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Coordonnées
Campus Scientifique
Bd des Aiguillettes
BP 239
54506 Vandoeuvre-lès-Nancy Cedex
+33 3 83 59 20 65
Territoire
Lorraine
Statut
Chercheur
Affiliation
Projets
Intégration sémantique et extraction de connaissances guidée par les connaissances du domaine pour l'interprétation des résultats de l'analyse transcriptomique des cancers colo-rectaux. (SEMCRC)
2007 - Porteur du projet : Dr DEVIGNES Marie-Dominique - Partenaire : Dr POCH Olivier
Publications
HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations.
Amaya-Ramirez D, Devriese M, Lhotte R, Usureau C, Smaïl-Tabbone M, Taupin JL, Devignes MD
Bioinform Adv. 2024 12 5;4(1):vbae186
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards.
Gaignard A, Rosnet T, De Lamotte F, Lefort V, Devignes MD
J Biomed Semantics. 2023 07 1;14(1):7
CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment.
Dhondge H, Chauvot de Beauchêne I, Devignes MD
Bioinform Adv. 2023 06 27;3(1):vbad081
Experiences with a training DSW knowledge model for early-stage researchers.
Devignes MD, Smaïl-Tabbone M, Dhondge H, Dolcemascolo R, Gavaldá-García J, Higuera-Rodriguez RA, Kravchenko A, Roca Martínez J, Messini N, Pérez-Ràfols A, Pérez Ropero G, Sperotto L, Chauvot de Beauchêne I, Vranken W
Open Res Eur. 2023 06 19;3:97
Molecular-evaluated and explainable drug repurposing for COVID-19 using ensemble knowledge graph embedding.
Islam MK, Amaya-Ramirez D, Maigret B, Devignes MD, Aridhi S, Smaïl-Tabbone M
Sci Rep. 2023 03 4;13(1):3643
Improving automatic GO annotation with semantic similarity.
Sarker B, Khare N, Devignes MD, Aridhi S
BMC Bioinformatics. 2022 12 12;23(Suppl 2):433
NT-proBNP and stem cell factor plasma concentrations are independently associated with cardiovascular outcomes in end-stage renal disease hemodialysis patients.
Rossignol P, Duarte K, Bresso E, A Å, Devignes MD, Eriksson N, Girerd N, Glerup R, Jardine AG, Holdaas H, Lamiral Z, Leroy C, Massy Z, März W, Krämer B, Wu PH, Schmieder R, Soveri I, Christensen JH, Svensson M, Zannad F, Fellström B
Eur Heart J Open. 2022 11;2(6):oeac069
Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project.
Bresso E, Ferreira JP, Girerd N, Kobayashi M, Preud'homme G, Rossignol P, Zannad F, Devignes MD, Smaïl-Tabbone M
J Biomed Inform. 2022 09 28;:104212
Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis.
Gheeraert A, Vuillon L, Chaloin L, Moncorgé O, Very T, Perez S, Leroux V, Chauvot de Beauchêne I, Mias-Lucquin D, Devignes MD, Rivalta I, Maigret B
J Chem Inf Model. 2022 06 27;62(12):3107-3122
Machine Learning-Derived Echocardiographic Phenotypes Predict Heart Failure Incidence in Asymptomatic Individuals.
Kobayashi M, Huttin O, Magnusson M, Ferreira JP, Bozec E, Huby AC, Preud'homme G, Duarte K, Lamiral Z, Dalleau K, Bresso E, Smaïl-Tabbone M, Devignes MD, Nilsson PM, Leosdottir M, Boivin JM, Zannad F, Rossignol P, Girerd N,
JACC Cardiovasc Imaging. 2021 Sep 8;:
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
Alborzi SZ, Ahmed Nacer A, Najjar H, Ritchie DW, Devignes MD
PLoS Comput Biol. 2021 Aug 9;17(8):e1008844
Head-to-head comparison of clustering methods for heterogeneous data: a simulation-driven benchmark.
Preud'homme G, Duarte K, Dalleau K, Lacomblez C, Bresso E, Smaïl-Tabbone M, Couceiro M, Devignes MD, Kobayashi M, Huttin O, Ferreira JP, Zannad F, Rossignol P, Girerd N
Sci Rep. 2021 Feb 18;11(1):4202
Sex differences in circulating proteins in heart failure with preserved ejection fraction.
Stienen S, Ferreira JP, Kobayashi M, Preud'homme G, Dobre D, Machu JL, Duarte K, Bresso E, Devignes MD, Andrés NL, Girerd N, Aakhus S, Ambrosio G, Rocca HB, Fontes-Carvalho R, Fraser AG, van Heerebeek L, de Keulenaer G, Marino P, McDonald K, Mebazaa A, Papp Z, Raddino R, Tschöpe C, Paulus WJ, Zannad F, Rossignol P
Biol Sex Differ. 2020 Aug 24;11(1):47
Circulating plasma proteins and new-onset diabetes in a population-based study: proteomic and genomic insights from the STANISLAS cohort.
