Publications

Jon Ison, Hans Ienasescu, Emil Rydza, Piotr Chmura, Kristoffer Rapacki, et al.. biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience, Oxford Univ Press, 2021, 10 (1), pp.giaa157. ⟨10.1093/gigascience/giaa157⟩. ⟨hal-03145289⟩

Marie Lefebvre, Alban Gaignard, Maxime Folschette, Jérémie Bourdon, Carito Guziolowski. Large-scale regulatory and signaling network assembly through linked open data. Database - The journal of Biological Databases and Curation, Oxford University Press, 2021, 2021, pp.baaa113. ⟨10.1093/database/baaa113⟩. ⟨hal-03107317v2⟩

Olivia Rousseau, Matilde Karakachoff, Alban Gaignard, Lise Bellanger, Philippe Bijlenga, et al.. Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population. Journal of Neurology, Neurosurgery and Psychiatry, BMJ Publishing Group, 2021, 92 (2), jnnp-2020-324371. ⟨10.1136/jnnp-2020-324371⟩. ⟨hal-03033899⟩

Vincent L'Allinec, Stéphanie Chatel, Matilde Karakachoff, Emmanuelle Bourcereau, Zeineb Es-Salah-Lamoureux, et al.. Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project. Neurosurgery, Lippincott, Williams & Wilkins, 2020. ⟨hal-02889889⟩

Alban Gaignard, Hala Skaf-Molli, Khalid Belhajjame. Findable and reusable workflow data products: A genomic workflow case study. Semantic Web – Interoperability, Usability, Applicability, IOS Press, 2020, pp.1-13. ⟨10.3233/SW-200374⟩. ⟨hal-02903805⟩

Benoit Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez-Bougie, Sophie Maiga, et al.. Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways. Journal of Hematology and Oncology, BioMed Central, 2018, 11 (1), pp.137. ⟨10.1186/s13045-018-0679-0⟩. ⟨inserm-01958772⟩

Romain Bourcier, Stéphanie Chatel, Emmanuelle Bourcereau, Solène Jouan, Hervé Le Marec, et al.. Understanding the Pathophysiology of Intracranial Aneurysm: The ICAN Project. Neurosurgery, Lippincott, Williams & Wilkins, 2017, 80 (4), pp.621-626. ⟨10.1093/neuros/nyw135⟩. ⟨hal-01768333⟩

Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, et al.. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, Elsevier, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩. ⟨hal-01516082⟩

Alban Gaignard, Johan Montagnat, Bernard Gibaud, Germain Forestier, Tristan Glatard. Domain-specific summarisation of Life-Science e-experiments from provenance traces. Journal of Web Semantics, Elsevier, 2014, 29, pp.19-30. ⟨10.1016/j.websem.2014.07.001⟩. ⟨hal-01027596⟩

Bernard Gibaud, Germain Forestier, Hugues Benoit-Cattin, Frédéric Cervenansky, Patrick Clarysse, et al.. OntoVIP: An ontology for the annotation of object models used for medical image simulation.. Journal of Biomedical Informatics, Elsevier, 2014, 52, pp.279-92. ⟨10.1016/j.jbi.2014.07.008⟩. ⟨inserm-01062371⟩

Tristan Glatard, Carole Lartizien, Bernard Gibaud, Rafael Ferreira da Silva, Germain Forestier, et al.. A virtual imaging platform for multi-modality medical image simulation.. IEEE Transactions on Medical Imaging, Institute of Electrical and Electronics Engineers, 2013, 32 (1), pp.110-8. ⟨10.1109/TMI.2012.2220154⟩. ⟨inserm-00762497⟩

Mathieu Acher, Philippe Collet, Alban Gaignard, Philippe Lahire, Johan Montagnat, et al.. Composing Multiple Variability Artifacts to Assemble Coherent Workflows. Software Quality Journal, Springer Verlag, 2012, 20 (3-4), pp.689-734. ⟨10.1007/s11219-011-9170-7⟩. ⟨hal-00733556⟩

Christian Barillot, Habib Benali, Michel Dojat, Alban Gaignard, Bernard Gibaud, et al.. Federating distributed and heterogeneous information sources in neuroimaging: the NeuroBase Project.. Studies in Health Technology and Informatics, IOS Press, 2006, 120, pp.3-13. ⟨inserm-00141685⟩

Alban Gaignard, Hala Skaf-Molli, Khalid Belhajjame. Découvrabilité et réutilisation de données produites par des workflows : un cas d’usage en génomique. Journées Francophones d'Ingénierie des Connaissances (IC) Plate-Forme Intelligence Artificielle (PFIA'21), Jun 2021, Bordeaux, France. pp 73-80. ⟨emse-03260542⟩

Fatima-Zahra Boujdad, Alban Gaignard, Mario Südholt, Wilmer Garzón-Alfonso, Luis Daniel Benavides Navarro, et al.. On distributed collaboration for biomedical analyses. CCGrid-Life 2019 Workshop on Clusters, Clouds and Grids for Life Sciences, May 2019, Larnaca, Cyprus. pp.1-10, ⟨10.1109/CCGRID.2019.00079⟩. ⟨hal-02080463⟩

