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2023
[j23]
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Alban Gaignard, Thomas Rosnet, Frédéric de Lamotte, Vincent Lefort, Marie-Dominique Devignes:
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards. J. Biomed. Semant. 14(1): 7 (2023)
2022
[j22]
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Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi:
Improving automatic GO annotation with semantic similarity. BMC Bioinform. 23-S(2): 433 (2022)
[j21]
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Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli:
Steps towards causal Formal Concept Analysis. Int. J. Approx. Reason. 142: 338-348 (2022)
[j20]
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Emmanuel Bresso, Joao-Pedro Ferreira, Nicolas Girerd, Masatake Kobayashi, Grégoire Preud'homme, Patrick Rossignol, Fayez Zannad, Marie-Dominique Devignes, Malika Smaïl-Tabbone:
Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project. J. Biomed. Informatics 135: 104212 (2022)
[j19]
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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:
Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. J. Chem. Inf. Model. 62(12): 3107-3122 (2022)
[j18]
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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:
On the design of a similarity function for sparse binary data with application on protein function annotation. Knowl. Based Syst. 238: 107863 (2022)
2021
[j17]
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Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes:
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PLoS Comput. Biol. 17(8) (2021)
2018
[j16]
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Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes:
Computational discovery of direct associations between GO terms and protein domains. BMC Bioinform. 19-S(14): 53-66 (2018)
2017
[j15]
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  - journals/biomedsem/PersoneniBDDSC17
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Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet:
Discovering associations between adverse drug events using pattern structures and ontologies. J. Biomed. Semant. 8(1): 29:1-29:13 (2017)
[j14]
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Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. BMC Bioinform. 18(1): 107:1-107:11 (2017)
2014
[j13]
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Marie-Dominique Devignes, Yves Moreau:
ECCB 2014: The 13^th European Conference on Computational Biology. Bioinform. 30(17): 345-348 (2014)
[j12]
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Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie:
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res. 42(Database-Issue): 389-395 (2014)
2013
[j11]
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Emmanuel Bresso, Renaud Grisoni, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Marie-Dominique Devignes, Malika Smaïl-Tabbone:
Integrative relational Machine-Learning Approach for Understanding Drug Side-Effect Profiles. BMC Bioinform. 14: 207 (2013)
2012
[j10]
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Marie-Dominique Devignes, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch:
Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. Int. J. Comput. Biol. Drug Des. 5(3/4): 245-260 (2012)
2011
[j9]
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Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie:
Spatial clustering of protein binding sites for template based protein docking. Bioinform. 27(20): 2820-2827 (2011)
2010
[j8]
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Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes:
IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinform. 11: 588 (2010)
[j7]
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Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Emmanuel Bresso, Amedeo Napoli, Malika Smaïl-Tabbone:
BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery. Int. J. Metadata Semant. Ontologies 5(3): 184-193 (2010)
[j6]
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Leo Ghemtio, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Michel Souchet, Vincent Leroux, Bernard Maigret:
Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case. J. Chem. Inf. Model. 50(5): 701-715 (2010)
[j5]
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  - journals/nar/MacindoeMVDR10
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Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie:
HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res. 38(Web-Server-Issue): 445-449 (2010)
2009
[j4]
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Saliha Yilmaz, Philippe Jonveaux, Cedric Bicep, Laurent Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes:
Gene-disease relationship discovery based on model-driven data integration and database view definition. Bioinform. 25(2): 230-236 (2009)
2008
[j3]
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Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes:
Ontology-guided data preparation for discovering genotype-phenotype relationships. BMC Bioinform. 9(S-4) (2008)
2006
[j2]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Treillis de concepts et ontologies pour interroger l'annuaire de sources de données biologiques BioRegistry. Ingénierie des Systèmes d Inf. 11(1): 39-60 (2006)
2002
[j1]
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Marie-Dominique Devignes, André Schaaff, Malika Smaïl:
Collecte et intégration de données biologiques hétérogènes sur le web. Ingénierie des Systèmes d Inf. 7(1-2): 45-61 (2002)

