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Alban Gaignard

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FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards

Alban Gaignard , Thomas Rosnet , Frédéric de Lamotte , Vincent Lefort , Marie-Dominique Devignes
Journal of Biomedical Semantics, 2023, 14 (1), pp.7. ⟨10.1186/s13326-023-00289-5⟩
Article dans une revue hal-04148181v1
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Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

Marine Djaffardjy , George Marchment , Clémence Sebe , Raphael Blanchet , Khalid Belhajjame
Computational and Structural Biotechnology Journal, 2023, 21, pp.2075-2085. ⟨10.1016/j.csbj.2023.03.003⟩
Article dans une revue hal-04037221v2
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A taxonomy of tools and approaches for distributed genomic analyses

Wilmer Garzón , Luis Daniel Benavides Navarro , Alban Gaignard , Richard Redon , Mario Südholt
Informatics in Medicine Unlocked, 2022, 32, pp.1-17. ⟨10.1016/j.imu.2022.101024⟩
Article dans une revue hal-03748752v1
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Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population

Olivia Rousseau , Matilde Karakachoff , Alban Gaignard , Lise Bellanger , Philippe Bijlenga
Journal of Neurology, Neurosurgery and Psychiatry, 2021, 92 (2), jnnp-2020-324371. ⟨10.1136/jnnp-2020-324371⟩
Article dans une revue hal-03033899v1
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Large-scale regulatory and signaling network assembly through linked open data

Marie Lefebvre , Alban Gaignard , Maxime Folschette , Jérémie Bourdon , Carito Guziolowski
Database - The journal of Biological Databases and Curation, 2021, 2021, pp.baaa113. ⟨10.1093/database/baaa113⟩
Article dans une revue hal-03107317v2
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biotoolsSchema: a formalized schema for bioinformatics software description

Jon Ison , Hans Ienasescu , Emil Rydza , Piotr Chmura , Kristoffer Rapacki
GigaScience, 2021, 10 (1), pp.giaa157. ⟨10.1093/gigascience/giaa157⟩
Article dans une revue hal-03145289v1

Findable and reusable workflow data products: A genomic workflow case study

Alban Gaignard , Hala Skaf-Molli , Khalid Belhajjame
Semantic Web – Interoperability, Usability, Applicability, 2020, pp.1-13. ⟨10.3233/SW-200374⟩
Article dans une revue hal-02903805v1
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Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project

Vincent L'Allinec , Stéphanie Chatel , Matilde Karakachoff , Emmanuelle Bourcereau , Zeineb Es-Salah-Lamoureux
Neurosurgery, 2020
Article dans une revue hal-02889889v1
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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

Benoit Tessoulin , Agnès Moreau-Aubry , Géraldine Descamps , Patricia Gomez-Bougie , Sophie Maiga
Journal of Hematology and Oncology, 2018, 11 (1), pp.137. ⟨10.1186/s13045-018-0679-0⟩
Article dans une revue inserm-01958772v1
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Article dans une revue hal-01516082v1
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Understanding the Pathophysiology of Intracranial Aneurysm: The ICAN Project

Romain Bourcier , Stéphanie Chatel , Emmanuelle Bourcereau , Solène Jouan , Hervé Le Marec
Neurosurgery, 2017, 80 (4), pp.621-626. ⟨10.1093/neuros/nyw135⟩
Article dans une revue hal-01768333v1
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Domain-specific summarisation of Life-Science e-experiments from provenance traces

Alban Gaignard , Johan Montagnat , Bernard Gibaud , Germain Forestier , Tristan Glatard
Journal of Web Semantics, 2014, 29, pp.19-30. ⟨10.1016/j.websem.2014.07.001⟩
Article dans une revue hal-01027596v1
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OntoVIP: An ontology for the annotation of object models used for medical image simulation.

Bernard Gibaud , Germain Forestier , Hugues Benoit-Cattin , Frédéric Cervenansky , Patrick Clarysse
Journal of Biomedical Informatics, 2014, 52, pp.279-92. ⟨10.1016/j.jbi.2014.07.008⟩
Article dans une revue inserm-01062371v1
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A virtual imaging platform for multi-modality medical image simulation.

