The chemistry
of holobionts.
A next-generation lab for integrative experimental and computational research at the intersection of mass spectrometry, multi-omics, and multi-agent AI — building open systems that decipher the metabolic interplay between hosts and their microbiomes, and that move toward autonomous scientific research.
Our mission is to build the next-generation toolbox for mass-spectrometry metabolomics — open, modular, and AI-native — to accelerate insights in health, ecology, and the bio-industries.
Four lines, one question.
12 people. Four disciplines.
Chemists, computer scientists, AI engineers, bioinformaticians — working under one roof. We celebrate diversity of thought and background; it is the engine of our research, not a side note.
Joined 2023Louis-Félix Nothias
Principal Investigator and Coordinator, HolobiomicsLab · Chaire de Professeur Junior CNRS · 3iA Côte d'Azur Affiliated Chair
Founder · MS metabolomics · AI for science
Elise Dumont
Principal Investigator, HolobiomicsLab · Professor, Université Côte d'Azur · Senior member, Institut Universitaire de France
Computational chemistry · Molecular dynamics
Joined 2024Tao Jiang
CNRS Research Engineer (Ingénieur d'Études · Chemistry)
Machine learning for MS data · MetaboT · Mimosa
Joined 2024Madina Bekbergenova
PhD researcher (Univ. Côte d'Azur & 3iA Côte d'Azur)
Agentic frameworks · RL for MS acquisition
Joined 2024Yousouf Taghzouti
Postdoctoral researcher (Univ. Côte d'Azur JEDI IdEx)
Semantic web · knowledge graphs for omics
Joined 2024Matthieu Ferraud
AI Research Engineer (CNRS)
Metabolomics × KG × AI · MetaboLinkAI
Joined 2025Martin Legrand
AI Research Engineer (HolobiomicsLab · CNRS)
Multi-agent systems · MetaboLinkAI
Joined 2025Thaiz Rodrigues Teixeira
Postdoctoral Fellow (Univ. Côte d'Azur IdEx Excellence fellowship)
RAPID-NP · antimicrobial peptides · marine BGCs
Joined 2025Benjamin Navet
Research engineer and doctoral researcher (MetaboLinkAI)
Neuro-symbolic LLM × knowledge graphs
Joined 2025Aleksandra Izdebska
Postdoctoral researcher (ANR POPS project)
LC-MS/MS · polyamines & bacterial virulence
Joined 2026Dina Boukhajou
Master 2 intern (February – August 2026)
Marine holobiont · transcriptomics × metabolomics × KG
Joined 2026Deniz Ertuğrul
Master 2 intern (February – August 2026)
Next-gen epigenetics · AI for clinical data
Where we sit, who we sit with.
HolobiomicsLab is part of the Institut de Chimie de Nice (ICN, UMR 7272) — a joint research unit of CNRS and Université Côte d'Azur — and an affiliated chair of the Interdisciplinary Institute for Artificial Intelligence (3iA Côte d'Azur).
We are based in the Valrose Parc — a botanical-garden campus in the heart of Nice, between the Mediterranean Sea and the Maritime Alps.
Since December 2025, we are a co-founding member of the eDIAM team — an alignment and expansion of our research vision that, since June 2026, also brings us into the Centre Inria de l'Université Côte d'Azur.
| Years | Amount | Source | Reference |
|---|---|---|---|
| 2025–28 | €450k | ANR–SNSF bilateral (MetaboLinkAI) | ANR-24-CE93-0012-01 · SNF 10002786 |
| 2025 | €120k | CNRS MITI — PhD fellowship | marine holobionts |
| 2024–25 | €70k | Académie 1 IdEx UniCA — KG-bot postdoc | ANR-15-IDEX-01 |
| 2025–28 | €191k | ANR — partnership with ANR POPS | ANR-24-CE44-1190 |
| 2024–28 | €200k | FNR Luxembourg — L. Pradi PhD | project 17994255 |
| 2024–27 | €120k | EUR Spectrum / 3iA — international PhD | with Prof. W. Bittremieux (Antwerp) |
| 2023–28 | €805k | CNRS Chaire Prof. Junior + IdEx UniCA | ANR-22-CPJ2-0048-01 · ANR-15-IDEX-01 |
Selected work.
- 2026Mimosa Framework: Toward Evolving Multi-Agent Systems for Scientific ResearchLegrand, M., …, Gandon, F., Nothias, L.-F.DOI arXiv (preprint)
- 2025MetaboT: An LLM-based Multi-Agent Framework for Interactive Analysis of Mass Spectrometry Metabolomics Knowledge GraphsBekbergenova, M., Pradi, L., Navet, B., Tysinger, E., …, Gandon, F., Nothias, L.-F.DOI Research Square (preprint)
- 2022High-confidence structural annotation of metabolites absent from spectral librariesHoffmann, M. A., Nothias, L.-F., Ludwig, M., et al.DOI Nature Biotechnology · 40 · 411–421
- 2022Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversityShaffer, J. P., Nothias, L.-F., Thompson, L. R., et al.DOI Nature Microbiology · 7 · 2128–2150
- 2021Systematic classification of unknown metabolites using high-resolution fragmentation mass spectraDührkop, K., Nothias, L.-F., Fleischauer, M., et al.DOI Nature Biotechnology · 39 · 462–471
- 2020Feature-based molecular networking in the GNPS analysis environmentNothias, L.-F., Petras, D., Schmid, R., et al.DOI Nature Methods · 17 · 905–908
We hire at all levels.
Postdoc, PhD, and staff positions appear regularly. We welcome applications from outstanding Master's students, MSCA postdoctoral candidates, prospective visiting scholars, and researchers preparing CNRS permanent applications.