Maxime Folschette, Kirsley Chennen, Alban Gaignard, Richard Redon, Hala Skaf-Molli, et al.. INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data. JOBIM 2019, Jul 2019, Nantes, France. ⟨hal-02330809⟩

Anass Nouri, Florent Autrusseau, Romain Bourcier, Alban Gaignard, Vincent L'Allinec, et al.. 3D bifurcations characterization for intra-cranial aneurysms prediction. SPIE Medical Imaging, Feb 2019, San Diego, CA, United States. ⟨10.1117/12.2504626⟩. ⟨hal-01896717⟩

Alban Gaignard, Khalid Belhajjame, Hala Skaf-Molli. SHARP: Harmonizing Galaxy and Taverna workflow provenance. SeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics, May 2017, Portoroz, Slovenia. ⟨hal-01768401⟩

Marie Lefebvre, Jérémie Bourdon, Carito Guziolowski, Alban Gaignard. Regulation and signalization graph assembly through Linked Open Data. JOBIM 2017, Jul 2017, Lille, France. ⟨hal-01768420⟩

Alban Gaignard, Khalid Belhajjame, Hala Skaf-Molli. SHARP: Harmonizing cross-workflow provenance. SeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics - 14th ESWC 2017, May 2017, Portoroz, Slovenia. ⟨hal-01768394⟩

yohann Lelièvre, Audrey Bihouée, Eric Charpentier, Alban Gaignard, Simon Souchet, et al.. Developing and sharing reproducible bioinformatics pipelines: best practices. JOBIM 2017, Jul 2017, Lille, France. ⟨hal-01768429⟩

Alban Gaignard, Hala Skaf-Molli, Audrey Bihouée. From scientific workflow patterns to 5-star linked open data. TaPP 2016: 8th USENIX Workshop on the Theory and Practice of Provenance, Jun 2016, Washington D.C., United States. ⟨hal-01768449⟩

S Cipiere, G. Ereteo, Alban Gaignard, Boujelben N., S. Gaspard, et al.. Global Initiative for Sentinel e-Health Network on Grid (GINSENG), Medical data integration and semantic developments for epidemiology. CCGRID, May 2014, Chicago, United States. ⟨hal-02083188⟩

Oumy Seye, Catherine Faron Zucker, Olivier Corby, Alban Gaignard. Publication, partage et réutilisation de règles sur le Web de données. 25èmes Journées francophones d'Ingénierie des Connaissances, May 2014, Clermont-Ferrand, France. pp.237-248. ⟨hal-01015281⟩

Alban Gaignard, Johan Montagnat, Catherine Faron Zucker, Olivier Corby. Fédération multi-sources en neurosciences : intégration de données relationnelles et sémantiques. IC pour l'Interopérabilité Sémantique dans les applications en e-Santé, Jun 2012, France. 6 p. ⟨hal-01018722⟩

Alban Gaignard, Johan Montagnat, Catherine Faron Zucker, Olivier Corby. Semantic Federation of Distributed Neurodata. MICCAI Workshop on Data- and Compute-Intensive Clinical and Translational Imaging Applications, Oct 2012, Nice, France. pp.41-50. ⟨hal-00746765⟩

Olivier Corby, Alban Gaignard, Catherine Faron Zucker, Johan Montagnat. KGRAM Versatile Inference and Query Engine for the Web of Linked Data. IEEE/WIC/ACM International Conference on Web Intelligence, Dec 2012, Macao, China. pp.1-8. ⟨hal-00746772⟩

Bernard Gibaud, Farooq Ahmad, Christian Barillot, Franck Michel, Bacem Wali, et al.. A federated system for sharing and reuse of images and image processing tools in neuroimaging. Computer Assisted Radiology and Surgery (CARS'11), Jun 2011, Berlin, Germany. ⟨hal-00690921⟩

Alban Gaignard, Johan Montagnat, Bacem Wali, Bernard Gibaud. Characterizing semantic service parameters with Role concepts to infer domain-specific knowledge at runtime. International Conference on Knowledge Engineering and Ontology Development (KEOD'11), Oct 2011, Paris, France. pp.12. ⟨hal-00677829⟩

Bernard Gibaud, Gilles Kassel, Michel Dojat, Bénédicte Batrancourt, Franck Michel, et al.. NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.. American Medical Informatics Association, Oct 2011, Washington DC, United States. pp.472-80. ⟨hal-00683087⟩

Michel Dojat, Mélanie Pélégrini-Issac, Farooq Ahmad, Christian Barillot, Bénédicte Batrancourt, et al.. NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimaging. Organization for Human Brain Mapping (HBM'11), Jun 2011, Quebec, Canada. ⟨hal-00813796⟩

Franck Michel, Alban Gaignard, Farooq Ahmad, Christian Barillot, Bénédicte Batrancourt, et al.. Grid-wide neuroimaging data federation in the context of the NeuroLOG project.. HealthGrid'10, Jun 2010, Paris, France. pp.112-123, ⟨10.3233/978-1-60750-583-9-112⟩. ⟨inserm-00512799⟩

