Publis – Marie-Dominique DEVIGNES

Liste Complète (1979-2023) via PubMed NCBI

Liste Complète (1999-2023) retournée par HAL-INRIA

Publications HAL de Marie-Dominique,Devignes; Marie-Dominique,Morch; Marie-Dominique,Morch-Devignes; Marie-Dominique,Devignes-Morch

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Criteria : Author : « Marie-Dominique,Devignes; Marie-Dominique,Morch; Marie-Dominique,Morch-Devignes; Marie-Dominique,Devignes-Morch », Publication year >= « 1980 » to « 2023 »
Number of occurrences founded : 146.

titre: FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards
auteur: Alban Gaignard, Thomas Rosnet, Frédéric de Lamotte, Vincent Lefort, Marie-Dominique Devignes
article: Journal of Biomedical Semantics, 2023, 14 (1), pp.7. ⟨10.1186/s13326-023-00289-5⟩
typdoc: Journal articles

titre: Molecular-evaluated and explainable drug repurposing for COVID-19 using ensemble knowledge graph embedding
auteur: Md Kamrul Islam, Diego Amaya-Ramirez, Bernard Maigret, Marie-Dominique Devignes, Sabeur Aridhi, Malika Smaïl-Tabbone
article: Scientific Reports, 2023, 13 (1), pp.3643. ⟨10.1038/s41598-023-30095-z⟩
typdoc: Journal articles

titre: CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment
auteur: Hrishikesh Dhondge, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes
article: Bioinformatics Advances, 2023, 3 (1), ⟨10.1093/bioadv/vbad081⟩
typdoc: Journal articles

titre: Experiences with a training DSW knowledge model for early-stage researchers
auteur: Marie-Dominique Devignes, Malika Smaïl-Tabbone, Hrishikesh Dhondge, Roswitha Dolcemascolo, Jose Gavaldá-García, R. Anahí Higuera-Rodriguez, Anna Kravchenko, Joel Roca Martínez, Niki Messini, Anna Pérez-Ràfols, Guillermo Pérez Ropero, Luca Sperotto, Isaure Chauvot de Beauchêne, Wim Vranken
article: Open Research Europe, 2023, 3, pp.97. ⟨10.12688/openreseurope.15609.1⟩
typdoc: Journal articles

titre: Improving automatic GO annotation with semantic similarity
auteur: Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
article: BMC Bioinformatics, 2022, 23 (S2), pp.433. ⟨10.1186/s12859-022-04958-7⟩
typdoc: Journal articles

titre: Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project
auteur: Emmanuel Bresso, Joao-Pedro Ferreira, Nicolas Girerd, Masatake Kobayashi, Grégoire Preud’homme, Patrick Rossignol, Fayez Zannad, Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: Journal of Biomedical Informatics, 2022, 135, pp.104212. ⟨10.1016/j.jbi.2022.104212⟩
typdoc: Journal articles

titre: Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis
auteur: 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
article: Journal of Chemical Information and Modeling, 2022, 62 (12), pp.3107-3122. ⟨10.1021/acs.jcim.2c00350⟩
typdoc: Journal articles

titre: Steps Towards Causal Formal Concept Analysis
auteur: Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
article: International Journal of Approximate Reasoning, 2022, 142, pp.338-348. ⟨10.1016/j.ijar.2021.12.007⟩
typdoc: Journal articles

titre: On the design of a similarity function for sparse binary data with application on protein function annotation
auteur: Marcelo Veras, Bishnu Sarker, Sabeur Aridhi, João Gomes, José Macêdo, Engelbert Mephu Nguifo, Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: Knowledge-Based Systems, 2022, 238, pp.107863. ⟨10.1016/j.knosys.2021.107863⟩
typdoc: Journal articles

titre: A Semi-supervised Graph Deep Neural Network for Automatic Protein Function Annotation
auteur: Akrem Sellami, Bishnu Sarker, Salvatore Tabbone, Marie-Dominique Devignes, Sabeur Aridhi
article: 9th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Jun 2022, Gran Canaria, Spain. pp.153-166, ⟨10.1007/978-3-031-07802-6_14⟩
typdoc: Conference papers

titre: CroMaSt: A workflow for domain family curation through cross-mapping of structural instances between protein domain databases
auteur: Hrishikesh Dhondge, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes
article: ECCB2022- 21st European Conference on Computational Biology, Sep 2022, Sitges, Spain. ⟨10.48546/WORKFLOWHUB.WORKFLOW.390.1⟩
typdoc: Poster communications

titre: Reduced structural flexibility of eplet amino acids in HLA proteins
auteur: Diego Amaya-Ramirez, Romain Lhotte, Magali Devriese, Constantin Hays, Jean-Luc Taupin, Marie-Dominique Devignes
article: ECCB 2022 21st European Conference on Computational Biology Planetary Health and Biodiversity, Sep 2022, Barcelona, Spain
typdoc: Poster communications

titre: FAIR-Checker : Checking and Inspecting metadata for FAIR bioinformatics resources
auteur: Thomas Rosnet, F de Lamotte, Marie-Dominique Devignes, Vincent Lefort, A Gaignard
article: Elixir AllHands 2022, Jun 2022, Amsterdam, Netherlands
typdoc: Poster communications

titre: Machine Learning-Derived Echocardiographic Phenotypes Predict Heart Failure Incidence in Asymptomatic Individuals
auteur: Masatake Kobayashi, Olivier Huttin, Martin Magnusson, João Pedro Ferreira, Erwan Bozec, Anne-Cecile Huby, Gregoire Preud’Homme, Kevin Duarte, Zohra Lamiral, Kevin Dalleau, Emmanuel Bresso, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Peter M Nilsson, Margret Leosdottir, Jean-Marc Boivin, Faiez Zannad, Patrick Rossignol, Nicolas Girerd
article: JACC: Cardiovascular Imaging, 2021, S1936-878X (21), pp.00556-8. ⟨10.1016/j.jcmg.2021.07.004⟩
typdoc: Journal articles

titre: Head-to-head comparison of clustering methods for heterogeneous data: a simulation-driven benchmark
auteur: Gregoire Preud’Homme, Kévin Duarte, Kevin Dalleau, Claire Lacomblez, Emmanuel Bresso, Malika Smaïl-Tabbone, Miguel Couceiro, Marie-Dominique Devignes, Masatake Kobayashi, Olivier Huttin, João Pedro Ferreira, Faiez Zannad, Patrick Rossignol, Nicolas Girerd
article: Scientific Reports, 2021, 11 (1), pp.4202. ⟨10.1038/s41598-021-83340-8⟩
typdoc: Journal articles

titre: PPIDomainMiner: Inferring domain-domain interactions from multiple sources of proteinprotein interactions
auteur: Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David Ritchie, Marie-Dominique Devignes
article: PLoS Computational Biology, 2021, 17 (8), pp.e1008844. ⟨10.1371/journal.pcbi.1008844⟩
typdoc: Journal articles

titre: A Hybrid Approach to Identifying the Most Predictive and Discriminant Features in Supervised Classification Problems
auteur: Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
article: ICCS 2021 – 26th International Conference on Conceptual Structures, Sep 2021, Virtual, France. ⟨10.1007/978-3-030-86982-3_4⟩
typdoc: Conference papers

