Publications

Batoul Haydar, Nanée Chahinian, Claude Pasquier (2026). From Imperfect Sewer Data to Coherent Topology: A Graph-Based Approach. EGU26-9507.

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Fadi Abou Choucha, Claude Pasquier (2026). MEAST: A Novel Framework for Analyzing Gene Set Stability in Single Cell Transcriptomics. Scientific Reports, Vol. 16, No. 1, pp. 18536.

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Fadi Abou Choucha, Rafaël Lopes Goncalves, Thomas Hermet, Jessica Mille, Laetitia Guardini, Mariem Benkhedher, Caroline Lacoux, Marine Gautier-Isola, Baharia Mograbi, Jérémie Roux, Françoise Cottrez, Bernard Mari, Hervé Groux, Claude Pasquier, Roger Rezzonico, Georges Vassaux (2026). Single-Cell Transcriptomics Reveals a Differential Response of Human Bronchial Epithelial Cell-Types to Cadmium Chloride. Archives of Toxicology, Vol. 100, No. 6, pp. 2307–2321.

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Batoul Haydar, Nanée Chahinian, Claude Pasquier (2026). Reconstructing Sewer Network Topology Using Graph Theory. Water, Vol. 18, No. 2, pp. 222.

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Batoul Haydar, Nanée Chahinian, Claude Pasquier (2025). Addressing Common Inconsistencies in Sewer Networks Data. EGU25-7012.

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Nina Singlan, Fadi Abou Choucha, Claude Pasquier (2025). A New Similarity Based Adapted Louvain Algorithm (SIMBA) for Active Module Identification in p-Value Attributed Biological Networks. Scientific Reports, Vol. 15, No. 1, pp. 11360.

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Romain Lombardi, Mathieu Jozwiak, Jean Dellamonica, Claude Pasquier (2025). Using Weak Signals to Predict Spontaneous Breathing Trial Success: A Machine Learning Approach. Intensive Care Medicine Experimental, Vol. 13, No. 1, pp. 34.

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Célia da Costa Pereira, Claude Pasquier, Andrea GB Tettamanzi (2025). Propagation-Based Domain-Transferable Gradual Sentiment Analysis. 17th International Conference on Agents and Artificial Intelligence.

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Batoul Haydar, Nanée Chahinian, Claude Pasquier (2024). From Standards to an Ontology-Based Data Access System for Sewer Networks. Actes Des 10ème Journées Doctorales En Hydrologie Urbaine.

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Laurent Turchi, Nathalie Sakakini, Gaelle Saviane, Béatrice Polo, Mirca Saras Saurty-Seerunghen, Mathieu Gabut, Corine Auge Gouillou, Vincent Guerlais, Claude Pasquier, Marie Luce Vignais (2023). CELF2 Sustains a Proliferating/OLIG2+ Glioblastoma Cell Phenotype via the Epigenetic Repression of SOX3. Cancers, Vol. 15, No. 20, pp. 5038.

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Claude Pasquier, Vincent Guerlais, Denis Pallez, Raphaël Rapetti-Mauss, Olivier Soriani (2023). A Network Embedding Approach to Identify Active Modules in Biological Interaction Networks. Life Science Alliance, Vol. 6, No. 9, pp. e202201550.

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Romain Lombardi, Mathieu Jozwiak, Jean Dellamonica, Claude Pasquier (2023). A Machine Learning Approach to Predict Weaning Outcome among Ventilated Patients in Intensive Care Unit. Reanimation 2023, the French Intensive Care Society International Congress, Vol. 13.

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Claude Pasquier, Alain Robichon (2022). Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species. International Journal of Molecular Sciences, Vol. 23, No. 22, pp. 14429.

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Álvaro Javier Feliz Morel, Anida Hasanovic, Aurélie Morin, Chloé Prunier, Virginie Magnone, Kevin Lebrigand, Amaury Aouad, Sarah Cogoluegnes, Judith Favier, Claude Pasquier, Isabelle Mus-Veteau (2022). Persistent Properties of a Subpopulation of Cancer Cells Overexpressing the Hedgehog Receptor Patched. Pharmaceutics, Vol. 14, No. 5, pp. 988.

