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70

Curriculum vitae


Journal articles14 documents

  • Christine Sinoquet. A method combining a random forest-based technique with the modeling of linkage disequilibrium through latent variables, to run multilocus genome-wide association studies. BMC Bioinformatics, BioMed Central, 2018, 19 (1), pp.106. ⟨10.1186/s12859-018-2054-0⟩. ⟨hal-01984726⟩
  • Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau. SMMB: a stochastic Markov blanket framework strategy for epistasis detection in GWAS. Bioinformatics, Oxford University Press (OUP), 2018, 34 (16), pp.2773-2780. ⟨10.1093/bioinformatics/bty154⟩. ⟨hal-01986668⟩
  • Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau. A survey about methods dedicated to epistasis detection. Frontiers in Genetics, Frontiers, 2015, 6 (Article 285), pp.19. ⟨10.3389/fgene.2015.00285⟩. ⟨hal-01205577⟩
  • Raphaël Mourad, Christine Sinoquet, N. Zhang, T. Liu, Philippe Leray. A survey on latent tree models and applications. Journal of Artificial Intelligence Research, Association for the Advancement of Artificial Intelligence, 2013, 47, pp.157-203. ⟨10.1613/jair.3879⟩. ⟨hal-00828445⟩
  • Vittorio Perduca, Christine Sinoquet, Raphaël Mourad, Grégory Nuel. Alternative methods for H1 simulations in genome wide association studies. Human Heredity, Karger, 2012, 73 (2), pp.95-104. ⟨10.1159/000336194⟩. ⟨hal-00915530⟩
  • Vittorio Perduca, Christine Sinoquet, Raphaël Mourad, Gregory Nuel. Alternative Methods for H1 Simulations in Genome-Wide Association Studies. Human Heredity, Karger, 2012, 73 (2), pp.95-104. ⟨10.1159/000336194⟩. ⟨hal-00686364⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Probabilistic graphical models for genetic association studies. Briefings in Bioinformatics, Oxford University Press (OUP), 2012, 13 (1), pp.20-33. ⟨10.1093/bib/BBR015⟩. ⟨hal-00573325⟩
  • Raphaël Mourad, Christine Sinoquet, Christian Dina, Philippe Leray. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.. PLoS ONE, Public Library of Science, 2011, 6 (12), pp.e27320. ⟨10.1371/journal.pone.0027320⟩. ⟨hal-00655876⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies.. BMC Bioinformatics, BioMed Central, 2011, 12 (1), pp.16. ⟨10.1186/1471-2105-12-16⟩. ⟨hal-00567988⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: Refining a qualitative simulation.. BioSystems, Elsevier, 2009, 98 (3), pp.149-159. ⟨10.1016/j.biosystems.2009.05.002⟩. ⟨hal-00415921⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: refining a qualitative simulation. BioSystems, Elsevier, 2009, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩. ⟨hal-00423353⟩
  • Christine Sinoquet. Iterative two-pass algorithm for missing data imputation in SNP arrays. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2009, 7 (5), pp.833-852. ⟨10.1142/S0219720009004357⟩. ⟨hal-00423339⟩
  • Christine Sinoquet, Sylvain Demey, Frédérique Braun. Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes. Nucleic Acids Research, Oxford University Press, 2008, 36 (10), pp.3332-3340. ⟨10.1093/nar/gkn135⟩. ⟨hal-00423408⟩
  • Anne Berry, Alain Sigayret, Christine Sinoquet. Maximal sub-triangulation in preprocessing phylogenetic data. Soft Computing, Springer Verlag, 2006, 10 (5), pp.461-468. ⟨10.1007/s00500-005-0507-7⟩. ⟨hal-00423418⟩