titre: Prot-A-GAN: Automatic Protein Function Annotation using GAN-inspired Knowledge Graph Embedding
auteur: Bishnu Sarker, Marie-Dominique Devignes, Guy Wolf, Sabeur Aridhi
article: ICML 2021 – Workshop on Computational Biology, Jul 2021, Virtual, United States
typdoc: Conference papers

titre: Data-driven identification of structural patterns associated with RNA binding in RNA Recognition Motif domains
auteur: Hrishikesh Dhondge, Martínez Joel Roca, Vranken Wim, Marie-Dominique Devignes, Isaure Chauvot de Beauchêne
article: Student Council Symposium (SCS) 2021, Jul 2021, Virtual, France
typdoc: Poster communications

titre: Sex differences in circulating proteins in heart failure with preserved ejection fraction
auteur: Susan Stienen, Joao Pedro Ferreira, Masatake Kobayashi, Gregoire Preud’homme, Daniela Dobre, Jean-Loup Machu, Kévin Duarte, Emmanuel Bresso, Marie-Dominique Devignes, Natalia López Andrés, Nicolas Girerd, Svend Aakhus, Giuseppe Ambrosio, Hans-Peter Brunner-La Rocca, Ricardo Fontes-Carvalho, Alan Fraser, Loek van Heerebeek, Gilles de Keulenaer, Paolo Marino, Kenneth Mcdonald, Alexandre Mebazaa, Zoltàn Papp, Riccardo Raddino, Carsten Tschöpe, Walter Paulus, Faiez Zannad, Patrick Rossignol
article: Biology of Sex Differences, 2020, 11 (1), pp.47. ⟨10.1186/s13293-020-00322-7⟩
typdoc: Journal articles

titre: Circulating plasma proteins and new-onset diabetes in a population-based study: proteomic and genomic insights from the STANISLAS cohort
auteur: Joao Pedro Ferreira, Zohra Lamiral, Constance Xhaard, Kévin Duarte, Emmanuel Bresso, Marie-Dominique Devignes, Edith Le Floch, Claire Dandine Roulland, Jean-François Deleuze, Sandra Wagner, Bruno Guerci, Nicolas Girerd, Faiez Zannad, Jean-Marc Boivin, Patrick Rossignol
article: European Journal of Endocrinology, 2020, 183 (3), pp.285-295. ⟨10.1530/EJE-20-0246⟩
typdoc: Journal articles

titre: 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)
auteur: Susan Stienen, Joao Pedro Ferreira, Masatake Kobayashi, Gregoire Preud’Homme, Daniela Dobre, Jean-Loup Machu, Kévin Duarte, Emmanuel Bresso, Marie-Dominique Devignes, Natalia López Andrés, Nicolas Girerd, Svend Aakhus, Giuseppe Ambrosio, Hans-Peter Brunner-La Rocca, Ricardo Fontes-Carvalho, Alan G Fraser, Loek van Heerebeek, Stephane Heymans, Gilles de Keulenaer, Paolo Marino, Kenneth Mcdonald, Alexandre Mebazaa, Zoltàn Papp, Riccardo Raddino, Carsten Tschöpe, Walter Paulus, Faiez Zannad, Patrick Rossignol
article: Biomarkers, 2020, 25 (2), pp.201-211. ⟨10.1080/1354750X.2020.1727015⟩
typdoc: Journal articles

titre: Insulin-like growth factor binding protein 2: A prognostic biomarker for heart failure hardly redundant with natriuretic peptides
auteur: Nicolas Girerd, Emmanuel Bresso, Marie-Dominique Devignes, Patrick Rossignol
article: International Journal of Cardiology, 2020, 300, pp.252-254. ⟨10.1016/j.ijcard.2019.11.100⟩
typdoc: Journal articles

titre: PGxCorpus, a manually annotated corpus for pharmacogenomics
auteur: Joël Legrand, Romain Gogdemir, Cedric Bousquet, Kevin Dalleau, Marie-Dominique Devignes, William Digan, Chia-Ju Lee, Ndeye-Coumba Ndiaye, Nadine Petitpain, Patrice Ringot, Malika Smaïl-Tabbone, Yannick Toussaint, Adrien Coulet
article: Scientific Data , 2020, 7, pp.3. ⟨10.1038/s41597-019-0342-9⟩
typdoc: Journal articles

titre: Application of Artificial Intelligence to Gastroenterology and Hepatology
auteur: Catherine Le Berre, William J. Sandborn, Sabeur Aridhi, Marie-Dominique Devignes, Laure Fournier, Malika Smail-Tabbone, Silvio Danese, Laurent Peyrin-Biroulet
article: Gastroenterology, 2020, 158 (1), pp.76-94.e2. ⟨10.1053/j.gastro.2019.08.058⟩
typdoc: Journal articles

titre: Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO‑TARGETS case–control analyses
auteur: Joao Pedro Ferreira, Anne Pizard, Jean-Loup Machu, Emmanuel Bresso, Hans-Peter Brunner-Larocca, Nicolas Girerd, Céline Leroy, Arantxa González, Javier Díez, Stephane Heymans, Marie-Dominique Devignes, Patrick Rossignol, Faiez Zannad
article: Clinical Research in Cardiology, 2020, 109 (1), pp.22-33. ⟨10.1007/s00392-019-01480-4⟩
typdoc: Journal articles

titre: Explaining Multicriteria Decision Making with Formal Concept Analysis
auteur: Alexandre Bazin, Miguel Couceiro, Marie-Dominique Devignes, Amedeo Napoli
article: Concept Lattices and Applications 2020, Jun 2020, Tallinn, Estonia
typdoc: Conference papers

titre: Graph Based Automatic Protein Function Annotation Improved by Semantic Similarity
auteur: Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
article: IWBBIO 2020 – 8th International Work-Conference on Bioinformatics and Biomedical Engineering, May 2020, GRANADA, Spain. pp.261-272, ⟨10.1007/978-3-030-45385-5_24⟩
typdoc: Conference papers

titre: Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs
auteur: Nicolas Soler, Emilie Robert, Isaure Chauvot de Beauchêne, Philippe Monteiro, Virginie Libante, Bernard Maigret, Johan Staub, David W. Ritchie, Gérard Guédon, Sophie Payot, Marie-Dominique Devignes, Nathalie N. Leblond-Bourget
article: Mobile DNA, 2019, 10 (1), pp.1-16. ⟨10.1186/s13100-019-0160-9⟩
typdoc: Journal articles

titre: The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
auteur: Naihui Zhou, Yuxiang Jiang, Timothy Bergquist, Alexandra Lee, Balint Kacsoh, Alex Crocker, Kimberley Lewis, George Georghiou, Huy Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet Rifaioglu, Alperen Dalkiran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca Hurto, Peter Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, Jose Fernandez, Branislava Gemovic, Vladimir Perovic, Radoslav Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C Mchardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex Freitas, Magdalena Antczak, Fabio Fabris, Mark Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel S. Roche, Jonas Reeb, David Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage Black, Dane Jo, Erica Suh, Jonathan Dayton, Dallas Larsen, Ashton Omdahl, Liam Mcguffin, Danielle Brackenridge, Patricia Babbitt, Jeffrey Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian M Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven Brenner, Christine Orengo, Constance Jeffery, Giovanni Bosco, Deborah Hogan, Maria Martin, Claire O’donovan, Sean Mooney, Casey Greene, Predrag Radivojac, Iddo Friedberg
article: Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩
typdoc: Journal articles