Tristan Glatard , Carole Lartizien , Bernard Gibaud , Rafael Ferreira da Silva , Germain Forestier
IEEE Transactions on Medical Imaging, 2013, 32 (1), pp.110-8. ⟨10.1109/TMI.2012.2220154⟩
Article dans une revue inserm-00762497v1
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Composing Multiple Variability Artifacts to Assemble Coherent Workflows

Mathieu Acher , Philippe Collet , Alban Gaignard , Philippe Lahire , Johan Montagnat
Software Quality Journal, 2012, 20 (3-4), pp.689-734. ⟨10.1007/s11219-011-9170-7⟩
Article dans une revue hal-00733556v1
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Federating distributed and heterogeneous information sources in neuroimaging: the NeuroBase Project.

Christian Barillot , Habib Benali , Michel Dojat , Alban Gaignard , Bernard Gibaud
Studies in Health Technology and Informatics, 2006, 120, pp.3-13
Article dans une revue inserm-00141685v1
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Extraction d'informations sur les workflows scientifiques à partir de la littérature

Clémence Sebe , Aurélie Névéol , Sarah Cohen-Boulakia , Alban Gaignard
23ème conférence francophone sur l'Extraction et la Gestion des Connaissances (EGC), Jan 2023, Lyon, France. pp.313-320
Communication dans un congrès hal-03991363v1

(more) Findable bioinformatics softwares with Bioschemas

Alban Gaignard
Elixir Tools platform, F2F meeting, Elixir, Mar 2023, Leyden, Netherlands
Communication dans un congrès hal-04057569v1
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Découvrabilité et réutilisation de données produites par des workflows : un cas d’usage en génomique

Alban Gaignard , Hala Skaf-Molli , Khalid Belhajjame
Journées Francophones d'Ingénierie des Connaissances (IC) Plate-Forme Intelligence Artificielle (PFIA'21), Jun 2021, Bordeaux, France. pp 73-80
Communication dans un congrès emse-03260542v1
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On distributed collaboration for biomedical analyses

Fatima-Zahra Boujdad , Alban Gaignard , Mario Südholt , Wilmer Garzón-Alfonso , Luis Daniel Benavides Navarro
CCGrid-Life 2019 Workshop on Clusters, Clouds and Grids for Life Sciences, May 2019, Larnaca, Cyprus. pp.1-10, ⟨10.1109/CCGRID.2019.00079⟩
Communication dans un congrès hal-02080463v1
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3D bifurcations characterization for intra-cranial aneurysms prediction

Anass Nouri , Florent Autrusseau , Romain Bourcier , Alban Gaignard , Vincent L'Allinec
SPIE Medical Imaging, Feb 2019, San Diego, CA, United States. ⟨10.1117/12.2504626⟩
Communication dans un congrès hal-01896717v1

INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data

Maxime Folschette , Kirsley Chennen , Alban Gaignard , Richard Redon , Hala Skaf-Molli
JOBIM 2019, Jul 2019, Nantes, France
Communication dans un congrès hal-02330809v1
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SHARP: Harmonizing cross-workflow provenance

Alban Gaignard , Khalid Belhajjame , Hala Skaf-Molli
SeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics - 14th ESWC 2017, May 2017, Portoroz, Slovenia
Communication dans un congrès hal-01768394v1
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Regulation and signalization graph assembly through Linked Open Data

Marie Lefebvre , Jérémie Bourdon , Carito Guziolowski , Alban Gaignard
JOBIM 2017, Jul 2017, Lille, France
Communication dans un congrès hal-01768420v1

Developing and sharing reproducible bioinformatics pipelines: best practices

Yohann Lelièvre , Audrey Bihouée , Eric Charpentier , Alban Gaignard , Simon Souchet
JOBIM 2017, Jul 2017, Lille, France
Communication dans un congrès hal-01768429v1
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SHARP: Harmonizing Galaxy and Taverna workflow provenance

