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).
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 15, 2024 | Paper accepted at EKAW 2024 on the modeling and comparison of FAIRness measures. [paper] |
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Jul 2, 2024 | Co-chairing the SOSEM workshop at PFIA2024. |
Jun 10, 2024 | Elixir All-Hands meeting, Uppsala. Best poster award for the EDAM control room. |
Apr 9, 2024 | Invited talk on Knowledge Graphs for intracranial aneurysms at Inria Lyon, team AIstrosight [slides] |
Mar 25, 2024 | Teaching at ETBII 2024 on Semantic Web for Life Sciences [slides] |
Feb 26, 2024 | Attending the SWAT4HCLS 2024 conference in Leiden. |
Nov 8, 2023 | Poster presented at the 22th International Semantic Web Conference (ISWC 2023) [paper], [poster] |
Oct 30, 2023 | Project coordination at Elixir BioHackathon [Project #23 report] |
Oct 23, 2023 | Marine Djaffardjy PhD defense |
Sep 27, 2023 | FAIR signposting hackathon held in the context of EOSC [report] |
selected publications
- FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standardsJournal of Biomedical Semantics, Dec 2023
- Developing and reusing bioinformatics data analysis pipelines using scientific workflow systemsComputational and Structural Biotechnology Journal, Dec 2023
- Large-scale regulatory and signaling network assembly through linked open dataDatabase: The Journal of Biological Databases and Curation, Dec 2021
- Findable and reusable workflow data products: A genomic workflow case studySemantic Web, Dec 2020
- Location of intracranial aneurysms is the main factor associated with rupture in the ICAN populationJournal of Neurology, Neurosurgery, and Psychiatry, Dec 2020
- Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunitiesFuture Generation Computer Systems, Dec 2017