titre: Blind prediction of homo‐ and hetero‐ protein complexes: The CASP13‐CAPRI experiment
auteur: Marc Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A.G. Chaleil, Tereza Gerguri, Paul Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐ran Liu, Xi‐ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng‐you Huang, Mireia Rosell, Luis Angel Rodríguez‐lumbreras, Miguel Romero‐durana, Lucía Díaz‐bueno, Juan Fernandez‐recio, Charles Christoffer, Genki Terashi, Woong‐hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subram, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathyn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain Moal, David Ritchie, Isaure Chauvot de Beauchêne, Bernard Maigret, Marie-Dominique Devignes, Maria Elisa Ruiz Echartea, Didier Barradas‐bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman‐duhovny, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Petras J. Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha Badal, Ilya A. Vakser, Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Zhiping Weng, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panos Koukos, Jorge Roel‐touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael Trellet, Adrien S.J. Melquiond, Li Xue, Brian Jiménez‐garcía, Charlotte Noort, Rodrigo Honorato, Alexandre M.J.J. Bonvin, Shoshana J. Wodak
article: Proteins – Structure, Function and Bioinformatics, 2019, 87 (12), pp.1200-1221. ⟨10.1002/prot.25838⟩
typdoc: Journal articles

titre: Extended persistence of antiphospholipid antibodies beyond the twelve‐week time interval: Association with baseline antiphospholipid antibodies titres
auteur: Jean Devignes, Malika Smaïl-Tabbone, Alex Hervé, Geoffroy Cagninacci, Marie-Dominique Devignes, Thomas Lecompte, Stéphane Zuily, Denis Wahl
article: International Journal of Laboratory Hematology, 2019, 41 (6), pp.726-730. ⟨10.1111/ijlh.13094⟩
typdoc: Journal articles

titre: The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus.
auteur: Charles Coluzzi, Julie Lao, Gérard Guédon, Marie-Dominique Devignes, Chloé Ambroset, Thomas Lacroix, Helene Chiapello, Sophie Payot, Nathalie N. Leblond-Bourget
article: 8th symposium on Antimicrobial Resistance in Animal and Environment, Jul 2019, Tours, France
typdoc: Conference papers

titre: The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus
auteur: Charles Coluzzi, Julie Lao, Gérard Guédon, Marie-Dominique Devignes, Chloé Ambroset, Thomas Lacroix, Helene Chiapello, Sophie Payot, Nathalie N. Leblond-Bourget
article: 4th International Workshop on Streptococcus suis, Jun 2019, Montréal, Canada.
typdoc: Poster communications

titre: Computational Discovery of Direct Associations between GO terms and Protein Domains
auteur: Seyed Ziaeddin Alborzi, David Ritchie, Marie-Dominique Devignes
article: BMC Bioinformatics, 2018, 19 (Suppl 14), pp.413. ⟨10.1186/s12859-018-2380-2⟩
typdoc: Journal articles

titre: Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach
auteur: Gabin Personeni, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jonveaux, Céline Bonnet, Adrien Coulet
article: Proceedings of the 11th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018), Dec 2018, Antwerp, Belgium
typdoc: Conference papers

titre: First steps toward finding relevant pathology-gene pairs using analogy
auteur: Marie-Dominique Devignes, Yohann Fransot, Yves Lepage, Jean Lieber, Emmanuel Nauer, Malika Smaïl-Tabbone
article: EvoCBR 2018 : Workshop on Evolutionary Computation and CBR at the International Conference on Case-Based Reasoning (ICCBR 2018), Jul 2018, Stockholm, Sweden
typdoc: Conference papers

titre: Découverte d’associations entre Evénements Indésirables Médicamenteux par les structures de patrons et les ontologies
auteur: Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
article: Journée I.A. et Santé, Jul 2018, Nancy, France
typdoc: Conference papers

titre: PPI DomainMiner: predicting domain-domain interactions from protein-protein interactions using tripartite graph modeling and vector similarity
auteur: Seyed Ziaeddin Alborzi, Sabeur Aridhi, Dave Ritchie, Marie-Dominique Devignes
article: ECCB 2018 – 17th European Conference on Computational Biology, Sep 2018, Athènes, Greece
typdoc: Poster communications

titre: A data science approach for exploring differential expression profiles of genes in transcriptomic studies-Application to the understanding of ageing in obese and lean rats in the FIGHT-HF project
auteur: Emmanuel Bresso, Claire Lacomblez, Anne Pizard, Patrick Rossignol, Faiez Zannad, Malika Smaïl-Tabbone, Marie-Dominique Devignes
article: JOBIM 2018 – Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France
typdoc: Poster communications

titre: ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains
auteur: Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie
article: BMC Bioinformatics, 2017, 18 (1), pp.107. ⟨10.1186/s12859-017-1519-x⟩
typdoc: Journal articles

titre: Low-dose alkylphenol exposure promotes mammary epithelium alterations and transgenerational developmental defects, but does not enhance tumorigenic behaviour of breast cancer cells
auteur: Clémence Chamard-Jovenin, Charlène Thiébaut, Amand Chesnel, Emmanuel Bresso, Chloé Morel, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Taha Boukhobza, Hélène Dumond
article: Frontiers in Endocrinology, 2017, 8, pp.272. ⟨10.3389/fendo.2017.00272⟩
typdoc: Journal articles

titre: A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins
auteur: Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Chloé C. Ambroset, Valentin Loux, Thomas Lacroix, Sophie Payot, Nathalie N. Leblond-Bourget
article: Frontiers in Microbiology, 2017, 8, pp.16. ⟨10.3389/fmicb.2017.00443⟩
typdoc: Journal articles

titre: Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models
auteur: Marwa El Houasli, Bernard Maigret, Marie-Dominique Devignes, Anisah W Ghoorah, Sergei Grudinin, David Ritchie
article: Proteins: Structure, Function, and Genetics, 2017, Special Issue: Sixth Meeting on the Critical Assessment of Predicted Interactions 85 (3), pp.463-469. ⟨10.1002/prot.25182⟩
typdoc: Journal articles

titre: Discovering associations between adverse drug events using pattern structures and ontologies
auteur: Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
article: Journal of Biomedical Semantics, 2017, 93, pp.539 – 546. ⟨10.1186/s13326-017-0137-x⟩
typdoc: Journal articles

titre: Validation de ER$\alpha comme marqueur prédictif de susceptibilité aux nonylphénols in vivo et in vitro
auteur: Clémence Chamard-Jovenin, Charlène Thiébaut, Amand Chesnel, Emmanuel Bresso, Chloé Morel, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Taha Boukhobza, Hélène Dumond
article: Journée PNR-EST de l’ANSES, Oct 2017, Paris, France
typdoc: Conference papers

titre: Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations
auteur: Seyed Ziaeddin Alborzi, Sabeur Aridhi, Marie-Dominique Devignes, Rabie Saidi, Alexandre Renaux, Maria-Jesus Martin, David W. Ritchie
article: Function-SIG ISMB/ECCB 2017, biofunctionprediction.org, Jul 2017, Prague, Czech Republic
typdoc: Conference papers