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Véronique Braud, Frédéric Cazals, Maria Duca, Isabelle Mus-Veteau, Claude Pasquier, Olivier Soriani (2022). L’essentiel du symposium UCAncer 2021 sur les approches multidisciplinaires de la recherche sur le cancer. Bulletin du Cancer, Vol. 109, No. 4, pp. 505–509.

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Oriane Lié, Thierry Virolle, Mathieu Gabut, Claude Pasquier, Ilyess Zemmoura, Corinne Augé-Gouillou (2022). SETMAR Shorter Isoform: A New Prognostic Factor in Glioblastoma. Frontiers in Oncology, Vol. 11, pp. 638397.

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Claude Pasquier, Alain Robichon (2021). Temporal and Sequential Order of Nonoverlapping Gene Networks Unraveled in Mated Female Drosophila. Life Science Alliance, Vol. 5, No. 2, pp. e202101119.

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Claude Pasquier, Vincent Guerlais, Denis Pallez, Raphaël Rapetti-Mauss, Olivier Soriani (2021). Identification of Active Modules in Interaction Networks Using Node2vec Network Embedding. bioRxiv, pp. 2021.09.22.461345.

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Claude Pasquier, Alain Robichon (2021). Computational Search of Hybrid Human/SARS-CoV-2 dsRNA Reveals Unique Viral Sequences That Diverge from Those of Other Coronavirus Strains. Heliyon, Vol. 7, No. 6, pp. e07284.

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Claude Pasquier, Alain Robichon (2020). Computational Prediction of miRNA / mRNA Duplexomes at the Whole Human Genome Scale Reveals Functional Subnetworks of Interacting Genes with Embedded miRNA Annealing Motifs. Computational Biology and Chemistry, Vol. 88, pp. 107366.

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Frédéric Flouvat, Nazha Selmaoui-folcher, Jérémy Sanhes, Chengcheng Mu, Claude Pasquier, Jean-François Boulicaut (2020). Mining Evolutions of Complex Spatial Objects Using a Single-Attributed Directed Acyclic Graph. Knowledge and Information Systems, Vol. 62, No. 10, pp. 3931–3971.

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Claude Pasquier, Célia da Costa Pereira, Andrea G.B. Tettamanzi (2020). Extending a Fuzzy Polarity Propagation Method for Multi-Domain Sentiment Analysis with Word Embedding and POS Tagging. 24th European Conference on Artificial Intelligence (ECAI 2020).

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Claude Pasquier, Alain Robichon (2020). Computational Search of Hybrid Human/ SARS-CoV-2 dsRNA Reveals Unique Viral Sequences That Diverge from Other Coronavirus Strains. bioRxiv, pp. 1–15.

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Claude Pasquier, Sandra Agnel, Alain Robichon (2020). Transcriptome-Wide-Scale-Predicted dsRNAs Potentially Involved in RNA Homoeostasis Are Remarkably Excluded from Genes with No/Very Low Expression in All Developmental Stages. RNA Biology, Vol. 17, No. 4, pp. 554–570.

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Leandro Correa, Denis Pallez, Laurent Tichit, Olivier Soriani, Claude Pasquier (2019). Population-Based Meta-Heuristic for Active Modules Identification. Proceedings of the Tenth International Conference on Computational Systems-Biology and Bioinformatics, pp. 1–8.

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Claude Pasquier (2018). Contributions à la fouille de données complexes. Université Côte d’Azur.

Denis Pallez, Julien Gardès, Claude Pasquier (2017). Prediction of miRNA-disease Associations Using an Evolutionary Tuned Latent Semantic Analysis.. Scientific reports, Vol. 7, No. 1, pp. 10548.

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Claude Pasquier, Sandra Agnel, Alain Robichon (2017). The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes. G3: Genes, Genomes, Genetics, Vol. 7, No. 7, pp. 2295–2304.

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Claude Pasquier, Frédéric Flouvat, Jérémy Sanhes, Nazha Selmaoui-folcher (2017). Attributed Graph Mining in the Presence of Automorphism. Knowledge and Information Systems, Vol. 50, No. 2, pp. 569–584.

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Claude Pasquier, Julien Gardès (2016). Prediction of miRNA-disease Associations with a Vector Space Model.. Scientific reports, Vol. 6, pp. 27036.

