
  T. Schiex, A. Moisan , L. Duret et P. Rouzé
  Proc. of the second "Georgia Tech International Conference on Bioinformatics - In silico Biology".
  Atlanta. November 1999 (extended abstract).
• A note on CSP graph parameters
  T. Schiex
  Technical report 1999/03, INRA, July 1999.

1998

• Reversible DAC and Other Improvements for Solving MAX-CSP
  J. Larrosa, P. Meseguer, T. Schiex and G. Verfaillie
  Proc. of AAAI'98. Madison (USA), 1998.
• Non-monotonic reasoning: from complexity to algorithms (long version)
  C. Cayrol, M-C. Lagasquie et T. Schiex
  Annals of artificial intelligence and mathematics, vol. 22 (1998).
• Maximizing the reversible DAC lower bound in Max-CSP is NP-complete
  T. Schiex
  Tech. Report 1998/02, INRA, July 1998.
• Introduction to a Benchmark Column in CONSTRAINTS
  Claude Le Pape, James M. Crawford, Barry Fox, Thomas Schiex
  Constraints 3(2/3): 255-256 (1998).
• A Composite Genetic Map of the Parasitoid Wasp Trichogramma brassicae Based on RAPD Markers
  V. Laurent, E. Wajnberg, B. Mangin, T. Schiex, C. Gaspin et F. Vanlerberghe-Masutti
  Genetics (1998) vol 150 - n. 1: 275-282.

1997

• Bounding the Optimum of Constraint Optimization Problems
  S. de Givry, G. Verfaillie and T. Schiex
  Proc. of CP'97. Schloss Hagenberg, Austria, 1997.
• Problèmes de satisfaction de contraintes valués (in french)
  T. Schiex, H. Fargier et G. Verfaillie
  Revue d'Intelligence Artificielle. Vol. 11 - n. 3/1997.
• Traitement de problèmes de décision sous incertitude par des problèmes de satisfaction de contraintes (in french)
  H. Fargier, J. Lang, R. Martin-Clouaire et T. Schiex,
  Revue d'Intelligence Artificielle. Vol. 11 - n. 3/1997.
• Constructing and Joining Maximum Likelihood Genetic Maps
  T. Schiex, C. Gaspin, V. Laurent and B. Mangin
  Proc. of EUCARPIA'97, Poznan, Poland, May 1997.
• CARThAGENE: Constructing and Joining Maximum Likelihood Genetic Maps
  T. Schiex & C. Gaspin
  Proc. of ISMB'97. Halkidiki, Greece, June 1997.
• Genetic Algorithms for Genetic Mapping
  C. Gaspin & T. Schiex
  Proc. of the third conference on Evolutionary Computing, Nà®mes, France, 1997
• Postscript source
  of slides prepared for the "Séminaire de l'Institut Pasteur" on multiple alignment and secondary structure prediction of related RNA moledules. Organized by Marie-France Sagot. December 1997.

1996

• Russian Doll Search
  G. Verfaillie, M. Lemaitre et T. Schiex
  Proc. of AAAI'96. Portland (OR), 1996.
• Lazy Arc Consistency
  T. Schiex, J-C. Régin, C. Gaspin and G. Verfaillie
  Proc. of AAAI'96. Portland (OR), 1996.
• Mixed Constraint Satisfaction: a framework for decision problems under incomplete knowledge
  H. Fargier, J. Lang and T. Schiex
  Proc. of AAAI'96. Portland (OR), 1996.
• Semiring-based CSPs and Valued CSPs: Basic Properties and Comparison.
  S. Bistarelli, H. Fargier, U. Montanari, F. Rossi, T. Schiex, et G. Verfaillie
  In M. Jampel, E. Freuder, and M. Maher, editors, Over-Constrained Systems (LNCS 1106, Selected papers from the Workshop on Over-Constrained Systems at CP'95, reprints and background papers), pages 111-150. Springer, 1996.
• Constraint programming
  P. Esquirol, H. Fargier, P. Lopez et T. Schiex
  Belgian journal of operation research, statistics and computer science, 1996.
• Non-monotonic reasoning: from complexity to algorithms
  C. Cayrol, M-C. Lagasquie et T. Schiex
  Proceedings of the 4th international symposium on artificial intelligence and mathematics, Fort Lauderdale (FL), January 1996.

1995

• Valued Constraint Satisfaction Problems: hard and easy problems
  T. Schiex, H. Fargier et G. Verfaillie
  Proc. of the International joint Conference in AI, Montreal, Canada, August 1995.
• A constraint satisfaction framework for decision under uncertainty
  H. Fargier, J. Lang, R. Martin-Clouaire et T. Schiex
  Proc. of the 11th Int. Conf. on Uncertainty in Artificial Intelligence, Montreal, Canada, August 1995.
• Maintien de solution dans les problèmes dynamiques de satisfaction de contraintes : bilan de quelques approches (in french).
  G. Verfaillie et T. Schiex
  Revue d'Intelligence Artificielle, 1995.
• Satisfaction de contraintes et biologie moléculaire (in french)
  C. Gaspin, C. Bessière, A. Moisan et T. Schiex
  Revue d'Intelligence Artificielle, 1995.