titre: Associating Gene Ontology Terms with Pfam Protein Domains
auteur: Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David Ritchie
article: 5th International Work-Conference on Bioinformatics and Biomedical Engineering – IWBBIO 2017, Apr 2017, Granada, Spain. pp.127-138, ⟨10.1007/978-3-319-56154-7_13⟩
typdoc: Conference papers

titre: Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations
auteur: Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Sabeur Aridhi, Rabie Saidi, Alexandre Renaux, Maria J. Martin, David W. Ritchie
article: Function-SIG ISMB/ECCB 2017, Jul 2017, Prague, Czech Republic. 2017
typdoc: Poster communications

titre: Neighborhood-Based Label Propagation in Large Protein Graphs
auteur: Sabeur Aridhi, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, Marie-Dominique Devignes, David Ritchie
article: Function SIG @ ISMB/ECCB 2017, Jul 2017, Prague, Czech Republic. pp.2
typdoc: Poster communications

titre: Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment
auteur: Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovy, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A.G. Chaleil, Paul A Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra Negi S., Thom Vreven, Brian G Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Zhiping Weng, Raphaël Guérois, Anna Vangone, João P.G.L.M. Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S. J. Melquiond, Koen Visscher, Panagiotis L Kastritis, Alexandre M. J. J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Sheng, Lenna X. Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodríguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebbecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H Moal, Juan Fernández-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J Wodak
article: Proteins – Structure, Function and Bioinformatics, 2016, Special Issue: Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, 84 (S1), pp.323-348. ⟨10.1002/prot.25007⟩
typdoc: Journal articles

titre: Kbdock – Searching and organising the structural space of protein-protein interactions
auteur: Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie
article: ERCIM News, 2016, 104, pp.24-25
typdoc: Journal articles

titre: New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration
auteur: Chloé C. Ambroset, Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Valentin Loux, Thomas Lacroix, Sophie Payot, Nathalie N. Leblond-Bourget
article: Frontiers in Microbiology, 2016, 6 (6), pp.1483. ⟨10.3389/fmicb.2015.01483⟩
typdoc: Journal articles

titre: Characterization of the ICESt3 relaxase active site indicates evolutionary relationship between MOBT relaxases and rolling circle replication proteins of the Rep-trans family.
auteur: Nicolas Soler, Philippe Monteiro, Emilie Robert, Marie-Dominique Devignes, Bernard Maigret, Dave Ritchie, Gérard Guédon, Sophie Payot, Nathalie N. Leblond-Bourget
article: Type IV Secretion in Gram-Negative and Gram-Positive Bacteria conference, Dec 2016, Beilngries, Germany
typdoc: Conference papers

titre: Transgenerational effects of ERalpha36 over-expression on mammary gland development and molecular phenotype: clinical perspective for breast cancer risk and therapy.
auteur: Clémence Chamard-Jovenin, Amand Chesnel, Emmanuel Bresso, Chloé Morel, Charlène Thiébaut, Malika Smail-Tabbone, El-Hadi Djermoune, Marie-Dominique Devignes, Taha Boukhobza, Hélène Dumond
article: 21st World Congress on Advances in Oncology and 19th International Symposium on Molecular Medicine, Oct 2016, Athens, Greece
typdoc: Conference papers

titre: Discovering ADE associations from EHRs using pattern structures and ontologies
auteur: Gabin Personeni, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
article: Phenotype Day, Bio-Ontologies SIG, ISMB, Jul 2016, Orlando, United States
typdoc: Conference papers

titre: Using aggregation functions on structured data: a use case in the FIGHT-HF project
auteur: Kevin Dalleau, Miguel Couceiro, Marie-Dominique Devignes, Chedy Raïssi, Malika Smaïl-Tabbone
article: International Symposium on Aggregation and Structures (ISAS 2016) , Jul 2016, Luxembourg, Luxembourg
typdoc: Conference papers

titre: Extraction d’association d’EIM à partir de dossiers patients : expérimentation avec les structures de patrons et les ontologies
auteur: Gabin Personeni, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
article: Deuxième Atelier sur l’Intelligence Artificielle et la Santé, Jun 2016, Montpellier, France
typdoc: Conference papers

titre: Long chain alkylphenol mixture promotes breast cancer initiation and progression through an ERα36-mediated mechanism
auteur: Clémence Chamard-Jovenin, Amand Chesnel, Chloé Morel, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Taha Boukhobza, Hélène Dumond
article: 2nd French Workshop on Endocrine disruption in wildlife and human health, Jan 2016, Paris, France
typdoc: Conference papers

titre: Classification and Exploration of 3D Protein Domain Interactions Using Kbdock
auteur: Anisah W Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie
article: O. Carugo; F. Eisenhaber. Data Mining Techniques for the Life Sciences, 1415, Springer Science+Business Media New York, pp.91-105, 2016, Methods in Molecular Biology, 978-1-4939-3570-3. ⟨10.1007/978-1-4939-3572-7_5⟩
typdoc: Book sections

titre: Using Content-Based Filtering to Infer Direct Associations between the CATH, Pfam, and SCOP Domain Databases
auteur: Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes
article: ECCB 2016, Sep 2016, The Hague, Netherlands
typdoc: Poster communications

titre: A glimpse into an unexplored world: very high diversity of integrative and mobilizable elements in Streptococci
auteur: Charles Coluzzi, Gérard Guédon, Chloé Ambroset, Marie-Dominique Devignes, Sophie Payot, Nathalie N. Leblond-Bourget
article: 8th ASM conference on Streptococcal Genetics, Jul 2016, Washington, United States
typdoc: Poster communications

titre: A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
auteur: Anisah Ghoorah, Marie-Dominique Devignes, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, David Ritchie
article: Biology, 2015, 4 (2), pp.327-343. ⟨10.3390/biology4020327⟩
typdoc: Journal articles

titre: Long chain alkyphenol mixture promotes breast cancer initiation and progression through an ER$\alpha-mediated mechanism
auteur: Clémence Chamard-Jovenin, Amand Chesnel, Chloé Morel, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Taha Boukobza, Hélène Dumond
article: 2nd International Symposium of the Cancer Research Center of Lyon, Sep 2015, Lyon, France
typdoc: Conference papers

titre: EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains
auteur: Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David Ritchie
article: JOBIM 2015, Jul 2015, Clermont-Ferrand, France. ⟨10.1101/022343⟩
typdoc: Conference papers

titre: Long chain alkylphenol mixture promotes breast cancer initiation and progression through an ER36-mediated mechanism
auteur: Clémence Chamard-Jovenin, Amand Chesnel, Chloé Morel, Emmanuel Bresso, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Taha Boukobza, Hélène Dumond
article: 4ème Colloque Inter-Régional Grand-Est de Recherche Translationnelle en Oncologie, Oncotrans 2015, Jun 2015, Dijon, France
typdoc: Conference papers

titre: ECCB 2014: The 13th European Conference on Computational Biology
auteur: Marie-Dominique Devignes, Yves Moreau
article: Bioinformatics, 2014, 30 (17), pp.4. ⟨10.1093/bioinformatics/btu512⟩
typdoc: Journal articles

titre: Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery
auteur: Thibault Caradec, Maude Pupin, Aurélien Vanvlassenbroeck, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jacques, Valérie Leclère
article: PLoS ONE, 2014, 9 (1), pp.e85667. ⟨10.1371/journal.pone.0085667⟩
typdoc: Journal articles