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Claude Pasquier, Jérémy Sanhes, Frédéric Flouvat, Nazha Selmaoui-folcher (2015). Frequent Pattern Mining in Attributed Trees: Algorithms and Applications. Knowledge and Information Systems, Vol. 46, No. 3, pp. 491–514.

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Claude Pasquier, Mathilde Clément, Aviv Dombrovsky, Stéphanie Penaud, Martine Da Rocha, Corinne Rancurel, Neil Ledger, Maria Capovilla, Alain Robichon (2014). Environmentally Selected Aphid Variants in Clonality Context Display Differential Patterns of Methylation in the Genome. PLOS ONE, Vol. 9, No. 12, pp. e115022.

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Frédéric Flouvat, Jérémy Sanhes, Claude Pasquier, Nazha Selmaoui-folcher, Jean-François Boulicaut (2014). Improving Pattern Discovery Relevancy by Deriving Constraints from Expert Models. 21st European Conference on Artificial Intelligence (ECAI'14), Proceedings Published by IOS Press in Frontiers in Artificial Intelligence and Applications Serie Volume 263, pp. 327–332.

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Frédéric Flouvat, Jérémy Sanhes, Claude Pasquier, Nazha Selmaoui-folcher, Jean-François Boulicaut (2014). Les modèles des experts au service de l’extraction de motifs pertinents. 19ème congrès sur la Reconnaissance de Formes et l’Intelligence Artificielle (RFIA'14).

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Claude Pasquier, Frédéric Flouvat, Jérémy Sanhes, Nazha Selmaoui-folcher (2014). Extraction de motifs dans des graphes orientés attribués en présence d’automorphisme. 14ème Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC'14), Revue des Nouvelles Technologies de l’Information, volume E-26, pp. 371–382.

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Jérémy Sanhes, Frédéric Flouvat, Claude Pasquier, Nazha Selmaoui-folcher, Jean-François Boulicaut (2013). Weighted Path as a Condensed Pattern in a Single Attributed DAG. 23rd International Joint Conference on Artificial Intelligence (IJCAI'13), pp. 1642–8.

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Claude Pasquier, Jérémy Sanhes, Frédéric Flouvat, Nazha Selmaoui-folcher (2013). Frequent Pattern Mining in Attributed Trees. 17th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD'13), J. Pei et al. (Eds.): PAKDD 2013, Part I, LNAI 7818, Pp. 26–37. Springer, Heidelberg (2013), pp. 26–37.

Claude Pasquier, Jérémy Sanhes, Frédéric Flouvat, Nazha Selmaoui-folcher (2013). Extraction de motifs fréquents dans des arbres attribués. 13ème Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC'13). Revue des Nouvelles Technologies de l’Information, volume E-24, pp. 193–204.

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Jérémy Sanhes, Frédéric Flouvat, Claude Pasquier, Nazha Selmaoui-folcher, Jean-François Boulicaut (2013). Extraction de motifs condensés dans un unique graphe orienté acyclique attribué. 13ème Conférence Francophone sur l’Extraction et la Gestion des Connaissances (EGC'13), Revue des Nouvelles Technologies de l’Information, volume E-24.

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Claude Pasquier (2011). Applying Semantic Web Technologies to Biological Data Integration and Visualization. Data Management in Semantic Web, pp. 131–151.

Claude Pasquier (2010). Single Document Keyphrase Extraction Using Sentence Clustering and Latent Dirichlet Allocation. 5th International Workshop on Semantic Evaluation, SemEval 2010 (ACL'10), pp. 154–157.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier (2009). Mining Association Rule Bases from Integrated Genomic Data and Annotations (Extended Version). Lecture Notes in Bioinformatics, Vol. 5488, pp. 78–90.

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Nicolas Pasquier, Claude Pasquier, Laurent Brisson, Martine Collard (2008). Mining Gene Expression Data Using Domain Knowledge. International Journal of Software and Informatics (IJSI), Vol. 2, No. 2, pp. 215–231.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier (2008). GenMiner: Mining Non-Redundant Association Rules from Integrated Gene Expression Data and Annotations.. Bioinformatics (Oxford, England), Vol. 24, No. 22, pp. 2643–4.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier (2008). Mining Association Rule Bases from Integrated Genomic Data and Annotations. 5th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB'08), pp. 33–43.