Ferreira JP, Lamiral Z, Xhaard C, Duarte K, Bresso E, Devignes MD, Lefloch E, Roulland CD, Deleuze JF, Wagner S, Guerci B, Girerd N, Zannad F, Boivin JM, Rossignol P
Eur. J. Endocrinol.. 2020 Jun 1;:
Enhanced clinical phenotyping by mechanistic bioprofiling in heart failure with preserved ejection fraction: insights from the MEDIA-DHF study (The Metabolic Road to Diastolic Heart Failure).
Stienen S, Ferreira JP, Kobayashi M, Preud'homme G, Dobre D, Machu JL, Duarte K, Bresso E, Devignes MD, López N, Girerd N, Aakhus S, Ambrosio G, Brunner-La Rocca HP, Fontes-Carvalho R, Fraser AG, van Heerebeek L, Heymans S, de Keulenaer G, Marino P, McDonald K, Mebazaa A, Papp Z, Raddino R, Tschöpe C, Paulus WJ, Zannad F, Rossignol P
Biomarkers. 2020 Feb 16;:1-11
PGxCorpus, a manually annotated corpus for pharmacogenomics.
Legrand J, Gogdemir R, Bousquet C, Dalleau K, Devignes MD, Digan W, Lee CJ, Ndiaye NC, Petitpain N, Ringot P, Smaïl-Tabbone M, Toussaint Y, Coulet A
Sci Data. 2020 Jan 2;7(1):3
Insulin-like growth factor binding protein 2: A prognostic biomarker for heart failure hardly redundant with natriuretic peptides.
Girerd N, Bresso E, Devignes MD, Rossignol P
Int. J. Cardiol.. 2019 Nov 13;:
Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Raghavendra Maddhuri Venkata Subraman S, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Echartea MER, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, DapkŪnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ
Proteins. 2019 Oct 14;:
Application of Artificial Intelligence to Gastroenterology and Hepatology.
Le Berre C, Sandborn WJ, Aridhi S, Devignes MD, Fournier L, Smaïl-Tabbone M, Danese S, Peyrin-Biroulet L
Gastroenterology. 2019 Oct 5;:
Extended persistence of antiphospholipid antibodies beyond the 12-week time interval: Association with baseline antiphospholipid antibodies titres.
Devignes J, Smaïl-Tabbone M, Hervé A, Cagninacci G, Devignes MD, Lecompte T, Zuily S, Wahl D
Int J Lab Hematol. 2019 Sep 15;:
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses.
Ferreira JP, Pizard A, Machu JL, Bresso E, Rocca HB, Girerd N, Leroy C, González A, Diez J, Heymans S, Devignes MD, Rossignol P, Zannad F,
Clin Res Cardiol. 2019 May 6;:
Characterization of a relaxase belonging to the MOB family, a widespread family in Firmicutes mediating the transfer of ICEs.
Soler N, Robert E, Chauvot de Beauchêne I, Monteiro P, Libante V, Maigret B, Staub J, Ritchie DW, Guédon G, Payot S, Devignes MD, Leblond-Bourget N
Mob DNA. 2019 ;10:18
Computational discovery of direct associations between GO terms and protein domains.
Alborzi SZ, Ritchie DW, Devignes MD
BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):413
Discovering associations between adverse drug events using pattern structures and ontologies.
Personeni G, Bresso E, Devignes MD, Dumontier M, Smaïl-Tabbone M, Coulet A
J Biomed Semantics. 2017 Aug;8(1):29
Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.
El Houasli M, Maigret B, Devignes MD, Ghoorah AW, Grudinin S, Ritchie DW
Proteins. 2017 Mar;85(3):463-469
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
Alborzi SZ, Devignes MD, Ritchie DW
BMC Bioinformatics. 2017 Feb;18(1):107
A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.
Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N
Front Microbiol. 2017 ;8:443
Low-Dose Alkylphenol Exposure Promotes Mammary Epithelium Alterations and Transgenerational Developmental Defects, But Does Not Enhance Tumorigenic Behavior of Breast Cancer Cells.
Chamard-Jovenin C, Thiebaut C, Chesnel A, Bresso E, Morel C, Smail-Tabbone M, Devignes MD, Boukhobza T, Dumond H
Front Endocrinol (Lausanne). 2017 ;8:272
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ
Proteins. 2016 Sep;84 Suppl 1:323-48
Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.
Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW
Methods Mol. Biol.. 2016 ;1415:91-105
A structure-based classification and analysis of protein domain family binding sites and their interactions.
Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW
Biology (Basel). 2015 Apr;4(2):327-43
New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.
Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N
Front Microbiol. 2015 ;6:1483
ECCB 2014: The 13th European Conference on Computational Biology.
Devignes MD, Moreau Y
Bioinformatics. 2014 Sep 1;30(17):i345-8
KBDOCK 2013: a spatial classification of 3D protein domain family interactions.
Ghoorah AW, Devignes MD, Smail-Tabbone M, Ritchie DW
Nucleic Acids Res. 2014 Jan;42(Database issue):D389-95
Prediction of monomer isomery in Florine: a workflow dedicated to nonribosomal peptide discovery.