Alban Gaignard , Khalid Belhajjame , Hala Skaf-Molli
SeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics, May 2017, Portoroz, Slovenia
Communication dans un congrès hal-01768401v1
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From scientific workflow patterns to 5-star linked open data

Alban Gaignard , Hala Skaf-Molli , Audrey Bihouée
TaPP 2016: 8th USENIX Workshop on the Theory and Practice of Provenance, Jun 2016, Washington D.C., United States
Communication dans un congrès hal-01768449v1

Global Initiative for Sentinel e-Health Network on Grid (GINSENG), Medical data integration and semantic developments for epidemiology

S Cipiere , G. Ereteo , Alban Gaignard , Boujelben N. , S. Gaspard
CCGRID, May 2014, Chicago, United States
Communication dans un congrès hal-02083188v1
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Publication, partage et réutilisation de règles sur le Web de données

Oumy Seye , Catherine Faron Zucker , Olivier Corby , Alban Gaignard
25èmes Journées francophones d'Ingénierie des Connaissances, May 2014, Clermont-Ferrand, France. pp.237-248
Communication dans un congrès hal-01015281v1
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Semantic Federation of Distributed Neurodata

Alban Gaignard , Johan Montagnat , Catherine Faron Zucker , Olivier Corby
MICCAI Workshop on Data- and Compute-Intensive Clinical and Translational Imaging Applications, Oct 2012, Nice, France. pp.41-50
Communication dans un congrès hal-00746765v1
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Fédération multi-sources en neurosciences : intégration de données relationnelles et sémantiques

Alban Gaignard , Johan Montagnat , Catherine Faron Zucker , Olivier Corby
IC pour l'Interopérabilité Sémantique dans les applications en e-Santé, Jun 2012, France. 6 p
Communication dans un congrès hal-01018722v1
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KGRAM Versatile Inference and Query Engine for the Web of Linked Data

Olivier Corby , Alban Gaignard , Catherine Faron Zucker , Johan Montagnat
IEEE/WIC/ACM International Conference on Web Intelligence, Dec 2012, Macao, China. pp.1-8
Communication dans un congrès hal-00746772v1

NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimaging

Michel Dojat , Mélanie Pélégrini-Issac , Farooq Ahmad , Christian Barillot , Bénédicte Batrancourt
Organization for Human Brain Mapping (HBM'11), Jun 2011, Quebec, Canada
Communication dans un congrès hal-00813796v1

A federated system for sharing and reuse of images and image processing tools in neuroimaging

Bernard Gibaud , Farooq Ahmad , Christian Barillot , Franck Michel , Bacem Wali
Computer Assisted Radiology and Surgery (CARS'11), Jun 2011, Berlin, Germany
Communication dans un congrès hal-00690921v1
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NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.

Bernard Gibaud , Gilles Kassel , Michel Dojat , Bénédicte Batrancourt , Franck Michel
American Medical Informatics Association, Oct 2011, Washington DC, United States. pp.472-80
Communication dans un congrès hal-00683087v1
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Characterizing semantic service parameters with Role concepts to infer domain-specific knowledge at runtime

Alban Gaignard , Johan Montagnat , Bacem Wali , Bernard Gibaud
International Conference on Knowledge Engineering and Ontology Development (KEOD'11), Oct 2011, Paris, France. pp.12
Communication dans un congrès hal-00677829v1
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Grid-wide neuroimaging data federation in the context of the NeuroLOG project.

