Marie-Dominique Devignes

56 papers A 2C 2Misc 3Journal 27Unranked 22

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	GEODES: Geometric Descriptors for the Assessment of Global and Local Flexibility of Proteins During Molecular Dynamics Simulation. IEEE Access Karina Pats, Igor Glukhov, Stepan Petrosian, Maria Mamaeva, Alexey A. Sergushichev, Marie-Dominique Devignes, Ferdinand Molnár
2023	J	`jnl`	FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards. J. Biomed. Semant. Alban Gaignard, Thomas Rosnet, Frédéric de Lamotte, Vincent Lefort, Marie-Dominique Devignes
2022	—	`conf`	A Semi-supervised Graph Deep Neural Network for Automatic Protein Function Annotation. IWBBIO (2) Akrem Sellami, Bishnu Sarker, Salvatore Tabbone, Marie-Dominique Devignes, Sabeur Aridhi
2022	J	`jnl`	Improving automatic GO annotation with semantic similarity. BMC Bioinform. Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
2022	J	`jnl`	Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project. J. Biomed. Informatics Emmanuel Bresso, Joao-Pedro Ferreira, Nicolas Girerd, Masatake Kobayashi, Grégoire Preud'homme, Patrick Rossignol, Fayez Zannad, Marie-Dominique Devignes, Malika Smaïl-Tabbone
2022	J	`jnl`	On the design of a similarity function for sparse binary data with application on protein function annotation. Knowl. Based Syst. Marcelo B. A. Veras, Bishnu Sarker, Sabeur Aridhi, João P. P. Gomes, José A. F. de Macêdo, Engelbert Mephu Nguifo, Marie-Dominique Devignes, Malika Smaïl-Tabbone
2022	J	`jnl`	Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. J. Chem. Inf. Model. Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, Serge Perez, Vincent Leroux, Isaure Chauvot de Beauchêne, Dominique Mias-Lucquin, Marie-Dominique Devignes, Ivan Rivalta, Bernard Maigret
2022	J	`jnl`	Steps towards causal Formal Concept Analysis. Int. J. Approx. Reason. Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
2021	Misc	`conf`	An Approach to Identifying the Most Predictive and Discriminant Features in Supervised Classification Problems. ICCS Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
2021	J	`jnl`	PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PLoS Comput. Biol. Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes
2020	—	`conf`	Explaining Multicriteria Decision Making with Formal Concept Analysis. CLA Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
2020	—	`conf`	Graph Based Automatic Protein Function Annotation Improved by Semantic Similarity. IWBBIO Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
2018	J	`jnl`	Computational discovery of direct associations between GO terms and protein domains. BMC Bioinform. Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes
2018	—	`conf`	Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. SWAT4LS Gabin Personeni, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jonveaux, Céline Bonnet, Adrien Coulet
2017	—	`conf`	Associating Gene Ontology Terms with Pfam Protein Domains. IWBBIO (2) Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie
2017	J	`jnl`	Discovering associations between adverse drug events using pattern structures and ontologies. J. Biomed. Semant. Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
2017	J	`jnl`	ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. BMC Bioinform. Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie
2017	J	`jnl`	Neighborhood-Based Label Propagation in Large Protein Graphs. CoRR Sabeur Aridhi, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, Marie-Dominique Devignes, David W. Ritchie
2016	J	`jnl`	Kbdock - Searching and Organising the Structural Space of Protein-Protein Interactions. ERCIM News Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
2014	J	`jnl`	ECCB 2014: The 13 Bioinform. Marie-Dominique Devignes, Yves Moreau
2014	J	`jnl`	KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res. Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
2014	—	`conf`	Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability. DILS Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Adrien Coulet
2013	—	`conf`	Clustering optimal de gènes fondé sur une mesure de similarité sémantique. CORIA Rachid Hafiane, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Salvatore Tabbone
2013	J	`jnl`	Integrative relational Machine-Learning Approach for Understanding Drug Side-Effect Profiles. BMC Bioinform. Emmanuel Bresso, Renaud Grisoni, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Marie-Dominique Devignes, Malika Smaïl-Tabbone
2012	—	`conf`	Formal Concept Analysis for the Interpretation of Relational Learning Applied on 3D Protein-binding Sites. KDIR Emmanuel Bresso, Renaud Grisoni, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2012	J	`jnl`	Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. Int. J. Comput. Biol. Drug Des. Marie-Dominique Devignes, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch
2012	C	`conf`	ILP Characterization of 3D Protein-Binding Sites and FCA-Based Interpretation. IC3K Emmanuel Bresso, Renaud Grisoni, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2011	—	`conf`	Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis. BIBM Workshops Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch
2011	J	`jnl`	Spatial clustering of protein binding sites for template based protein docking. Bioinform. Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
2011	—	`conf`	Use of Domain Knowledge for Dimension Reduction - Application to Mining of Drug Side Effects. KDIR Emmanuel Bresso, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Amedeo Napoli, Marie-Dominique Devignes
2010	J	`jnl`	BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery. Int. J. Metadata Semant. Ontologies Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Emmanuel Bresso, Amedeo Napoli, Malika Smaïl-Tabbone
2010	J	`jnl`	Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case. J. Chem. Inf. Model. Leo Ghemtio, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Michel Souchet, Vincent Leroux, Bernard Maigret
2010	—	`conf`	Connaissances de domaine et treillis de concepts pour l'exploration progressive de données complexes. IC Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2010	J	`jnl`	HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res. Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie
2010	J	`jnl`	IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinform. Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
2010	A	`conf`	Using Domain Knowledge to Guide Lattice-based Complex Data Exploration. ECAI Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2009	—	`conf`	A KDD Approach for Designing Filtering Strategies to Improve Virtual Screening. KDIR Leo Ghemtio, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Michel Souchet, Bernard Maigret
2009	—	`conf`	Analyse de données transcriptomiques: Modélisation floue de profils d'expression différentielle et analyse fonctionnelle. INFORSID Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch, Ngoc-Hoan Nguyen, Wolfgang Raffelsberger
2009	J	`jnl`	Gene-disease relationship discovery based on model-driven data integration and database view definition. Bioinform. Saliha Yilmaz, Philippe Jonveaux, Cedric Bicep, Laurent Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes
2008	C	`conf`	BioRegistry: automatic extraction of metadata for biological database retrieval and discovery. iiWAS Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Amedeo Napoli, Malika Smaïl-Tabbone
2008	Misc	`conf`	Extending Attribute Dependencies for Lattice-Based Querying and Navigation. ICCS Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2008	A	`conf`	Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval. ECAI Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2008	—	`conf`	Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics. Description Logics Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
2008	J	`jnl`	Ontology-guided data preparation for discovering genotype-phenotype relationships. BMC Bioinform. Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
2008	—	`conf`	Role Assertion Analysis: a proposed method for ontology refinement through assertion learning. STAIRS Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
2007	—	`conf`	Traitement d'attributs inter-dépendants pour la recherche d'information par treillis. Actes d'IC Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2007	—	`conf`	Workshop PC Chairs' Message. WISE Workshops Marie-Dominique Devignes, Malika Smaïl-Tabbone
2006	—	`conf`	SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies. DILS Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
2006	—	`conf`	Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. OTM Workshops (1) Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
2006	J	`jnl`	Treillis de concepts et ontologies pour interroger l'annuaire de sources de données biologiques BioRegistry. Ingénierie des Systèmes d Inf. Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2005	—	`conf`	BioRegistry: A Structured Metadata Repository for Bioinformatic Databases. CompLife Malika Smaïl-Tabbone, Shazia Osman, Nizar Messai, Amedeo Napoli, Marie-Dominique Devignes
2005	—	`conf`	Méthode sémantique pour la classification et l'iinterrogation de sources de données biologiques. EGC (Ateliers) Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2005	Misc	`conf`	Querying a Bioinformatic Data Sources Registry with Concept Lattices. ICCS Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2005	J	`jnl`	Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de données biologiques (BioRegistry) CoRR Nizar Messai, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli
2005	—	`conf`	Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de données biologiques (BioRegistry). INFORSID Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
2002	J	`jnl`	Collecte et intégration de données biologiques hétérogènes sur le web. Ingénierie des Systèmes d Inf. Marie-Dominique Devignes, André Schaaff, Malika Smaïl