Alban Gaignard, Johan Montagnat. Intégration des connaissances en neurosciences dans un environnement multi-centrique. Journées francophones d'Ingénierie des Connaissances (IC 2010), Jun 2010, Nîmes, France. pp.21-30. ⟨hal-00691827⟩

Alban Gaignard, Johan Montagnat. A distributed security policy for neuroradiological data sharing. HealthGrid 2009, Jun 2009, Berlin, Germany. pp.257-262, ⟨10.3233/978-1-60750-027-8-257⟩. ⟨hal-00677795⟩

Johan Montagnat, Alban Gaignard, Diane Lingrand, Javier Rojas Balderrama, Philippe Collet, et al.. NeuroLOG: a community-driven middleware design. HealthGrid, Jun 2008, Chicago, United States. pp.49--58. ⟨hal-00461611⟩

Brice Morin, Gilles Vanwormhoudt, Philippe Lahire, Alban Gaignard, Olivier Barais, et al.. Managing Variability Complexity in Aspect Oriented Modelling. 12th International Conference on Model Driven Engineering Languages and Systems (MODELS'2009), ACM/IEEE, Sep 2008, Toulouse, France. pp.797-812. ⟨hal-00415774⟩

Brice Morin, Gilles Vanwormhoudt, Philippe Lahire, Alban Gaignard, Olivier Barais, et al.. Managing Variability Complexity in Aspect-Oriented Modeling. In Proceedings of ACM/IEEE 11th International Conference on Model Driven Engineering Languages and Systems (MoDELS 08), 2008, Toulouse, France, France. ⟨inria-00457129⟩

Philippe Lahire, Brice Morin, Gilles Vanwormhoudt, Alban Gaignard, Olivier Barais, et al.. Introducing variability into Aspect-Oriented Modeling approaches. In Proceedings of ACM/IEEE 10th International Conference on Model Driven Engineering Languages and Systems (MoDELS 07), 2007, Nashville, TN, USA, United States. ⟨inria-00477562⟩

Bernard Gibaud, Christian Barillot, Habib Benali, Michel Dojat, Alban Gaignard, et al.. Sharing data and image processing tools in neuroimaging.. CARS 2006 - Computer Assisted Radiology and Surgery, Jun 2006, Osaka, Japan. pp.41-42. ⟨inserm-00152138⟩

Lucie Lamothe, Alban Gaignard, Mads Kierkegaard, Hager Eldakroury, Melissa Black, et al.. EDAM, the life-science ontology for data analysis and management. JOBIM, Jul 2022, Rennes, France. ⟨10.5281/zenodo.6769072⟩. ⟨hal-03702557⟩

Matúš Kalaš, Laure Plantard, Nataša Sladoje, Joakim Lindblad, Moritz Alexander Kirschmann, et al.. EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2020). ELIXIR All Hands 2020, Jun 2020, Virtual, United Kingdom. ⟨hal-02910948⟩

Matúš Kalaš, Laure Plantard, Nataša Sladoje, Joakim Lindblad, Moritz Alexander Kirschmann, et al.. EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2019). 3rd NEUBIAS Bioimage Analysis Community Conference 2019, Jun 2020, Luxembourg, Luxembourg. ⟨hal-02910949⟩

Alban Gaignard, Julie D. Thompson, Kirsley Chennen, Maxime Folschette, Jocelyn Laporte, et al.. INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical data. JOBIM 2019, Jul 2019, Nantes, France. ⟨hal-02330853⟩

Matúš Kalaš, Laure Plantard, Nataša Sladoje, Joakim Lindblad, Moritz Alexander Kirschmann, et al.. EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats. NEUBIAS, Feb 2019, Luxembourg, Luxembourg. ⟨10.7490/f1000research.1115257.1⟩. ⟨hal-02267597⟩

Alban Gaignard, Khalid Belhajjame, Hala Skaf-Molli. SHARP: Harmonizing and Bridging Cross-Workflow Provenance. The Semantic Web: ESWC 2017 Satellite Events Portorož, Slovenia, May 28 – June 1, 2017, Revised Selected Papers, 2017. ⟨hal-01768385⟩

Aurélien Cornet, Christian Barillot, Olivier Dameron, Alban Gaignard, Camille Maumet, et al.. État des lieux MoDaL (Multi-Scale Data Links). [Rapport de recherche] IRISA, Inria Rennes. 2020. ⟨hal-02557351⟩

Aurélien Cornet, Christian Barillot, Olivier Dameron, Alban Gaignard, Camille Maumet, et al.. Atelier MoDaL (Multi-Scale Data Links). [Rapport de recherche] IRISA, Inria Rennes. 2020. ⟨inserm-02507799v4⟩

Alban Gaignard. Distributed knowledge sharing and production through collaborative e-Science platforms. Other [cs.OH]. Université Nice Sophia Antipolis, 2013. English. ⟨NNT : 2013NICE4010⟩. ⟨tel-00827926v2⟩

Alban Gaignard. Sharing massive data analysis: 
from provenance to linked experiment reports. Doctoral. France. 2018. ⟨cel-02069606⟩