Franck Michel , Alban Gaignard , Farooq Ahmad , Christian Barillot , Bénédicte Batrancourt
HealthGrid'10, Jun 2010, Paris, France. pp.112-123, ⟨10.3233/978-1-60750-583-9-112⟩
Communication dans un congrès inserm-00512799v1
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Intégration des connaissances en neurosciences dans un environnement multi-centrique

Alban Gaignard , Johan Montagnat
Journées francophones d'Ingénierie des Connaissances (IC 2010), Jun 2010, Nîmes, France. pp.21-30
Communication dans un congrès hal-00691827v1
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A distributed security policy for neuroradiological data sharing

Alban Gaignard , Johan Montagnat
HealthGrid 2009, Jun 2009, Berlin, Germany. pp.257-262, ⟨10.3233/978-1-60750-027-8-257⟩
Communication dans un congrès hal-00677795v1
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Managing Variability Complexity in Aspect-Oriented Modeling

Brice Morin , Gilles Vanwormhoudt , Philippe Lahire , Alban Gaignard , Olivier Barais
In Proceedings of ACM/IEEE 11th International Conference on Model Driven Engineering Languages and Systems (MoDELS 08), 2008, Toulouse, France, France
Communication dans un congrès inria-00457129v1

Managing Variability Complexity in Aspect Oriented Modelling

Brice Morin , Gilles Vanwormhoudt , Philippe Lahire , Alban Gaignard , Olivier Barais
12th International Conference on Model Driven Engineering Languages and Systems (MODELS'2009), ACM/IEEE, Sep 2008, Toulouse, France. pp.797-812
Communication dans un congrès hal-00415774v1
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NeuroLOG: a community-driven middleware design

Johan Montagnat , Alban Gaignard , Diane Lingrand , Javier Rojas Balderrama , Philippe Collet
HealthGrid, Jun 2008, Chicago, United States. pp.49--58
Communication dans un congrès hal-00461611v1
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Introducing variability into Aspect-Oriented Modeling approaches

Philippe Lahire , Brice Morin , Gilles Vanwormhoudt , Alban Gaignard , Olivier Barais
In Proceedings of ACM/IEEE 10th International Conference on Model Driven Engineering Languages and Systems (MoDELS 07), 2007, Nashville, TN, USA, United States
Communication dans un congrès inria-00477562v1
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Sharing data and image processing tools in neuroimaging.

Bernard Gibaud , Christian Barillot , Habib Benali , Michel Dojat , Alban Gaignard
CARS 2006 - Computer Assisted Radiology and Surgery, Jun 2006, Osaka, Japan. pp.41-42
Communication dans un congrès inserm-00152138v1
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Schema.org : How is it used?

Minh-Hoang Dang , Alban Gaignard , Hala Skaf-Molli , Pascal Molli
International Semantic Web Conference (ISWC) 2023, Nov 2023, Athens, France. CEUR Workshop Proceedings, 2023
Poster de conférence hal-04250523v1
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EDAM, the life-science ontology for data analysis and management

Lucie Lamothe , Alban Gaignard , Mads Kierkegaard , Hager Eldakroury , Melissa Black
JOBIM, Jul 2022, Rennes, France. ⟨10.5281/zenodo.6769072⟩
Poster de conférence hal-03702557v1

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2019)

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
3rd NEUBIAS Bioimage Analysis Community Conference 2019, Jun 2020, Luxembourg, Luxembourg
Poster de conférence hal-02910949v1

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2020)

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
ELIXIR All Hands 2020, Jun 2020, Virtual, United Kingdom
Poster de conférence hal-02910948v1
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EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats

Matúš Kalaš , Laure Plantard , Nataša Sladoje , Joakim Lindblad , Moritz Alexander Kirschmann
NEUBIAS, Feb 2019, Luxembourg, Luxembourg. ⟨10.7490/f1000research.1115257.1⟩
Poster de conférence hal-02267597v1
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INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical data

Alban Gaignard , Julie D. Thompson , Kirsley Chennen , Maxime Folschette , Jocelyn Laporte
JOBIM 2019, Jul 2019, Nantes, France
Poster de conférence hal-02330853v1
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SHARP: Harmonizing and Bridging Cross-Workflow Provenance

Alban Gaignard , Khalid Belhajjame , Hala Skaf-Molli
The Semantic Web: ESWC 2017 Satellite Events Portorož, Slovenia, May 28 – June 1, 2017, Revised Selected Papers, 2017
Chapitre d'ouvrage hal-01768385v1