titre: KBDOCK 2013: A spatial classification of 3D protein domain family interactions
auteur: Anisah Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie
article: Nucleic Acids Research, 2014, 42 (D1), pp.389-395. ⟨10.1093/nar/gkt1199⟩
typdoc: Journal articles

titre: Long chain alkylphenol mixture promotes mammary epithelial cell metaplastic phenotype through an ERalpha36-mediated mechanism.
auteur: Clémence Chamard, Emmanuel Bresso, Taha Boukobza, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amand Chesnel, Hélène Dumond
article: 8e Forum du Canceropôle Grand Est, Nov 2014, Strasbourg, France
typdoc: Conference papers

titre: ILP for Mining Linked Open Data: a biomedical Case Study
auteur: Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Adrien Coulet
article: The 24th International Conference on Inductive Logic Programming (ILP 2014), Sep 2014, Nancy, France
typdoc: Conference papers

titre: Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability
auteur: Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Adrien Coulet
article: Data Integration in the Life Sciences – 10th International Conference, DILS 2014, Jul 2014, Lisbon, Portugal. pp.16 – 31, ⟨10.1007/978-3-319-08590-6_2⟩
typdoc: Conference papers

titre: Long chain alkylphenol mixture promotes mammary epithelial cell metaplastic phenotype through an estrogen receptor alpha 36 mediated mechanism
auteur: Clémence Chamard, Emmanuel Bresso, Taha Boukhobza, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amand Chesnel, Hélène Dumond
article: 23rd Biennial Congress of the European Association for Cancer Research, EACR-23, Jul 2014, Munich, Germany. pp.S118, ⟨10.1016/S0959-8049(14)50435-2⟩
typdoc: Conference papers

titre: Mining Linked Open Data: a Case Study with Genes Responsible for Intellectual Disability
auteur: Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Adrien Coulet
article: ECCB’14 (European Conference on Computational Biology 2014), Sep 2014, Strasbourg, France. , 2014
typdoc: Poster communications

titre: Proceedings of ECCB 2014: The 13th European Conference on Computational Biology
auteur: Marie-Dominique Devignes
article: The 13th European Conference on Computational Biology, Sep 2014, Strasbourg, France. 30 (17), Oxford University Press, 2014, Bioinformatics
typdoc: Proceedings

titre: Extended spectrum of MBD5 mutations in neurodevelopmental disorders
auteur: Céline Bonnet, Asma Ali Khan, Emmanuel Bresso, Charlène Vigouroux, Mylène Béri, Sarah Lejczak, Bénédicte Deemer, Joris Andrieux, Christophe Philippe, Anne Moncla, Irina Giurgea, Marie-Dominique Devignes, Bruno Leheup, Philippe Jonveaux
article: European Journal of Human Genetics, 2013, 21 (12), pp.1457 – 1461. ⟨10.1038/ejhg.2013.22⟩
typdoc: Journal articles

titre: Protein Docking Using Case-Based Reasoning
auteur: Anisah Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie
article: Proteins – Structure, Function and Bioinformatics, 2013, 81 (12), pp.2150-2158. ⟨10.1002/prot.24433⟩
typdoc: Journal articles

titre: Integrative relational machine-learning for understanding drug side-effect profiles
auteur: Emmanuel Bresso, Renaud Grisoni, Gino Marchetti, Arnaud-Sinan Karaboga, Michel Souchet, Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: BMC Bioinformatics, 2013, 14 (1), pp.207. ⟨10.1186/1471-2105-14-207⟩
typdoc: Journal articles

titre: Clustering optimal de gènes fondé sur une mesure de similarité sémantique
auteur: Rachid Hafiane, Malika Smaïl-Tabbone, Marie-Dominique Devignes, Salvatore Tabbone
article: 10ème édition de la COnférence en Recherche d’Information et Applications – CORIA 2013, Apr 2013, Neufchâtel, Suisse. 15 p
typdoc: Conference papers

titre: Functional classification of genes using semantic distance and fuzzy clustering approach: Evaluation with reference sets and overlap analysis
auteur: Marie-Dominique Devignes, Benabderrahmane Sidahmed, Malika Smail-Tabbone, Amedeo Napoli, Poch Olivier
article: International journal of computational biology and drug design, 2012, 5 (3/4), pp.245-260
typdoc: Journal articles

titre: Formal Concept Analysis for the Interpretation of Relational Learning applied on 3D Protein-Binding Sites
auteur: Emmanuel Bresso, Renaud Grisoni, Marie-Dominique Devignes, Amedeo Napoli, Malika Smail-Tabbone
article: 4th international conference on Knowledge Discovery and Information Retrieval – KDIR 2012, Oct 2012, Barcelona, Spain. 12 p
typdoc: Conference papers

titre: NRPS toolbox for the discovery of new nonribosomal peptides and synthetases
auteur: Maude Pupin, Malika Smaïl-Tabbone, Philippe Jacques, Marie-Dominique Devignes, Valérie Leclère
article: Journées Ouvertes en Biologie, l’Informatique et les Mathématiques – JOBIM 2012, Jul 2012, Rennes, France. pp.89-93
typdoc: Conference papers

titre: Spatial clustering of protein binding sites for template based protein docking
auteur: Anisah Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie
article: Bioinformatics, 2011, 27 (20), pp.2820-2827. ⟨10.1093/bioinformatics/btr493⟩
typdoc: Journal articles

titre: HIV-PDI: A Protein-Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 1. Concepts and Associated Database
auteur: Leo Ghemtio, Malika Smaïl-Tabbone, Appolinaire Djikeng, Marie-Dominique Devignes, Lionel Keminse, Patricia Kelbert, Joseph Fokam, Bernard Maigret, Odile Ouwe-Missi-Oukem-Boyer
article: Journal of Health & Medical Informatics, 2011, 2 (1), pp.1000104. ⟨10.4172/2157-7420.1000104⟩
typdoc: Journal articles

titre: Ontology-based functional classification of genes: evaluation with reference sets and overlap analysis
auteur: Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch
article: The second workshop on Integrative Data in Systems Biology held in conjunction with the IEEE BIBM 2011 conference, Nov 2011, Atlanta, United States
typdoc: Conference papers

titre: Use of domain knowledge for dimension reduction: application to mining of drug side effects
auteur: Emmanuel Bresso, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Amedeo Napoli, Marie-Dominique Devignes
article: International Conference on Knowledge Discovery and Information Retrieval – KDIR 2011, Oct 2011, Paris, France. pp.8
typdoc: Conference papers

titre: Benchmarking a new semantic similarity measure using fuzzy clustering and reference sets: Application to cancer expression data
auteur: Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smail-Tabbone, Olivier Poch, Amedeo Napoli, Wolfgang Raffelsberger, Dominique Guenot, Nguyen Hoan, Eric Guerin
article: 11ème Conférence Internationale Francophone sur l’Extraction et la Gestion des Connaissances – EGC 2011, Jan 2011, Brest, France
typdoc: Conference papers

titre: Ontology-based knowledge discovery in pharmacogenomics.
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
article: Hamid R. Arabnia and Quoc-Nam Tran. Software Tools and Algorithms for Biological Systems, 696, Springer, pp.357-66, 2011, Advances in Experimental Medicine and Biology, 978-1-4419-7046-6. ⟨10.1007/978-1-4419-7046-6_36⟩
typdoc: Book sections