Conference papers32 documents

  • Hugo Boisaubert, Christine Sinoquet. Detection of gene-gene interactions: methodological comparison on real-world data and insights on synergy between methods.. International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC2019, Feb 2019, Prague, Czech Republic. pp.30-42. ⟨hal-01986665⟩
  • Christine Sinoquet, Clément Niel. Ant colony optimization for Markov blanket-based feature selection. Application for precision medicine. 4th International Conference on Machine Learning, Optimization, and Data Science, LOD2018, Sep 2018, Volterra, Tuscany, Italy. 12 p. ⟨hal-01986649⟩
  • Christine Sinoquet, Kamel Mekhnacha. Random forest framework customized to handle highly correlated variables: an extensive experimental study applied to feature selection in genetic data.. IEEE 5th International Conference on Data Science and Advanced Analytics, DSAA2018, Oct 2018, Turin, Italy. pp.217-226. ⟨hal-01986653⟩
  • Christine Sinoquet, Kamel Mekhnacha. Random forests with latent variables to foster feature selection in the context of highly correlated variables. Illustration with a bioinformatics application.. 17th International Symposium on Intelligent Data Analysis, IDA2018, Oct 2018, 's-Hertogenbosch, Netherlands. pp.290-302. ⟨hal-01986660⟩
  • Clément Niel, Christine Sinoquet. Enhanced ensemble approach to learn Markov blankets for feature subset selection in high-dimensional settings. Illustration with an application to mine genetic data.. Cap2018 (French Conference on Machine Learning), Jun 2018, Rouen, France. ⟨hal-01986670⟩
  • Clément Niel, Christine Sinoquet. Optimisation par colonie de fourmis pour la sélection de variables par construction stochastique de couverture de Markov - Application pour la médecine de précision.. 19th edition of the annual congress of the French Society for Operation Research and Decision Assistance, ROADEF2018, Feb 2018, Lorient, France. ⟨hal-01986671⟩
  • Christine Sinoquet, Kamel Mekhnacha. Combining latent tree modeling with a random forest-based approach, for genetic association studies. 26th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, ESANN2018, Apr 2018, Bruges, Belgium. pp.225-230. ⟨hal-01984665⟩
  • Christine Sinoquet, Clément Niel. Enhancement of a stochastic Markov blanket framework with ant colony optimization, to uncover epistasis in genetic association studies.. ESANN 2018 - 26th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Apr 2018, Bruges, Belgium. pp.673-678. ⟨hal-01984753⟩
  • Duc-Thanh Phan, Philippe Leray, Christine Sinoquet. Impact du choix de la méthode de partitionnement pour les forêts d'arbres latents. SFC2015, P. Kuntz, Sep 2015, Nantes, France. pp.24-27. ⟨hal-01205544⟩
  • Duc-Thanh Phan, Philippe Leray, Christine Sinoquet. Modeling genetical data with forests of latent trees for applications in association genetics at a large scale. Which clustering method should be chosen?. International Conference on Bioinformatics Models, Methods and Algorithms, Bioinformatics2015, Nov 2014, Lisbon, Portugal. pp.12. ⟨hal-01084907⟩
  • Christine Sinoquet, Raphaël Mourad, Philippe Leray. Modeling of genotype data with forests of latent trees to detect genetic causes of diseases. Ado2013 (Machine Learning and Omics Data), Dec 2013, Lille, France. 6 p. ⟨hal-00915538⟩
  • Vittorio Perduca, Raphaël Mourad, Christine Sinoquet, Grégory Nuel. Simulation of phenotypes under H1 in genome wide association studies and applications.. Fourth edition of workshop Statistical Methods for Post Genomics Analysis, SMPGD2012, France, Lyon, january 26-27, Jan 2012, Lyon, France. ⟨hal-00915541⟩
  • Christine Sinoquet, Raphaël Mourad, Philippe Leray. Forests of latent tree models for the detection of genetic associations. International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012), Feb 2012, Vilamoura, Portugal. pp.1-10, ⟨10.5220/0003703400050014⟩. ⟨hal-00637500⟩
  • Vittorio Perduca, Raphaël Mourad, Christine Sinoquet, Grégory Nuel. Waffect : a method to simulate case-control samples in genome-wide association studies.. 43ème édition des journées de la Société Française de Statistique, May 2011, Gammarth, Tunisia. ⟨hal-00915543⟩
