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Publications

PhD

1. Pasquier C: Gestion et conception de documents structurés par le contexte. PhD thesis. University of Nice - Sophia Antipolis; 1994.

International journals

2. Pasquier C, Sanhes J, Flouvat F, Selmaoui-Folcher N: Frequent Pattern Mining in Attributed trees: algorithms and applications. Knowledge and Information Systems, 2015, doi: 10.1007/s10115-015-0831-x. IF2014 = 1.782

3. Pasquier, C., Clément, M., Dombrovsky, A., Penaud, S., Da Rocha, M., Rancurel, C., Ledger, N., Capovilla, M., and Robichon, A. Environmentally Selected Aphid Variants in Clonality Context Display Differential Patterns of Methylation in the Genome. PLoS ONE 9(12) 2014, doi: 10.1371/journal.pone.0115022. IF2014 = 3.234

4. Martinez R, Pasquier N, Pasquier C: Mining Association Rule Bases from Integrated Genomic Data and Annotations (extended version). Lecture Notes in Bioinformatics 2009, 5488:78–90.

5. Pasquier N, Pasquier C, Brisson L, Collard M: Mining Gene Expression Data using Domain Knowledge. International Journal of Software and Informatics (IJSI) 2008, 2:215–231.

6. Martinez R, Pasquier N, Pasquier C: GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. Bioinformatics (Oxford, England) 2008, 24:2643–4. IF2008 = 4.328

7. Pasquier C: Biological data integration using Semantic Web technologies. Biochimie 2008, 90:584–94. IF2008 = 3.071

8. Martinez R, Pasquier N, Collard M, Pasquier C, Lopez-Perez L: Co-expressed gene groups analysis (CGGA): An automatic tool for the interpretation of microarray experiments. Journal of Integrative Bioinformatics 2006, 3:1–12.

9. Pasquier C, Girardot F, Jevardat De Fombelle K, Christen R: THEA: ontology-driven analysis of microarray data. Bioinformatics (Oxford, England) 2004, 20:2636–43. IF2004 = 5.742

10. Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA: Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (Oxford, England) 2003, 19:717–26. IF2003 = 6.701

11. Liakopoulos T, Pasquier C, Hamodrakas S: A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein engineering 2001, 14:387–90. IF2001 = 2.718

12. Pasquier C, Promponas V, Hamodrakas S: PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications. Proteins 2001, 44:361–9. IF2001 = 3.894

13. Pasquier C, Promponas V, Palaios G, Hamodrakas I, Hamodrakas S: A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein engineering 1999, 12:381–5. IF1999 = 3.202

14. Pasquier C, Hamodrakas SJ: An hierarchical artificial neural network system for the classification of transmembrane proteins. Protein engineering 1999, 12:631–4. IF1999 = 3.202

15. Promponas V, Palaios G, Pasquier C, Hamodrakas I, Hamodrakas S: CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods. In Silico Biology 1999, 1:159–162.

16. Pasquier C, Promponas V, Varvayannis N, Hamodrakas S: A web server to locate periodicities in a sequence. Bioinformatics (Oxford, England) 1998, 14:749–50.

International Conferences

17. Flouvat F, Sanhes J, Pasquier C, Selmaoui-Folcher N, Boulicaut J-F: Improving pattern discovery relevancy by deriving constraints from expert models. In proceedings of the 21st European Conference on Artificial Intelligence (ECAI’14); 2014. Rank A

18. Pasquier C, Sanhes J, Flouvat F, Selmaoui-Folcher N: Frequent Pattern Mining in Attributed trees. In proceedings of the 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD’13) J Pei et al (Eds): PAKDD 2013, Part I, LNAI 7818. Gold Coast Australia: Springer-Verlag; 2013:26–37. Rank A

19. Sanhes J, Flouvat F, Pasquier C, Selmaoui-Folcher N, Boulicaut J-F: Weighted Path as a Condensed Pattern in a Single Attributed DAG. In proceedings of the 23rd International Joint Conference on Artificial Intelligence (IJCAI’13), Beijing, China, August 3-9, 2013. Beijing, China; 2013. Rank A*

