Alban Gaignard

I’m CNRS researcher engineer working at l’Institut du Thorax in Nantes. I’m a member of the BiRD bioinformatics facility, an active contributor to IFB (Institut Français de Bioinformatique), and Elixir (European infrastructure for bioinformatics).

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I obtained a Ph.D. in Computer Science from the University of Nice-Sophia Antipolis. My research interests cover knowledge graphs and distributed systems (workflows, provenance) in the context of life sciences.

From 2018 to 2020, I co-lead the INEXMED integrative bioinformatics project funded by IFB (Institut Français de Bioinformatique) to design a FAIR data infrastructure bridging imaging and sequencing data.

Since 2019 I co-lead the IFB interoperability working group and represents the french activities in this domain for the European ELIXIR infrastructure.

Since 2020, I co-lead the R2P2 interdisciplinary project funded by CNRS, and aimed at better sharing and citing scientific workflows.

news

Sep 8, 2023 Invited talk to present Provenance metadata in workflows at CNRS “Reproducibility and Replicability in Science” workshop.
Sep 4, 2023 “Schema.org: How is it used ?” poster accepted at ISWC2023.
Aug 19, 2023 Invited talk on intracranial aneurysm knowledge graph and ontologies at ICS (Interdisciplinary Cerbrovascular Symposium) [Slides]
Jul 7, 2023 FAIR-Checker presented at SOSEM, the Open Science workshop associated to PFIA 2023. [(slides)]
Jul 7, 2023 FAIR-Checker paper published in Journal of Biomedical Semantics. https://doi.org/10.1186/s13326-023-00289-5
May 31, 2023 Invited talk to present Bioschemas at “machine actionable software management plans” Elixir workshop in Cologne.
Apr 27, 2023 Invited talk to present Bioschemas at the Elixir Machine Learning SIS kick-off meeting in Padova.
Mar 28, 2023 Invited talk to present Bioschemas at the Elixir Tools Platform face-to-face meeting in Leiden.
Nov 29, 2022 Invited talk to present FAIR-Checker at the EOSC General Assembly.
Aug 29, 2022 Invited talk to present FAIR-Checker at the Agro-Hackathon in Montpellier.

selected publications

  1. FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards
    Alban Gaignard, Thomas Rosnet, Frédéric Lamotte, and 2 more authors
    Journal of Biomedical Semantics, Dec 2023
  2. Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems
    Marine Djaffardjy, George Marchment, Clémence Sebe, and 5 more authors
    Computational and Structural Biotechnology Journal, Dec 2023
  3. Large-scale regulatory and signaling network assembly through linked open data
    Marie Lefebvre, Alban Gaignard, Maxime Folschette, and 2 more authors
    Database: The Journal of Biological Databases and Curation, Dec 2021
  4. Findable and reusable workflow data products: A genomic workflow case study
    Alban Gaignard, Hala Skaf-Molli, and Khalid Belhajjame
    Semantic Web, Dec 2020
  5. Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population
    Olivia Rousseau, Matilde Karakachoff, Alban Gaignard, and 15 more authors
    Journal of Neurology, Neurosurgery, and Psychiatry, Dec 2020
  6. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
    Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, and 11 more authors
    Future Generation Computer Systems, Dec 2017