  • Vittorio Perduca, Raphaël Mourad, Christine Sinoquet, Gregory Nuel. Waffect: a method to simulate case-control samples in genome-wide association studies.. JOBIM, Jun 2011, Paris, France. 7 p. ⟨hal-01986673⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Apprentissage de réseaux bayésiens hiérarchiques latents pour les études d'association pangénomiques. 5èmes Journées Francophones sur les Réseaux Bayésiens (JFRB2010), May 2010, Nantes, France. ⟨hal-00467399⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Réseaux bayésiens hiérarchiques avec variables latentes pour la modélisation des dépendances entre SNP: une approche pour les études d'association pangénomiques. Proc. SFC 2010, XVIIth Join Meeting of the French Society of Classification, France, Saint-Denis de la Réunion, 9-11 june, Jun 2010, Saint-Denis de la Réunion, France. pp.25-29. ⟨hal-00484705⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Apprentissage de réseaux bayésiens hiérarchiques latents pour les études d'association pangénomiques. Proc. JFRB 2010, 5th French-speaking meeting on Bayesian networks, Nantes, May 2010, Nantes, France. pp.11-12. ⟨hal-00484706⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Learning Hierarchical Bayesian Networks for Genome-Wide Association Studies. COMPSTAT, Nineteenth International Conference on Computational Statististics, Aug 2010, Paris, France. pp.549-556. ⟨hal-00484696⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Hierarchical Bayesian networks applied to association genetics. MODGRAPH 2010 (Modèles graphiques probabilistes pour l'intégration de données hétérogènes et la découverte de modèles causaux en biologie), Journée satellite de JOBIM 2010, Sep 2010, Montpellier, France. ⟨hal-00915546⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. A Bayesian network approach to model local dependencies among SNPs. MODGRAPH 2009 Probabilistic graphical models for integration of complex data and discovery of causal models in biology, satellite meeting of JOBIM 2009, Jun 2009, Nantes, France. ⟨hal-00470528⟩
  • Christine Sinoquet. SNPShuttle: bi-directional scan of SNP arrays to gain accuracy in missing genotype inference. Proc. Seventh Asia-Pacific Bioinformatics Conference, APBC2009, ISBN 978-7-302-19048-6, Jan 2009, Beijing, China. pp.915-925. ⟨hal-00423431⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Modélisation des dépendances locales entre SNP à l'aide d'un réseau bayésien. Proc. SFC'09, XVIth Join Meeting of the French Society of Classification, actes des 16èmes rencontres de la Société Francophone de Classification, Sep 2009, Grenoble, France. pp.169-172. ⟨hal-00423461⟩
  • Guillaume Blin, Guillaume Fertin, Irena Rusu, Christine Sinoquet. Extending the Hardness of RNA Secondary Structure Comparison. 1st International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE 2007), Apr 2007, Hangzhou, China. pp.140-151. ⟨hal-00418248⟩
  • Christine Sinoquet. A novel approach for structured consensus motif inference under specificity and quorum constraints. Proc. Fourth Asia-Pacific Bioinformatics Conference, APBC2006, Advances in Bioinformatics and Computational Biology, ISBN 1-86094-623-2, Feb 2006, Taipei, Taiwan. pp.207-216. ⟨hal-00423435⟩
  • Christine Sinoquet. A cooperative strategy dedicated to structured motif discovery in genomic data. Proc. Fith ALIO-EURO Conference on Combinatorial Optimization, Oct 2005, Paris, France. pp.106-107. ⟨hal-00423457⟩
  • Christine Sinoquet. When chance helps inferring a structured consensus motif from DNA sequences: study of the metaheuristics approach Kaos. Proc. CompBioNets2005, Algorithms and Computational Methods for Biochemical and Evolutionary Networks, ISBN 1904987311, Dec 2005, Lyon, France. pp.107-132. ⟨hal-00423436⟩
  • Christine Sinoquet. Révélation de motif consensus fonctionnel dans un génome. FRANCORO IV, International French-speaking Conference on Operational Research, Oct 2004, Fribourg, Switzerland. pp.89-90. ⟨hal-00423458⟩
  • Christine Sinoquet. Maximal sub-triangulation as preprocessing phylogenetic data. Proc. Fourth International Conference on Knowledge Discovery and Discrete Mathematics, Sep 2003, Metz, France. pp.267-275. ⟨hal-00423456⟩
  • Anne Berry, Alain Sigayret, Christine Sinoquet. Maximal sub-triangulation as preprocessing phylogenetic data. International Conference Journées de l'Informatique Messine, Sep 2003, Metz, France. ⟨hal-00522361⟩
  • Christine Sinoquet. Reverse translation of amino-acid sequences: a method guided by an n-gram model. Proc. JOBIM 2000 : Journées Ouvertes pour la Biologie, l'Informatique et les Mathématiques Open workshop for Biology, Computer Science and Mathematics, May 2000, Montpellier, France. pp.343-350. ⟨hal-00423459⟩
  • A. Durbec, Christine Sinoquet, M. Lafont. Interdépendances nappe-gravières en région Alsace. Forum scientifique «bravo l'eau», 29 mars 1990, au Conseil Général du Haut-Rhin à Colmar, 1990, France. 8 p. ⟨hal-02609014⟩