titre: IntelliGO: a new vector-based semantic similarity measure including annotation origin
auteur: Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
article: BMC Bioinformatics, 2010, 11, 11 (1), pp.588. ⟨10.1186/1471-2105-11-588⟩
typdoc: Journal articles

titre: Comparison of three preprocessing filters efficiency in virtual screening: identification of new putative LXR$\beta$ regulators as a test case
auteur: Leo Ghemtio, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Michel Souchet, Vincent Leroux, Bernard Maigret
article: Journal of Chemical Information and Modeling, 2010, 50 (5), pp.701-715. ⟨10.1021/ci900356m⟩
typdoc: Journal articles

titre: HexServer: an FFT-based protein docking server powered by graphics processors
auteur: Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David Ritchie
article: Nucleic Acids Research, 2010, 38, pp.W445-W449. ⟨10.1093/nar/gkq311⟩
typdoc: Journal articles

titre: BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery
auteur: Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Emmanuel Bresso, Amedeo Napoli, Malika Smaïl-Tabbone
article: International Journal of Metadata, Semantics and Ontologies, 2010, 5 (3), pp.184–193. ⟨10.1504/IJMSO.2010.034043⟩
typdoc: Journal articles

titre: Using Domain Knowledge to Guide Lattice-based Complex Data Exploration
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 19th European Conference on Artificial Intelligence – ECAI 2010, Aug 2010, Lisbon, Portugal. pp.847–852, ⟨10.3233/978-1-60750-606-5-847⟩
typdoc: Conference papers

titre: Connaissances de domaine et treillis de concepts pour l’exploration progressive de données complexes
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 21es Journées francophones d’Ingénierie des Connaissances – IC 2010, Jun 2010, Nîmes, France. pp.233 – 244
typdoc: Conference papers

titre: Gene-Disease Relationship Discovery based on Model-driven Data Integration and Database View Definition
auteur: Saliha Yilmaz, Philippe Jonveaux, Cedric Bicep, Laurent Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes
article: Bioinformatics, 2009, 25 (2), pp.230 – 236. ⟨10.1093/bioinformatics/btn612⟩
typdoc: Journal articles

titre: A KDD Approach for Designing Filtering Strategies to Improve Virtual Screening
auteur: Léo Ghemtio, Malika Smail-Tabbone, Marie-Dominique Devignes, Michel Souchet, Bernard Maigret
article: KDIR – International Conference on Knowledge Discovery and Information Retrieval, Oct 2009, Madeira, Portugal
typdoc: Conference papers

titre: Analyse de données transcriptomiques: Modélisation floue de profils d’expression différentielle et analyse fonctionnelle.
auteur: Sidahmed Benabderrahmane, Marie-Dominique Devignes, Malika Smaïl-Tabbone, O. Poch, Amedeo Napoli, N. Nguyen N.-H, W. Raffelsberger
article: Actes du XXVIIième congrès Informatique des Organisations et Systèmes d’information et de décision – INFORSID 2009, IRIT-Toulouse, May 2009, Toulouse, France. pp.413-428
typdoc: Conference papers

titre: Maîtriser les ressources numériques : biologie « in silico
auteur: Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: Magali Roux. Biologie L’ère numérique, CNRS Editions, pp.189-222, 2009, 9782271067791
typdoc: Book sections

titre: Ontology-guided data preparation for discovering genotype-phenotype relationships
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
article: BMC Bioinformatics, 2008, 9 (Suppl 4), pp.S3. ⟨10.1186/1471-2105-9-S4-S3⟩
typdoc: Journal articles

titre: Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment.
auteur: Alexandre Beautrait, Vincent Leroux, Matthieu Chavent, Léo Ghemtio, Marie-Dominique Devignes, Malika Smail-Tabbone, Wensheng Cai, Xuegang Shao, Gilles Moreau, Peter Bladon, Jianhua Yao, Bernard Maigret
article: Journal of Molecular Modeling, 2008, 14 (2), pp.135-148. ⟨10.1007/s00894-007-0257-9⟩
typdoc: Journal articles

titre: BioRegistry: Automatic Extraction of Metadata for Biological Database Retrieval and Discovery
auteur: Marie-Dominique Devignes, Philippe Franiatte, Nizar Messai, Amedeo Napoli, Malika Smail-Tabbone
article: 1st international workshop on Ressource Discovery (RED), Joint to iiWAS 2008, Nov 2008, Linz, Austria
typdoc: Conference papers

titre: Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 18th European Conference in Artificial Intelligence – ECAI 2008, Jul 2008, Patras, Greece. pp.127-131
typdoc: Conference papers

titre: Extending Attribute Dependencies for Lattice-Based Querying and Navigation
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 16th International Conference on Conceptual Structures – ICCS 2008, Jul 2008, Toulouse, France. pp.189-202, ⟨10.1007/978-3-540-70596-3_13⟩
typdoc: Conference papers

titre: Model-driven data integration for mining protein-ligand and protein-protein interactions in a drug design context.
auteur: Leo Ghemtio, Emmanuel Bresso, Michel Souchet, Bernard Maigret, Malika Smaïl-Tabbone, Marie-Dominique Devignes
article: Journées Ouvertes Biologie Informatique Mathématiques – JOBIM 2008, Jun 2008, Lille, France
typdoc: Conference papers

titre: Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics
auteur: Adrien Coulet, Malika Smail-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
article: 21st International Workshop on Description Logics – DL2008, May 2008, Dresden, Germany
typdoc: Conference papers

titre: Correction et complétude d’un algorithme de recherche d’information par treillis de concepts
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: Revue des Nouvelles Technologies de l’Information, 2007
typdoc: Journal articles

titre: Workshop PC Chairs’ Message. Web Data Integration for Mining in the Life Sciences (WebDIM4LS)
auteur: Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: International Workshops on Web Information Systems Engineering – WISE 2007 Workshops, Dec 2007, Nancy, France. pp.3-4, ⟨10.1007/978-3-540-77010-7_1⟩
typdoc: Conference papers

titre: Traitement d’attributs inter-dépendants pour la recherche d’information par treillis
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 18es Journées Francophones d’Ingénierie des Connaissances – IC 2007, Jul 2007, Grenoble, France. pp.109-120
typdoc: Conference papers

titre: Ontology-guided Data Preparation for Discovering Genotype-Phenotype Relationships
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
article: Network Tools and Applications in Biology: A Semantic Web for Bioinformatics – NETTAB 2007, Jun 2007, Pisa, Italy
typdoc: Conference papers

titre: Immunoselection and characterization of a human genomic PPAR binding fragment located within POTE genes
auteur: Hossam Murad, Philippe Collet, Emilie Brunner, Hervé Schohn, Philippe Becuwe, Marie-Dominique Devignes, Michel Dauça, Lionel Domenjoud
article: Biochimie, 2006, ⟨10.1016/j.biochi.2006.09.017⟩
typdoc: Journal articles

titre: A transgenic mouse model engineered to investigate human brain-derived neurotrophic factor in vivo
auteur: Fabrice Guillemot, Italina Cerutti, Charles Auffray, Marie-Dominique Devignes
article: Transgenic Research, 2006, ⟨10.1007/s11248-006-9060-0⟩
typdoc: Journal articles