1994

• Nogood Recording for Static and Dynamic Constraint Satisfaction Problems
  T. Schiex et G. Verfaillie
  International Journal of Artificial Intelligence Tools 3 (2), p. 187-207, 1994
• Stubborness: an enhancement scheme for Backjumping and Nogood Recording
  T. Schiex et G. Verfaillie
  Proc. of the 12th ECAI, p. 165-169, Amsterdam, Netherlands, 1994.
• Solution reuse in dynamic constraint satisfaction problems
  G. Verfaillie et T. Schiex
  Proc. of AAAI'94. p. 307-312, Seattle (WA), 1994.
• Penalty logic and its link with Dempster-Shafer theory
  F. Dupin de Saint-Cyr, J. Lang et T. Schiex
  Proc. of the 10th International Conference on Uncertainty in Artificial Intelligence, 1994.
• Gestion de l'inconsistance dans les bases de connaissances: une approche syntaxique basée sur la logique des pénalités (in french)
  F. Dupin de Saint-Cyr, J. Lang et T. Schiex
  p. 507-518, Actes du congrès Reconnaissance des Formes et Intelligence Artificielle, 1994.
• Dynamic Backtracking for Dynamic CSPs
  G. Verfaillie et T. Schiex
  Proceedings ECAI'94 Workshop on Constraint Satisfaction Issues raised by Practical Applications, Amsterdam, Netherlands, August 1994.
• Solution and Reasoning Reuse in Space Planning and Scheduling Applications
  G. Verfaillie et T. Schiex
  Proc. of the Third International Symposium on Artificial Intelligence, Robotics, and Automation for Space (i-SAIRAS94), Pasadena (CA), 1994.
• Autour du problème de satisfaction de contraintes (in french)
  L'équipe du groupe de recherche CSP'Flex du PRC-IA
  Actes des cinquièmes journées nationales du PRC GDR Intelligence Artificielle, p. 159-178, Fevrier 1995

1993

• Intelligence Artificielle et Informatique Théorique (in french)
  J-M. Alliot et T. Schiex
  Ed. CEPADUES, ISBN: 2-85-428-324-4. 1993. First edition.
• A fixed point semantics for the ATMS
  M. Cayrol, O. Palmade et T. Schiex
  Journal of Logic and Computation 2 (30), p. 115-130, avril 1993.
• Nogood recording for static and dynamic CSP
  T. Schiex et G. Verfaillie
  Proceeding of the 5th IEEE International Conference on Tools with Artificial Intelligence (ICTAI'93), p. 48-55, Boston, MA, november 1993.
• Selecting preferred solutions in Fuzzy Constraint Satisfaction Problems
  H. Fargier, J. Lang, T. Schiex
  Proc. of the first European Congress on Fuzzy and Intelligent Technologies. 1993.
• Two Approaches to the Solution Maintenance Problem in Dynamic Constraint Satisfaction Problems
  T. Schiex et G. Verfaillie
  Proc. of the IJCAI-93/SIGMAN Workshop on Knowledge-based Production Planning, Scheduling and Control, p.305-316, Chambery, France, August 1993.

1992 and before

• Possibilistic Constraint Satisfaction Problems or ``How to handle soft constraints?''
  T. Schiex
  Proc. of the 8th Int. Conf. on Uncertainty in Artificial Intelligence, Stanford, CA, July 1992.
• A Synchronous-Asynchronous Programming Approach for Intelligent Real-Time Systems
  M. Adelantado, F. Boniol, M. Cubero-Castan, V. David, N. Hifdi, B. Lecussan, R. Porche et T. Schiex
  Proc. of the ECAI'92 Workshop on real-time intelligent systems, Vienna (Austria), 1992
• Satisfaction de contraintes souples(in french)
  H. Fargier, R. Martin-Clouaire et T. Schiex
  Journées nationales sur les applications des ensembles flous, p. 183-191, Octobre 1992.
• Représentation et traitement pratique de la flexibilité dans les problèmes sous contraintes (in french)
  L'équipe du groupe de recherche CSP'Flex du PRC-IA
  Actes des quatrièmes journées nationales du PRC GDR Intelligence Artificielle, Octobre 1992.
• Psil: un héritier de Scheme (in french)
  T. Schiex
  Bigre, numéro spécial consacré à  Scheme, 1991.
• Psil: l'infini en programmation (in french)
  M. Cayrol et T. Schiex
  Actes du sixième congrès Reconnaissance des Formes et Intelligence Artificielle, 1987.