Books1 document

Book sections7 documents

  • Hugo Boisaubert, Christine Sinoquet. Machine learning and combinatorial optimization to detect gene-gene interactions in genome-wide real data: looking through the prism of four methods and two protocols. Biomedical Engineering Systems and Technologies, 12th International Joint Conference, BIOSTEC2019, Czech Republic, Prague, 22-24 february, Extended Selected Papers, Communication in Computer and Information Science, A. Fred and H. Gamboa (eds.), Springer, 29 pages, In press. ⟨hal-02455132⟩
  • Duc-Thanh Phan, Philippe Leray, Christine Sinoquet. Latent Forests to Model Genetical Data for the Purpose of Multilocus Genome-wide Association Studies. Which clustering should be chosen?. Communication in Computer and Information Science, Springer, pp.17, 2015, BIOSTEC2015. ⟨hal-01204956⟩
  • Christine Sinoquet. Probabilistic graphical models for next-generation genomics and genetics.. Oxford University Press. Probabilistic graphical models for genetics, genomics, and postgenomics, 2014. ⟨hal-01166517⟩
  • Christine Sinoquet. Essentials to understand probabilistic graphical models: a tutorial about inference and learning.. Probabilistic graphical models for genetics, genomics, and postgenomics, Oxford University Press, pp.30-82, 2014. ⟨hal-01168741⟩
  • Christine Sinoquet, Raphaël Mourad. Modeling linkage disequilibrium and performing association studies through probabilistic graphical models: a visiting tour of recent advances.. Probabilistic graphical models for genetics, genomics, and postgenomics, Oxford University Press, pp.217-246, 2014. ⟨hal-01168755⟩
  • Christine Sinoquet. Probabilistic graphical modeling in systems biology: a framework for integrative approaches . A. Prokop and B. Csukas (eds.). Systems Biology : integrative biology and simulation tools, Springer, pp.241-272, 2013, Systems Biology: integrative biology and simulation tools. ⟨hal-01168778⟩
  • Christine Sinoquet, Raphaël Mourad, Philippe Leray. Forests of latent tree models to decipher genotype-phenotype associations. J. Gariel, J. Schier, S. Van Huffel, E. Conchon, C. Correia, A. Fred and H. Gamboa. Biomedical Engineering Systems and Technologies, Communication in Computer and Information Science 357, Springer Berlin Heidelberg, pp.113-134, 2013, 978-3-642-38255-0. ⟨10.1007/978-3-642-38256-7_8⟩. ⟨hal-00915532⟩