20. Pasquier C: Single Document Keyphrase Extraction Using Sentence Clustering and Latent Dirichlet Allocation. In proceedings of the 5th International Workshop on Semantic Evaluation. Uppsala, Sweden: Association for Computational Linguistics; 2010:154–157. Rank A

21. Martinez R, Pasquier N, Pasquier C: Mining Association Rule Bases from Integrated Genomic Data and Annotations. In proceedings of the 5th international conference on computational intelligence methods for bioinformatics and biostatistics (CIBB’08). Edited by Berlin S. Vietri sul Mare, Salerno, Italy; 2008:33–43. [vol. 1]

22. Martinez R, Pasquier C, Pasquier N: GenMiner: Mining Informative Association Rules from Genomic Data. In proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’07). Fremont, Silicon Valley, CA, USA: IEEE; 2007:15–22.

23. Martinez R, Pasquier N, Pasquier C, Lopez-Perez L: Interpreting microarray experiments via co-expressed gene groups analysis. In proceedings of the 9th International Conference of Discovery Science (DS’06) Lecture Notes in Computer Science. Volume 4265. Berlin, Heidelberg: Lecture Notes in Computer Science, Springer Verlag, vol. 4265, pp. 316-320; Springer Berlin Heidelberg; 2006:316–320. [Lecture Notes in Computer Science]

24. Martinez R, Christen R, Pasquier C, Pasquier N: Exploratory Analysis of Cancer SAGE Data. In proceedings of the 9th European Conferences on Principles and Practice of Knowledge Discovery in Databases (PKDD’05), Discovery Challenge. Porto, Portugal; 2005. Rank A

25. Anand S, Christen R, Pasquier C: Distributed BLAST with ProActive. In 1st Grid PlugTest ETSI Headquarters ProActive User Group. Sophia Antipolis, France; 2004.

26. Pasquier C, Christen R: Analysis of microarray data with THEA. In proceedings of Lyon’s International Multidisciplinary Meeting on Post-Genomics (IPG’04). La Doua, Lyon, France; 2004.

27. Parigot D, Courbis C, Degenne P, Fau A, Pasquier C, Fillon J, Held C, Attali I: Aspect and XML-oriented Semantic Framework GeneratorSmartTools. In proceedings of the second Workshop on Language Descriptions, Tools and Applications (LDTA’02; Satellite Event of ETAPS’02) Electronic Notes in Theoretical Computer Science. Volume 65. Grenoble, France: Electronic Notes in Theoretical Computer Science, Elsevier, vol. 65, issue 3, pp. 97-116; Electronic Notes in Theoretical Computer Science, Elsevier, vol. 65, issue 3, pp. 97-116; 2002:97–116. [vol. 3] Rank B

28. Attali I, Courbis C, Degenne P, Fau A, Fillon J, Parigot D, Pasquier C, Sacerdoti Cohen C: SmartTools: A Development Environment Generator based on XML Technologies. In proceedings of the 10th International Conference on Compiler Construction (CC’01): Held as Part of the Joint European Conferences on Theory and Practice of Software (ETAPS 2001). Genova, italy: Lecture Notes in Computer Science, Springer Verlag, vol. 2027, pp. 355-360; Lecture Notes in Computer Science, Springer Verlag, vol. 2027, pp. 355-360; 2001. Rank A

29. Attali I, Courbis C, Degenne P, Fau A, Parigot D, Pasquier C: SmartTools: A Generator of Interactive Environments Tools. In proceedings of the first workshop on Language Descriptions, Tools and Applications (LDTA’01) Electronic Notes in Theoretical Computer Science. Genova, Italy: Electronic Notes in Theoretical Computer Science, Elsevier, vol. 44, issue 2, pp. 225-231; Electronic Notes in Theoretical Computer Science, Elsevier, vol. 44, issue 2, pp. 225-231; 2001:225–231. Rank B

30. Pasquier C, Théry L: A Distributed Editing Environment for XML Documents. In proceedings of the first ECOOP Workshop on XML and Object Technology (XOT’00). Sophia-Antipolis, France; 2000.

31. Pasquier C: BIBLE: a system for Design and Management of Context-Controlled Documents. In proceedings of the first international conference on Principles of Document Processing (PODP’92). Washington D. C., USA; 1992.