Caradec T, Pupin M, Vanvlassenbroeck A, Devignes MD, Smail-Tabbone M, Jacques P, Leclere V
PLoS One. 2014 Jan 21;9(1):e85667
Extended spectrum of MBD5 mutations in neurodevelopmental disorders.
Bonnet C, Ali Khan A, Bresso E, Vigouroux C, Beri M, Lejczak S, Deemer B, Andrieux J, Philippe C, Moncla A, Giurgea I, Devignes MD, Leheup B, Jonveaux P
Eur J Hum Genet. 2013 Dec;21(12):1457-61
Protein docking using case-based reasoning.
Ghoorah AW, Devignes MD, Smail-Tabbone M, Ritchie DW
Proteins. 2013 Dec;81(12):2150-8
Integrative relational machine-learning for understanding drug side-effect profiles.
Bresso E, Grisoni R, Marchetti G, Karaboga AS, Souchet M, Devignes MD, Smail-Tabbone M
BMC Bioinformatics. 2013 Jun 26;14:207
Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.
Devignes MD, Benabderrahmane S, Smail-Tabbone M, Napoli A, Poch O
Int J Comput Biol Drug Des. 2012;5(3-4):245-60
Spatial clustering of protein binding sites for template based protein docking.
Ghoorah AW, Devignes MD, Smail-Tabbone M, Ritchie DW
Bioinformatics. 2011 Oct 15;27(20):2820-7
HexServer: an FFT-based protein docking server powered by graphics processors.
Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W445-9
Comparison of three preprocessing filters efficiency in virtual screening: identification of new putative LXRbeta regulators as a test case.
Ghemtio L, Devignes MD, Smail-Tabbone M, Souchet M, Leroux V, Maigret B
J Chem Inf Model. 2010 May 24;50(5):701-15.
Activation of peroxisome proliferator-activated receptor gamma by human cytomegalovirus for de novo replication impairs migration and invasiveness of cytotrophoblasts from early placentas.
Rauwel B, Mariame B, Martin H, Nielsen R, Allart S, Pipy B, Mandrup S, Devignes MD, Evain-Brion D, Fournier T, Davrinche C
J Virol. 2010 Mar;84(6):2946-54
IntelliGO: a new vector-based semantic similarity measure including annotation origin.
Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD
BMC Bioinformatics. 2010 Dec 1;11:588.
Gene-disease relationship discovery based on model-driven data integration and database view definition.
Yilmaz S, Jonveaux P, Bicep C, Pierron L, Smail-Tabbone M, Devignes MD
Bioinformatics. 2009 Jan 15;25(2):230-6
Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment.
Beautrait A, Leroux V, Chavent M, Ghemtio L, Devignes MD, Smail-Tabbone M, Cai W, Shao X, Moreau G, Bladon P, Yao J, Maigret B
J Mol Model. 2008 Feb;14(2):135-48
Ontology-guided data preparation for discovering genotype-phenotype relationships.
Coulet A, Smail-Tabbone M, Benlian P, Napoli A, Devignes MD
BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S3.
Immunoselection and characterization of a human genomic PPAR binding fragment located within POTE genes.
Murad H, Collet P, Brunner E, Schohn H, Becuwe P, Devignes MD, Dauca M, Domenjoud L
Biochimie. 2007 Mar;89(3):329-36
Effects of PPAR and RXR ligands in semaphorin 6B gene expression of human MCF-7 breast cancer cells.
Murad H, Collet P, Huin-Schohn C, Al-Makdissy N, Kerjan G, Chedotal A, Donner M, Devignes MD, Becuwe P, Schohn H, Domenjoud L, Dauca M
Int J Oncol. 2006 Apr;28(4):977-84.
SNP-Converter: an Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies
Coulet A, Smail-Tabbone M, Benlian P, Napoli A, Devignes MD
in Proceedings of the third International Workshop on Data Integration in the Life Sciences 2006, Hinxton, UK (DILS'06), Lecture Notes in Computer Science 4075, Springer, pages 82-93, 2006
SNP-converter: An ontology-based solution to reconcile heterogeneous SNP descriptions for pharmacogenomic studies.
Coulet A, Smail-Tabbone M, Benlian P, Napoli A, Devignes MD
Lect Notes Comput Sc. 2006;4075:82-93.
BioRegistry : a structured metadata repository for bioinformatic databases
Sma
in First International Symposium on Computational Life Science - CompLife 2005, Konstanz, Germany, Lecture Notes in Computer Science 3695, pages 46-56, 2005.
BioRegistry: A structured metadata repository for bioinformatic databases.
Smail-Tabbone M, Osman S, Messai N, Napoli A, Devignes MD
Lect Notes Comput Sc. 2005;3695:46-56.
The human semaphorin 6B gene is down regulated by PPARs.
Collet P, Domenjoud L, Devignes MD, Murad H, Schohn H, Dauça M
Genomics. 2004 Jun;83(6):1141-50