Directions of work or proceedings3 documents

  • Oscar Pastor, Christine Sinoquet, Ana Fred, Hugo Gamboa, Dirk Elias. Proceedings of the 6th International Conference on Bioinformatics Models, Methods and Algorithms. O. Pastor, C. Sinoquet, A. Fred, H. Gamboa and D. Elias (eds.). Conference on Bioinformatics Models, Methods and Algorithms, Jan 2015, Lisbon, Portugal. 2015, 978-989-758-070-3. ⟨hal-01168947⟩
  • Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana Fred, et al.. Proceedings of the 5th International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics2014): O. Pastor, C. Sinoquet, G. Plantier, T. Schultz, A.L.N. Fred and H. Gamboa (eds.). Bioinformatics2014 – Proceedings of the 5th International Conference on Bioinformatics Models, Methods and Algorithms, Angers, Loire Valley, France, 3-6 mars, ISBN 978-989-758-012-3.. Bioinformatics2014, Mar 2014, Angers, France. 2014, 978-989-758-012-3. ⟨hal-01169027⟩
  • Alberto Cliquet Jr, Mário Forjaz Secca, Jan Schier, Oscar Pastor, Christine Sinoquet, et al.. Biomedical Engineering Systems and Technologies, 7th International Joint Conference, BIOSTEC2014, Extended Selected Papers. France. Springer, 2014, Communication in Computer and Information Science. ⟨hal-01169026⟩

Other publications5 documents

  • Christine Sinoquet. Approches par optimisation combinatoire et par apprentissage statistique en bioinformatique. Applications pour la fouille et la modélisation de données complexes en génomique et en génétique . 2014. ⟨hal-01168797⟩
  • Vittorio Perduca, Raphaël Mourad, Christine Sinoquet, Grégory Nuel. Waffect: a method to simulate case-control samples in genome-wide association studies. 2011. ⟨hal-00915533⟩
  • Christine Sinoquet. Bayesian multi-locus pattern selection and computation through reversible jump MCMC. 2010. ⟨hal-00524885⟩
  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Forests of hierarchical latent models for association genetics. 2010. ⟨hal-00503013⟩
  • Thomas Morisseau, Raphaël Mourad, Christian Dina, Philippe Leray, Christine Sinoquet. GWAS-AS: assistance for a thorough evaluation of advanced algorithms dedicated to genome-wide association studies. 2010. ⟨hal-00915535⟩

Preprints, Working Papers, ...6 documents

  • Raphaël Mourad, Christine Sinoquet, Philippe Leray. Learning a forest of Hierarchical Bayesian Networks to model dependencies between genetic markers. 2010. ⟨hal-00444087v2⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability. 2009. ⟨hal-00359530⟩
  • Christine Sinoquet. Improvement of missing genotype imputation through bi-directional parsing of large SNP panels. 2008. ⟨hal-00300596v3⟩
  • Christine Sinoquet, Sylvain Demey, Frédérique Braun. Genome-comparative computational approach for investigating prokaryotic ORF expression potentialities, in relation with potentially high transcription. 2007. ⟨hal-00163675⟩
  • Christine Sinoquet, Sylvain Demey, Frédérique Braun. A large-scale computational analysis for significance assessment of frequencies relative to potentially strong sigma 70 promoters - comparison between 32 bacterial genomes -. 2007. ⟨hal-00153303v3⟩
  • Christine Sinoquet. Gapped consensus motif discovery: evaluation of a new algorithm based on local multiple alignments and a sampling strategy. 2006. ⟨hal-00023162⟩

Reports2 documents

  • Christine Sinoquet. Performance analysis of methods to infer missing genotypes. [Research Report] 2008. ⟨inria-00326741v2⟩
  • Christine Sinoquet, Jacques Nicolas. Analyse syntaxique non déterministe utilisant un modèle de n-grams. [Rapport de recherche] RR-3262, INRIA. 1997. ⟨inria-00073427⟩