Claude Pasquier (2008). Biological Data Integration Using Semantic Web Technologies.. Biochimie, Vol. 90, No. 4, pp. 584–94.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier, Martine Collard, Lucero Lopez-Perez (2008). Analyse des groupes de gènes co-exprimés: un outil automatique pour l'interprétation des expériences de biopuces (version étendue). Revue des Nouvelles Technologies de l’Information (RNTI-C-2), Classification : points de vue croisés, Vol. 831, pp. 263–74.

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Ricardo Martinez, Claude Pasquier, Nicolas Pasquier (2007). GenMiner: Mining Informative Association Rules from Genomic Data. IEEE International Conference on Bioinformatics and Biomedicine (BIBM'07), pp. 15–22.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier, Lucero Lopez-Perez (2006). Interpreting Microarray Experiments via Co-Expressed Gene Groups Analysis. 9th International Conference of Discovery Science (ICDS'06), Lecture Notes in Computer Science, Vol. 4265, pp. 316–320.

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Ricardo Martinez, Nicolas Pasquier, Claude Pasquier, Martine Collard, Lucero Lopez-Perez (2006). Analyse des groupes de gènes co-exprimés (AGGC): un outil automatique pour l'interprétation des expériences de biopuces. 13ème Rencontres de la Société Francophone de Classification (SFC’06), pp. 267–276.

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Ricardo Martinez, Nicolas Pasquier, Martine Collard, Claude Pasquier, Lucero Lopez-Perez (2006). Co-Expressed Gene Groups Analysis (CGGA): An Automatic Tool for the Interpretation of Microarray Experiments. Journal of Integrative Bioinformatics, Vol. 3, No. 2, pp. 1–12.

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Ricardo Martinez, Richard Christen, Claude Pasquier, Nicolas Pasquier (2005). Exploratory Analysis of Cancer SAGE Data. 9th European Conferences on Principles and Practice of Knowledge Discovery in Databases (PKDD'05), Discovery Challenge.

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Claude Pasquier, Fabrice Girardot, Karim Jevardat de Fombelle, Richard Christen (2004). THEA: Ontology-Driven Analysis of Microarray Data.. Bioinformatics (Oxford, England), Vol. 20, No. 16, pp. 2636–43.

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Ioannis Iliopoulos, Sophia Tsoka, Miguel A Andrade, Anton J Enright, Mark Carroll, Patrick Poullet, Vassilis Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros Hamodrakas, Javier Tamames, Asutosh T Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A Ouzounis (2003). Evaluation of Annotation Strategies Using an Entire Genome Sequence. Bioinformatics (Oxford, England), Vol. 19, No. 6, pp. 717–26.

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Didier Parigot, Carine Courbis, Pascal Degenne, Alexandre Fau, Claude Pasquier, Joël Fillon, Christophe Held, Isabelle Attali (2002). Aspect and XML-oriented Semantic Framework Generator : Smarttools. 2nd Workshop on Language Descriptions, Tools and Applications (LDTA'02), (Satellite Event of ETAPS'02), Electronic Notes in Theoretical Computer Science, Elsevier, Vol. 65, No. 3, pp. 97–116.

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Claude Pasquier, Vassilis Promponas, Stavros Hamodrakas (2001). PRED-CLASS: Cascading Neural Networks for Generalized Protein Classification and Genome-Wide Applications.. Proteins: Structure, Function, and Bioinformatics, Vol. 44, No. 3, pp. 361–9.

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Isabelle Attali, Carine Courbis, Pascal Degenne, Alexandre Fau, Didier Parigot, Claude Pasquier (2001). SmartTools: A Generator of Interactive Environments Tools. 10th International Conference on Compiler Construction (CC'01): Held as Part of the Joint European Conferences on Theory and Practice of Software (ETAPS 2001), Electronic Notes in Theoretical Computer Science, Elsevier, Vol. 44, No. 2, pp. 355–360.

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Theodore Liakopoulos, Claude Pasquier, Stavros Hamodrakas (2001). A Novel Tool for the Prediction of Transmembrane Protein Topology Based on a Statistical Analysis of the SwissProt Database: The OrienTM Algorithm. Protein Engineering, Vol. 14, No. 6, pp. 387–390.

