Selected work.
A curated selection. The full record lives on Google Scholar , HAL, and ORCID.
2026
Legrand, M., …, Gandon, F., Nothias, L.-F.
Mimosa Framework: Toward Evolving Multi-Agent Systems for Scientific ResearcharXiv (preprint)
Taghzouti, Y., Jiang, T., Juigné, C., Navet, B., Gandon, F., …, Nothias, L.-F.
T2S-Metrics: Unified Library for Evaluating SPARQL Queries Generated From Natural LanguageHAL (preprint)
2025
Bekbergenova, M., Pradi, L., Navet, B., Tysinger, E., …, Gandon, F., Nothias, L.-F.
MetaboT: An LLM-based Multi-Agent Framework for Interactive Analysis of Mass Spectrometry Metabolomics Knowledge GraphsResearch Square (preprint)
Schmid, R., …, Nothias, L.-F., et al.
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries
Nature Methods
Taghzouti, Y., …, Gandon, F., Nothias, L.-F.
Q²Forge: Minting Competency Questions and SPARQL Queries for Question-Answering Over Knowledge GraphsKnowledge Capture Conference (K-CAP '25)
2024
Schmid, R., Heuckeroth, S., …, Nothias, L.-F., et al.
Reproducible mass spectrometry data processing and compound annotation in MZmine 3Nature Protocols
Allard, P.-M., …, Nothias, L.-F., et al.
Comprehensive mass spectrometric metabolomic profiling of a chemically diverse collection of plantsScientific Data
Nothias, L.-F., Schmid, R., Garlet, A., et al.
Functional metabolomics of the human scalp: a metabolic niche for Staphylococcus epidermidismSystems · 9(2) · e0035623
2023
Bittremieux, W., …, Dorrestein, P. C., Nothias, L.-F., et al.
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomicsNature Communications
2022
Hoffmann, M. A., Nothias, L.-F., Ludwig, M., et al.
High-confidence structural annotation of metabolites absent from spectral librariesNature Biotechnology · 40 · 411–421
Shaffer, J. P., Nothias, L.-F., Thompson, L. R., et al.
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversityNature Microbiology · 7 · 2128–2150
2021
Dührkop, K., Nothias, L.-F., Fleischauer, M., et al.
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectraNature Biotechnology · 39 · 462–471
Schmid, R., Petras, D., Nothias, L.-F., et al.
Ion identity molecular networking for mass-spectrometry-based metabolomics in the GNPS environmentNature Communications · 12 · 3832
2020
Nothias, L.-F., Petras, D., Schmid, R., et al.
Feature-based molecular networking in the GNPS analysis environmentNature Methods · 17 · 905–908
Jarmusch, A. K., …, Nothias, L.-F., et al.
ReDU: a framework to find and reanalyze public mass spectrometry dataNature Methods
2019
Morton, J. T., Aksenov, A. A., Nothias, L.-F., et al.
Learning representations of microbe–metabolite interactionsNature Methods · 16 · 1306–1314
Cao, L., Gurevich, A., Alexander, K. L., et al.
MetaMiner: a scalable peptidogenomics approach for discovery of ribosomal peptide natural products with blind modifications from microbial communitiesCell Systems · 9(6) · 600–608.e4