titre: Effects of PPAR and RXR ligands in semaphorin 6B gene expression of human MCF-7 breast cancer cells.
auteur: Hossam Murad, Philippe Collet, Cecile Huin-Schohn, Nehmann Al-Makdissy, Geraldine Kerjan, Alain Chedotal, Mireille Donner, Marie-Dominique Devignes, Philippe Becuwe, Hervé Schohn, Lionel Domenjoud, Michel Dauça
article: International Journal of Oncology, 2006, 28, pp.977-984
typdoc: Journal articles

titre: Treillis de concepts et ontologies pour interroger l’annuaire de sources de données biologiques BioRegistry
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: Revue des Sciences et Technologies de l’Information – Série ISI : Ingénierie des Systèmes d’Information, 2006, Systèmes d’information spécialisés, 11 (1), pp.39-60
typdoc: Journal articles

titre: BR-Explorer: An FCA-based algorithm for Information Retrieval
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: Fourth International Conference On Concept Lattices and Their Applications – CLA 2006, Oct 2006, Hammamet/Tunisia
typdoc: Conference papers

titre: Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes
article: Proceedings of International Workshop on Knowledge Systems in Bioinformatics – KSinBIT’06, Oct 2006, Montpellier, France
typdoc: Conference papers

titre: SNP-Ontology for semantic integration of genomic variation data
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
article: 14th Annual International Conference on Intelligent Systems for Molecular Biology – ISMB’06, Aug 2006, Fortaleza/Brésil
typdoc: Conference papers

titre: SNP-Converter: an Ontology-Based solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
article: 3rd International Workshop on Data Integration in the Life Sciences 2006 – DILS’06, Jul 2006, European Bioinformatics Institute (EBI), Hinxton/UK
typdoc: Conference papers

titre: Ontology-driven Data Integration for Pharmacogenomics: Application to Genome Variations
auteur: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
article: Journées Ouvertes : Biologie, Informatique et Mathématiques – JOBIM’06, Centre de Bioinformatique de Bordeaux (CBiB), Jul 2006, Bordeaux/France
typdoc: Conference papers

titre: BR-Explorer: A sound and complete FCA-based retrieval algorithm (Poster)
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 4th International Conference on Formal Concept Analysis – ICFCA 2006, Feb 2006, Dresden/Germany
typdoc: Conference papers

titre: Classification et interrogation de sources de données biologiques
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: Revue des Nouvelles Technologies de l’Information, 2005, Extraction des connaissances : Etat et perspectives, pp.43-47
typdoc: Journal articles

titre: User-designed web services to support heterogeneous biological data retrieval
auteur: Marie-Dominique Devignes, Hervé de Palma, Laurent Pierron, Lionel Domenjoud, Malika Smaïl-Tabbone
article: First International Workshop on workflows management: new abilities for the biological information overflow – NETTAB 2005, Oct 2005, Naples, Italy, pp.27-34
typdoc: Conference papers

titre: BioRegistry : a structured metadata repository for bioinformatic databases
auteur: Malika Smaïl-Tabbone, Shazia Osman, Nizar Messai, Amedeo Napoli, Marie-Dominique Devignes
article: First International Symposium on Computational Life Science – CompLife 2005, Sep 2005, Konstanz, Germany, pp.46-56
typdoc: Conference papers

titre: Querying a Bioinformatic Data Sources Registry with Concept Lattices
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: 3th International Conference on Conceptual Structures – ICCS 2005, Jun 2005, Kassel, Germany. pp.323-336, ⟨10.1007/11524564_22⟩
typdoc: Conference papers

titre: Treillis de concepts et ontologies pour l’interrogation d’un annuaire de sources de données biologiques (BioRegistry)
auteur: Nizar Messai, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli
article: Actes du XXIIIème congrès Informatique des Organisations et Systèmes d’information et de décision – INFORSID 2005, May 2005, Grenoble/France
typdoc: Conference papers

titre: Méthode sémantique pour la classification et l’interrogation de sources de données biologiques
auteur: Nizar Messai, Marie-Dominique Devignes, Amedeo Napoli, Malika Smaïl-Tabbone
article: EGC 2005 – Atelier Modélisation des Connaissances, Jan 2005, Paris
typdoc: Conference papers

titre: Extraction de données pharmacogénomiques à partir d’études cliniques : problématique
auteur: Adrien Coulet, Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: Deuxième atelier sur la « Fouille de données complexes dans un processus d’extraction des connaissances », Jan 2005, Paris/France
typdoc: Conference papers

titre: The human Semaphorin 6B gene is down regulated by PPARs
auteur: Philippe Collet, Lionel Domenjoud, Marie-Dominique Devignes, Hossam Murad, Hervé Schohn, Michel Dauça
article: Genomics, 2004, 83 (6), pp.1141-1150
typdoc: Journal articles

titre: Alternative usage of 5′ exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene
auteur: Odile Bertaux, Esther Toselli-Mollereau, Charles Auffray, Marie-Dominique Devignes
article: Gene, 2004, 334, pp.83-97
typdoc: Journal articles

titre: Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
auteur: Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O’Donovan, Satoshi Fukuchi, O. Koyanagi Kanako, A. Barrero Roberto, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino, Kei Yura, Satoru Miyazaki, Kazuho Ikeo, Keiichi Homma, Arek Kasprzyk, Tetsuo Nishikawa, Mika Hirakawa, Jean Thierry-Mieg, Danielle Thierry-Mieg, Jennifer Ashurst, Libin Jia, Mitsuteru Nakao, A. Thomas, Michael, Nicola Mulder, Youla Karavidopoulou, Lihua Jin, Sangsoo Kim, Tomohiro Yasuda, Boris Lenhard, Eric Eveno, Yoshiyuki Suzuki, Jun-Ichi Takeda, Craig Gough, Phillip Hilton, Yasuyuki Fujii, Hiroaki Sakai, Susumu Tanaka, Clara Amid, Matthew Bellgard,, Maria de Fatima Bonaldo, Hidemasa Bono, K. Bromberg Susan, J. Brookes Anthony, Elspeth Bruford, Piero Carninci, Claude Chelala, Christine Couillault, J. de Souza Sandro, Marie-Anne Debily, Marie-Dominique Devignes, Inna Dubchak, Toshinori Endo, Anne Estreicher, Eduardo Eyras, Kaoru Fukami-Kobayashi, R. Gopinath Gopal, Esther Graudens, Yoonsoo Hahn, Ze-Guang Han, Michael Han, Kousuke Hanada, Hideki Hanaoka, Erimi Harada, Katsuyuki Hashimoto, Chisato Yamasaki, Ursula Hinz, Momoki Hirai, Teruyoshi Hishiki, Ian Hopkinson, Sandrine Imbeaud, Hidetoshi Inoko, Alexander Kanapin, Yayoi Kaneko, Takeya Kasukawa, Janet Kelso, Paul Kersey, Reiko Kikuno, Kouichi Kimura, Bernhard Korn, Vladimir Kuryshev, Izabela Makalowska, Takashi Makino, Shuhei Mano, Regine Mariage-Samson, Jun Mashima, Hideo Matsuda, Hans-Werner Mewes, Shinsei Minoshima, Keiichi Nagai, Hideki Nagasaki, Naoki Nagata, Rajni Nigam, Osamu Ogasawara, Osamu Ohara, Masafumi Ohtsubo, Norihiro Okada, Toshihisa Okido, Satoshi Oota, Motonori Ota, Toshio Ota, Tetsuji Otsuki, Dominique Piatier-Tonneau, Annemarie Poustka, Shuang-Xi Ren, Naruya Saitou, Katsunaga Sakai, Shigetaka Sakamoto, Ryuichi Sakate, Ingo Schupp, Florence Servant, Stephen Sherry, Rie Shiba, Sumio Sugano
article: PLoS Biology, 2004, 2 (6), pp.856-875
typdoc: Journal articles