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Vassilis Promponas, Claude Pasquier, Stavros Hamodrakas (2001). PRED-CLASS: Bioinformatics Software for Generalized Protein Classification and Genome-Wide Applications. 23rd Conference of the Hellenic Society for Biological Sciences.

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Theodore Liakopoulos, N Harkiolakis, Vassilis Promponas, Claude Pasquier, Ioannis Hamodrakas, Nikolaos Papandreou, Vasiliki Iconomidou, N Papandreou, Elpida Tzafestas, S Tzafestas, Elias Eliopoulos, Stavros Hamodrakas (2001). DAM-BIO: Bioinformatics Internet Workbench for Protein Analysis. New Modules and Applications to Biological Problems. 23rd Conference of the Hellenic Society for Biological Sciences.

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Isabelle Attali, Carine Courbis, Pascal Degenne, Alexandre Fau, Joël Fillon, Didier Parigot, Claude Pasquier, Claudio Sacerdoti Cohen (2001). SmartTools: A Development Environment Generator Based on XML Technologies. XML Technologies and Software Engineering (XSE'01), ICSE'01, Workshop Proceedings.

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Claude Pasquier, Laurent Théry (2000). A Distributed Editing Environment for XML Documents. First ECOOP Workshop on XML and Object Technology (XOT'00).

Theodore Liakopoulos, Giorgos Palaios, Vassilis Promponas, Ioannis Hamodrakas, Claude Pasquier, Stavros Hamodrakas (2000). A Workbench for Computational Analysis of Protein Sequence and Structure on the Internet. 22nd Conference of the Hellenic Society for Biological Sciences.

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Claude Pasquier, Stavros Hamodrakas (1999). An Hierarchical Artificial Neural Network System for the Classification of Transmembrane Proteins. Protein Engineering, Vol. 12, No. 8, pp. 631–634.

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Claude Pasquier, Vassilis Promponas, Giorgos Palaios, Ioannis Hamodrakas, Stavros Hamodrakas (1999). PRED-TMR2: An Hierarchical Neural Network to Classify Proteins as Transmembrane and a Novel Method to Predict Transmembrane Segments. 21st Conference of the Hellenic Society for Biological Sciences.

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Theodore Liakopoulos, Claude Pasquier, Stavros Hamodrakas (1999). OrienTM: A Novel Method to Predict Transmembrane Protein Topology. 21st Conference of the Hellenic Society for Biological Sciences.

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Claude Pasquier, Vassilis Promponas, Giorgos Palaios, Ioannis Hamodrakas, Stavros Hamodrakas (1999). A Novel Method for Predicting Transmembrane Segments in Proteins Based on a Statistical Analysis of the SwissProt Database: The PRED-TMR Algorithm. Protein Engineering, Vol. 12, No. 5, pp. 381–385.

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Vasilis Promponas, Giorgos Palaios, Claude Pasquier, Ioannis Hamodrakas, Stavros Hamodrakas (1999). CoPreTHi: A Web Tool Which Combines Transmembrane Protein Segment Prediction Methods.. In silico biology, Vol. 1, No. 3, pp. 159–62.

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Claude Pasquier, Vassilis Promponas, Nikos Varvayannis, Stavros Hamodrakas (1998). A Web Server to Locate Periodicities in a Sequence. Bioinformatics, Vol. 14, No. 8, pp. 749–50.

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Vassilis Promponas, Giorgos Palaios, Claude Pasquier, Ioannis Hamodrakas, Stavros Hamodrakas (1998). CoPreTHi: A Program to Combine the Results of Transmembrane Protein Segment Prediction Methods. 20th Conference of the Hellenic Society for Biological Sciences.

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Claude Pasquier, Vassilis Promponas, Nikos Varvayannis, Stavros Hamodrakas (1998). A Web Interface for FT: A Tool Dedicated to the Study of Periodicities in Sequences. 20th Conference of the Hellenic Society for Biological Science.

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Claude Pasquier (1994). Gestion et conception de documents structurés par le contexte. University of Nice - Sophia Antipolis.

Claude Pasquier (1992). BIBLE: A System for Design and Management of Context-Controlled Documents. First International Conference on Principles of Document Processing (PODP'92).