Book Chapters

32. Pasquier C: Applying Semantic Web technologies to biological data integration and visualization. In Data Management in Semantic Web. Edited by Jin H, Zehua L. Nova Science Publishers, Inc. 2011:131–151.

National journals

33. Martinez R, Pasquier N, Pasquier C, Collard M, Lopez-Perez L: Analyse des groupes de gènes co-exprimés : un outil automatique pour l’interprétation des expériences de biopuces. In Revue des Nouvelles Technologies de l’Information (RNTI-C-2), Classification : points de vue croisés. Edited by Cépaduès Editions. 2008:267–276.

National Conferences

34. Flouvat F, Sanhes J, Pasquier C, Selmaoui-Folcher N, Boulicaut J-F: Les modèles des experts au service de l’extraction de motifs pertinents. In actes de la 19e conférence Reconnaissance de Formes et Intelligence Artificielle (RFIA’14); 2014.

35. Pasquier C, Flouvat F, Sanhes J, Selmaoui-folcher N: Extraction de motifs dans des graphes orientés attribués en présence d’automorphisme. In actes de la 14e Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC’14), Revue des Nouvelles Technologies de l’Information, volume E-26; 2014:371–382.

36. Pasquier C, Sanhes J, Flouvat F, Selmaoui-Folcher N: Extraction de motifs fréquents dans des arbres attribués. In actes de la 13e Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC’13), Revue des Nouvelles Technologies de l’Information, volume E-24. Toulouse; 2013:193–204.

37. Sanhes J, Flouvat F, Pasquier C, Selmaoui-Folcher N, Boulicaut J-F: Extraction de motifs condensés dans un seul graphe orienté acyclique attribué. In actes de la 13e Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC’13), 29 janvier - 01 février 2013, Toulouse, France; 2013.

38. Martinez R, Pasquier N, Pasquier C, Collard M, Lopez-Perez L: Analyse des groupes de gènes co-exprimés (AGGC) : un outil automatique pour l’interpretation des expériences de biopuces. In actes de la 13ème Rencontres de la Société Francophone de Classification (SFC’06). Metz, France; 2006.

39. Iliopoulos E, Tzafestas E, Papandreou NA, Iconomidou V, Papandreou NC, Liakopoulos T, Pasquier C, Hamodrakas S, Tzafestas S, Harkiolakis N, Promponas V, Hamodrakas I: DAM-BIO: Bioinformatics internet workbench for protein analysis. New modules and applications to biological problems. In proceedings of the 23rd conference of the Hellenic Society for Biological Sciences. Chios island, Greece; 2001.

40. Liakopoulos T, Palaios G, Promponas V, Hamodrakas I, Pasquier C, Hamodrakas S: A workbench for computational analysis of protein sequence and structure on the Internet. In proceedings of the 22nd Conference of the Hellenic Society for Biological Sciences. Skiathos island, Greece; 2000.

41. Pasquier C, Promponas V, Palaios G, Hamodrakas I, Hamodrakas S: PRED-TMR2: An hierarchical neural network to classify proteins as transmembrane and a novel method to predict transmembrane segments. In proceedings of the 21st conference of the Hellenic Society for Biological Sciences. Galissas, Syros island, Greece; 1999.

42. Liakopoulos T, Pasquier C, Hamodrakas S: OrienTM: A novel method to predict transmembrane protein topology. In proceedings of the 21st conference of the Hellenic Society for Biological Sciences. Galissas, Syros island, Greece; 1999.

43. Pasquier C, Promponas V, Varvayannis N, Hamodrakas S: A web interface for FT: a tool dedicated to the study of periodicities in sequences. In proceedings of the 20th conference of the Hellenic Society for Biological Science. Samos Island, Greece; 1998.

44. Promponas V, Palaios G, Pasquier C, Hamodrakas I, Hamodrakas S: CoPreTHi: a program to combine the results of transmembrane protein segment prediction methods. In proceedings of the 20th conference of the Hellenic Society for Biological Science. Samos Island, Greece; 1998.

45. Pasquier C: Projet d’utilisation de la norme ODA à la Caisse des Dépôts et Consignations. Échange et génération de documents. In actes du colloque Gestion des Documents Electroniques. Caen, France; 1991.