Conference and Workshop Papers

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2022
[c29]
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  - conf/iwbbio/SellamiSTDA22
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Akrem Sellami, Bishnu Sarker, Salvatore Tabbone, Marie-Dominique Devignes, Sabeur Aridhi:
A Semi-supervised Graph Deep Neural Network for Automatic Protein Function Annotation. IWBBIO (2) 2022: 153-166
2021
[c28]
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  - conf/iccs/BazinCDN21
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Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli:
An Approach to Identifying the Most Predictive and Discriminant Features in Supervised Classification Problems. ICCS 2021: 48-56
2020
[c27]
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  - conf/cla/BazinCDN20
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Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli:
Explaining Multicriteria Decision Making with Formal Concept Analysis. CLA 2020: 119-130
[c26]
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  - conf/iwbbio/SarkerKDA20
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Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi:
Graph Based Automatic Protein Function Annotation Improved by Semantic Similarity. IWBBIO 2020: 261-272
2018
[c25]
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  - conf/swat4ls/PersoneniDSJBC18
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Gabin Personeni, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jonveaux, Céline Bonnet, Adrien Coulet:
Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. SWAT4LS 2018
2017
[c24]
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Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
Associating Gene Ontology Terms with Pfam Protein Domains. IWBBIO (2) 2017: 127-138
2014
[c23]
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  - conf/dils/PersoneniDBJDSC14
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Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Adrien Coulet:
Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability. DILS 2014: 16-31
2013
[c22]
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  - conf/coria/RachidSDT13
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Rachid Hafiane, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Salvatore Tabbone:
Clustering optimal de gènes fondé sur une mesure de similarité sémantique. CORIA 2013: 323-336
2012
[c21]
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Emmanuel Bresso, Renaud Grisoni, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
ILP Characterization of 3D Protein-Binding Sites and FCA-Based Interpretation. IC3K 2012: 84-100
[c20]
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Emmanuel Bresso, Renaud Grisoni, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Formal Concept Analysis for the Interpretation of Relational Learning Applied on 3D Protein-binding Sites. KDIR 2012: 111-120
2011
[c19]
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Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch:
Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis. BIBM Workshops 2011: 201-208
[c18]
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Emmanuel Bresso, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Amedeo Napoli, Marie-Dominique Devignes:
Use of Domain Knowledge for Dimension Reduction - Application to Mining of Drug Side Effects. KDIR 2011: 271-276
2010
[c17]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Using Domain Knowledge to Guide Lattice-based Complex Data Exploration. ECAI 2010: 847-852
[c16]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Connaissances de domaine et treillis de concepts pour l'exploration progressive de données complexes. IC 2010: 233-244
2009
[c15]
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Leo Ghemtio, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Michel Souchet, Bernard Maigret:
A KDD Approach for Designing Filtering Strategies to Improve Virtual Screening. KDIR 2009: 146-151
[c14]
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Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch, Ngoc-Hoan Nguyen, Wolfgang Raffelsberger:
Analyse de données transcriptomiques: Modélisation floue de profils d'expression différentielle et analyse fonctionnelle. INFORSID 2009: 413-428
2008
[c13]
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Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes:
Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics. Description Logics 2008
[c12]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval. ECAI 2008: 127-131
[c11]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Extending Attribute Dependencies for Lattice-Based Querying and Navigation. ICCS 2008: 189-202
[c10]
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Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Amedeo Napoli, Malika Smaïl-Tabbone:
BioRegistry: automatic extraction of metadata for biological database retrieval and discovery. iiWAS 2008: 456-461
[c9]
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Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes:
Role Assertion Analysis: a proposed method for ontology refinement through assertion learning. STAIRS 2008: 47-58
2007
[c8]
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Traitement d'attributs inter-dépendants pour la recherche d'information par treillis. Actes d'IC 2007: 109-121
[c7]
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Marie-Dominique Devignes, Malika Smaïl-Tabbone:
Workshop PC Chairs' Message. WISE Workshops 2007: 3-4
2006
[c6]
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Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes:
SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies. DILS 2006: 82-93
[c5]
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Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes:
Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. OTM Workshops (1) 2006: 648-657
2005
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Malika Smaïl-Tabbone, Shazia Osman, Nizar Messai, Amedeo Napoli, Marie-Dominique Devignes:
BioRegistry: A Structured Metadata Repository for Bioinformatic Databases. CompLife 2005: 46-56
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Méthode sémantique pour la classification et l'iinterrogation de sources de données biologiques. EGC (Ateliers) 2005: 43-48
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Querying a Bioinformatic Data Sources Registry with Concept Lattices. ICCS 2005: 323-336
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Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone:
Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de données biologiques (BioRegistry). INFORSID 2005: 587-602

Informal and Other Publications

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2017
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Sabeur Aridhi, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, Marie-Dominique Devignes, David W. Ritchie:
Neighborhood-Based Label Propagation in Large Protein Graphs. CoRR abs/1708.07074 (2017)
2016
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Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie:
Kbdock - Searching and Organising the Structural Space of Protein-Protein Interactions. ERCIM News 2016(104) (2016)
2005
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  - journals/corr/abs-cs-0506017
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Nizar Messai, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli:
Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de données biologiques (BioRegistry). CoRR abs/cs/0506017 (2005)

Coauthor Index

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