Collecte et intégration de données biologiques hétérogènes sur le web. - Marie-Dominique Devignes; André Schaaff; Malika Smaïl (Ingénierie des Systèmes d Inf., 2002)

BioRegistry: A Structured Metadata Repository for Bioinformatic Databases. - Malika Smaïl-Tabbone; Shazia Osman; Nizar Messai; Amedeo Napoli; Marie-Dominique Devignes (CompLife, 2005)

Méthode sémantique pour la classification et l'iinterrogation de sources de données biologiques. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (EGC (Ateliers), 2005)

Querying a Bioinformatic Data Sources Registry with Concept Lattices. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (ICCS, 2005)

Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de données biologiques (BioRegistry). - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (INFORSID, 2005)

SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies. - Adrien Coulet; Malika Smaïl-Tabbone; Pascale Benlian; Amedeo Napoli; Marie-Dominique Devignes (DILS, 2006)

Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. - Adrien Coulet; Malika Smaïl-Tabbone; Amedeo Napoli; Marie-Dominique Devignes (OTM Workshops (1), 2006)

Treillis de concepts et ontologies pour interroger l'annuaire de sources de données biologiques BioRegistry. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (Ingénierie des Systèmes d Inf., 2006)

Traitement d'attributs inter-dépendants pour la recherche d'information par treillis. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (Actes d'IC, 2007)

Workshop PC Chairs' Message. - Marie-Dominique Devignes; Malika Smaïl-Tabbone (WISE Workshops, 2007)

Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics. - Adrien Coulet; Malika Smaïl-Tabbone; Amedeo Napoli; Marie-Dominique Devignes (Description Logics, 2008)

Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (ECAI, 2008)

Extending Attribute Dependencies for Lattice-Based Querying and Navigation. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (ICCS, 2008)

BioRegistry: automatic extraction of metadata for biological database retrieval and discovery. - Marie-Dominique Devignes; Philippe Franiatte; Nizar Messai; Amedeo Napoli; Malika Smaïl-Tabbone (iiWAS, 2008)

Role Assertion Analysis: a proposed method for ontology refinement through assertion learning. - Adrien Coulet; Malika Smaïl-Tabbone; Amedeo Napoli; Marie-Dominique Devignes (STAIRS, 2008)

Ontology-guided data preparation for discovering genotype-phenotype relationships. - Adrien Coulet; Malika Smaïl-Tabbone; Pascale Benlian; Amedeo Napoli; Marie-Dominique Devignes (BMC Bioinform., 2008)

A KDD Approach for Designing Filtering Strategies to Improve Virtual Screening. - Leo Ghemtio; Malika Smaïl-Tabbone; Marie-Dominique Devignes; Michel Souchet; Bernard Maigret (KDIR, 2009)

Analyse de données transcriptomiques: Modélisation floue de profils d'expression différentielle et analyse fonctionnelle. - Sidahmed Benabderrahmane; Marie-Dominique Devignes; Malika Smaïl-Tabbone; Amedeo Napoli; Olivier Poch; Ngoc-Hoan Nguyen; Wolfgang Raffelsberger (INFORSID, 2009)

Gene-disease relationship discovery based on model-driven data integration and database view definition. - Saliha Yilmaz; Philippe Jonveaux; Cedric Bicep; Laurent Pierron; Malika Smaïl-Tabbone; Marie-Dominique Devignes (Bioinform., 2009)

Using Domain Knowledge to Guide Lattice-based Complex Data Exploration. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (ECAI, 2010)

Connaissances de domaine et treillis de concepts pour l'exploration progressive de données complexes. - Nizar Messai; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (IC, 2010)

IntelliGO: a new vector-based semantic similarity measure including annotation origin. - Sidahmed Benabderrahmane; Malika Smaïl-Tabbone; Olivier Poch; Amedeo Napoli; Marie-Dominique Devignes (BMC Bioinform., 2010)

BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery. - Marie-Dominique Devignes; Philippe Franiatte; Nizar Messai; Emmanuel Bresso; Amedeo Napoli; Malika Smaïl-Tabbone (Int. J. Metadata Semant. Ontologies, 2010)

Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case. - Leo Ghemtio; Marie-Dominique Devignes; Malika Smaïl-Tabbone; Michel Souchet; Vincent Leroux; Bernard Maigret (J. Chem. Inf. Model., 2010)

HexServer: an FFT-based protein docking server powered by graphics processors. - Gary Macindoe; Lazaros Mavridis; Vishwesh Venkatraman; Marie-Dominique Devignes; David W. Ritchie (Nucleic Acids Res., 2010)

Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis. - Sidahmed Benabderrahmane; Marie-Dominique Devignes; Malika Smaïl-Tabbone; Amedeo Napoli; Olivier Poch (BIBM Workshops, 2011)

Use of Domain Knowledge for Dimension Reduction - Application to Mining of Drug Side Effects. - Emmanuel Bresso; Sidahmed Benabderrahmane; Malika Smaïl-Tabbone; Gino Marchetti; Arnaud Sinan Karaboga; Michel Souchet; Amedeo Napoli; Marie-Dominique Devignes (KDIR, 2011)

Spatial clustering of protein binding sites for template based protein docking. - Anisah W. Ghoorah; Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (Bioinform., 2011)

Formal Concept Analysis for the Interpretation of Relational Learning Applied on 3D Protein-binding Sites. - Emmanuel Bresso; Renaud Grisoni; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (KDIR, 2012)