titre: Intelligent access to genomic sources on the web
auteur: Marie-Dominique Devignes, Nizar Messai, Amedeo Napoli, Shazia Osman, Malika Smaïl-Tabbone
article: W3C Workshop on Semantic Web for Life Sciences, Oct 2004, Cambridge, Massachusetts USA
typdoc: Conference papers

titre: Integration of biological data from web resources : management of multiple answers through metadata retrieval
auteur: Marie-Dominique Devignes, Malika Smaïl-Tabbone
article: 12th International Conference on Intelligent Systems for Molecular Biology – 3rd European Conference on Computational Biology – ISMB-ECCB 2004, 2004, Glasgow, Scotland, United Kingdom. pp.3
typdoc: Conference papers

titre: A Generic Solution for Automated Collecting and Integration of Biological Data from Web Sources
auteur: Marie-Dominique Devignes, Yvan Norsa, Malika Smaïl-Tabbone, Philippe Collet, Lionel Domenjoud, Michel Dauça
article: European Conference on Computational Biology – ECCB’03, Sep 2003, Paris, France. pp.2
typdoc: Conference papers

titre: Collecte et intégration de données biologiques hétérogènes sur le web : application dans le domaine de la cartographie du génome humain
auteur: Marie-Dominique Devignes, André Schaaff, Malika Smaïl
article: Revue des Sciences et Technologies de l’Information – Série ISI : Ingénierie des Systèmes d’Information, 2002, 7 (1-2), pp.45-61
typdoc: Journal articles

titre: Inconsistencies between maps of human chromosome 22 correlate with increased frequency of disease-related Loci
auteur: Claude Chelala, Marie-Dominique Devignes, Sandrine Imbeaud, Rima Zoorob, David Cox, Charles Auffray, Emmanuel Curis, Simone Benazeth
article: Journal of Biological Systems, 2002, 10, pp.303-317. ⟨10.1142/S0218339002000743⟩
typdoc: Journal articles

titre: Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes.
auteur: Nicole-Adeline Fayein, Bernard Stankoff, Charles Auffray, Marie-Dominique Devignes
article: Gene, 2002, 289 (1-2), pp.119-129. ⟨10.1016/S0378-1119(02)00507-3⟩
typdoc: Journal articles

titre: Collecte de données biologiques à partir de sources multiples et hétérogènes. Vers une structure de médiation conviviale et orientée source
auteur: Marie-Dominique Devignes, Malika Smaïl, Nacer Boudjlida
article: Journées scientifiques sur le Web sémantique, J. Charlet, P. Laublet, C. Raynaud, Oct 2002, Paris, France, 5 p
typdoc: Conference papers

titre: From putative promoter sequence to genomic context : biological data collection on the web using a generic application (Xprom)
auteur: Marie-Dominique Devignes, Yvan Norsa, Malika Smaïl, Philippe Collet, Lionel Domenjoud
article: European Conference on Computational Biology – ECCB’2002. Session Posters, Sep 2002, Saarbrücken, Germany, 2 p
typdoc: Conference papers

titre: Refined localization of twenty-one genes in subregion p13.1 of human chromosome 1
auteur: Claude Chelala, Sandrine Imbeaud, Marie-Dominique Devignes, Rima Zoorob, Charles Auffray
article: Cytogenetics and Cell Genetics, 2001, 92 (3-4), pp.209-212. ⟨10.1159/000056904⟩
typdoc: Journal articles

titre: Services for a Genomics Open Distributed Environment
auteur: Nacer Boudjlida, Malika Smaïl-Tabbone, Marie-Dominique Devignes
article: XEWA’2000: IEEE Workshop on XML-Enabled Wide Area Search in Bioinformatics, 2000, League City, Texas, 2 p
typdoc: Conference papers

titre: Detailed transcript map of a 810-kb region at 11p14 involving identification of 10 novel human 3′ exons
auteur: Fabrice Guillemot, Charles Auffray, Marie-Dominique Devignes
article: European Journal of Human Genetics, 1999, 7 (4), pp.487-495
typdoc: Journal articles

titre: The Genexpress IMAGE Knowledge base of human brain transcriptome : a prototype of integrated resource for functional and computational genomics
auteur: Geneviève Pietu, Régine Mariage-Samson, Nicole Fayein, Christiane Matingou, Eric Eveno, Rémi Houlgatte, Charles Decraene, Yves Vandenbrouck, Fariza Tahi, Marie-Dominique Devignes, Utte Wirkner, Wilhelm Ansorge, David Cox, Takahiro Nagase, Nobuo Nomura, Charles Auffray
article: Genome Research, 1999, 9 (2), pp.195-209
typdoc: Journal articles

titre: Querying Heterogeneous Databases : a user oriented system for collecting and structuring genome information
auteur: Marie-Dominique Devignes, André Schaaff, Malika Smaïl
article: Intelligent Systems for Molecular Biology 1999 – ISMB’99, 1999, Heidelberg, Germany, pp.30
typdoc: Conference papers

titre: Can Plant RNA Viruses Exchange Genetic Material?
auteur: Jean-Christophe Boyer, Marie-Dominique Morch, Anne-Lise Haenni
article: Evolutionary Tinkering in Gene Expression, 70 (5), Springer US, pp.175-192, 1989, ⟨10.1007/978-1-4684-5664-6_17⟩
typdoc: Book sections

titre: Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA
auteur: Marie-Dominique Morch, Jean-Christophe Boyer, Anne-Lise Haenni
article: Nucleic Acids Research, 1988, 16 (13), pp.6157-6173. ⟨10.1093/nar/16.13.6157⟩
typdoc: Journal articles

titre: Plant viruses and new perspectives in cross-protection
auteur: Rosaura P.C. Valle, Jacek Skrzeczkowski, Marie-Dominique Morch, Rajiv L Joshi, Radhia Gargouri, Gabrièle Drugeon, Jean-Christophe Boyer, François Chapeville, Anne-Lise Haenni
article: Biochimie, 1988, 70 (5), pp.695-703. ⟨10.1016/0300-9084(88)90255-6⟩
typdoc: Journal articles

titre: Phospholipid transfer protein: full-length cDNA and amino acid sequence in maize
auteur: Françoise Tchang, Patrice This, Virginia Stiefel, Vincent Arondel, Marie-Dominique Morch, Montserrat Pages, Pere Puigdomenech, Françoise Grellet, Michel Delseny, Philippe Bouillon, Jean-Claude Huet, Francoise Guerbette, Françoise Beauvais-Cante, Henri Duranton, J Claude Pernollet, Jean-Claude Kader
article: Journal of Biological Chemistry, 1988, 263 (32), pp.16849-16855
typdoc: Journal articles