ILP Characterization of 3D Protein-Binding Sites and FCA-Based Interpretation. - Emmanuel Bresso; Renaud Grisoni; Marie-Dominique Devignes; Amedeo Napoli; Malika Smaïl-Tabbone (IC3K, 2012)

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. - Marie-Dominique Devignes; Sidahmed Benabderrahmane; Malika Smaïl-Tabbone; Amedeo Napoli; Olivier Poch (Int. J. Comput. Biol. Drug Des., 2012)

Clustering optimal de gènes fondé sur une mesure de similarité sémantique. - Rachid Hafiane; Malika Smaïl-Tabbone; Marie-Dominique Devignes; Salvatore Tabbone (CORIA, 2013)

Integrative relational Machine-Learning Approach for Understanding Drug Side-Effect Profiles. - Emmanuel Bresso; Renaud Grisoni; Gino Marchetti; Arnaud Sinan Karaboga; Michel Souchet; Marie-Dominique Devignes; Malika Smaïl-Tabbone (BMC Bioinform., 2013)

Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability. - Gabin Personeni; Simon Daget; Céline Bonnet; Philippe Jonveaux; Marie-Dominique Devignes; Malika Smaïl-Tabbone; Adrien Coulet (DILS, 2014)

ECCB 2014: The 13th European Conference on Computational Biology. - Marie-Dominique Devignes; Yves Moreau (Bioinform., 2014)

KBDOCK 2013: a spatial classification of 3D protein domain family interactions. - Anisah W. Ghoorah; Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (Nucleic Acids Res., 2014)

Kbdock - Searching and Organising the Structural Space of Protein-Protein Interactions. - Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (ERCIM News, 2016)

Associating Gene Ontology Terms with Pfam Protein Domains. - Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; David W. Ritchie (IWBBIO (2), 2017)

Discovering associations between adverse drug events using pattern structures and ontologies. - Gabin Personeni; Emmanuel Bresso; Marie-Dominique Devignes; Michel Dumontier; Malika Smaïl-Tabbone; Adrien Coulet (J. Biomed. Semant., 2017)

ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. - Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; David W. Ritchie (BMC Bioinform., 2017)

Neighborhood-Based Label Propagation in Large Protein Graphs. - Sabeur Aridhi; Seyed Ziaeddin Alborzi; Malika Smaïl-Tabbone; Marie-Dominique Devignes; David W. Ritchie (CoRR, 2017)

Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. - Gabin Personeni; Marie-Dominique Devignes; Malika Smaïl-Tabbone; Philippe Jonveaux; Céline Bonnet; Adrien Coulet (SWAT4LS, 2018)

Computational discovery of direct associations between GO terms and protein domains. - Seyed Ziaeddin Alborzi; David W. Ritchie; Marie-Dominique Devignes (BMC Bioinform., 2018)

Explaining Multicriteria Decision Making with Formal Concept Analysis. - Alexandre Bazin; Miguel Couceiro; Marie-Dominique Devignes; Amedeo Napoli (CLA, 2020)

Graph Based Automatic Protein Function Annotation Improved by Semantic Similarity. - Bishnu Sarker; Navya Khare; Marie-Dominique Devignes; Sabeur Aridhi (IWBBIO, 2020)

An Approach to Identifying the Most Predictive and Discriminant Features in Supervised Classification Problems. - Alexandre Bazin; Miguel Couceiro; Marie-Dominique Devignes; Amedeo Napoli (ICCS, 2021)

PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. - Seyed Ziaeddin Alborzi; Amina Ahmed Nacer; Hiba Najjar; David W. Ritchie; Marie-Dominique Devignes (PLoS Comput. Biol., 2021)

A Semi-supervised Graph Deep Neural Network for Automatic Protein Function Annotation. - Akrem Sellami; Bishnu Sarker; Salvatore Tabbone; Marie-Dominique Devignes; Sabeur Aridhi (IWBBIO (2), 2022)

Improving automatic GO annotation with semantic similarity. - Bishnu Sarker; Navya Khare; Marie-Dominique Devignes; Sabeur Aridhi (BMC Bioinform., 2022)

Steps towards causal Formal Concept Analysis. - Alexandre Bazin; Miguel Couceiro; Marie-Dominique Devignes; Amedeo Napoli (Int. J. Approx. Reason., 2022)

Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project. - Emmanuel Bresso; Joao-Pedro Ferreira; Nicolas Girerd; Masatake Kobayashi; Grégoire Preud'homme; Patrick Rossignol; Fayez Zannad; Marie-Dominique Devignes; Malika Smaïl-Tabbone (J. Biomed. Informatics, 2022)

Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. - 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 (J. Chem. Inf. Model., 2022)

On the design of a similarity function for sparse binary data with application on protein function annotation. - 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 (Knowl. Based Syst., 2022)

FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards. - Alban Gaignard; Thomas Rosnet; Frédéric de Lamotte; Vincent Lefort; Marie-Dominique Devignes (J. Biomed. Semant., 2023)

GEODES: Geometric Descriptors for the Assessment of Global and Local Flexibility of Proteins During Molecular Dynamics Simulation. - Karina Pats; Igor Glukhov; Stepan Petrosian; Maria Mamaeva; Alexey A. Sergushichev; Marie-Dominique Devignes; Ferdinand Molnár (IEEE Access, 2025)