Dr. Louis-Félix Nothias is a CNRS junior group leader based at the University Côte d’Azur & the Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d’Azur, France. In 2023, he founded the Holobiomics Lab, which develops experimental and computational methods for studying host/microbial metabolism in holobionts and their microbiomes. The lab is pioneering advanced mass spectrometry-based metabolomics techniques in multi-omics studies using artificial intelligence. Prior to this, Dr. Nothias was a postdoctoral researcher at the University of California San Diego with Prof. Pieter Dorrestein (2016-2021), where he contributed to the GNPS ecosystem GNPS ecosystem, and a research associate at the University of Geneva with Prof. Jean-Luc Wolfender (2021-2023). He has contributed to both experimental and computational methods for MS-based metabolomics annotation (collaboration with the SIRIUS team/Boecker lab, see CASMI 2022) and has pioneered integrative multi-omics studies for studying microbiota metabolites in ecosystems, including through the collaborative Earth Microbiome Project.

Dr. Tao Jiang is a passionated computational chemist and CNRS engineer with extensive expertise in applying machine learning to chemical research. He earned his Ph.D. in Computational Chemistry, followed by several postdoctoral positions, before joining the Centre National de la Recherche Scientifique (CNRS) as an Ingénieur d'Études (IE) in 2017. His initial role was at the Chemistry Laboratory of École Normale Supérieure de Lyon, where he has been actively involved in projects leveraging machine learning for chemical applications. His work took an international turn during his assignment at the CNRS-Syensqo Joint Lab, the Eco-Efficient Products and Processes Laboratory (E2P2L) in Shanghai. There, he focused on the machine learning-driven development of biodegradation processes for specialty polymers. In September 2024, Dr. Jiang joined the Holobiomic Lab at the University Côte d'Azur, where he supports the lab’s research initiatives. He is currently engaged in multiple projects, including ScienceXGuide and the application of machine learning to mass spectrometry data. His work continues to advance the integration of computational tools and artificial intelligence in chemical and biochemical research.

Madina Bekbergenova has Master in Applied Mathematics: Stochastic Modelling in Neuroscience, Erasmus Mundus InterMaths program (University of L'Aquila, University of Hamburg, University of Côte d'Azur). She is currently undertaking a joint international PhD program in Chemistry and Computer Science at the University of Côte d'Azur and University of Antwerp, under the supervsion of Dr. Nothias and Dr. Wout Bittremieux, and supported by Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur. Her research focuses on artificial intelligence for mass spectrometry, including the development of agentic framework for mass spectrometry interpretation and the use reinforcement learning techniques to optimize data acquisition processes in mass spectrometry.

Pharmacist and Master in Chemistry from the Federal University of Santa Catarina, Brazil, with academic and professional experience in natural products, chemistry, and metabolomics. Currently a PhD candidate in Chemistry at Université Côte d'Azur, supported by AFR FNR Luxembourg (project 17994255). My PhD research focuses on developing an innovative LC-MS acquisition method to enhance metabolite detection and annotation by improving MS2 spectral quality and coverage. I am dedicated to advancing next-generation tools in metabolomics, pushing the boundaries of mass spectrometry-based analysis to deepen our understanding of metabolic processes.

Yousouf Tagzhouti has a PhD degree in Computer Science (École des Mines, Saint-Etienne, FR) and has strong expertise in semantic web technologies. He has joined the HolobiomicsLab and the Wimmics team at the INRIA Sophia-Antipolis. since November 2024, with funding from the UCA JEDI Initiative d'Excellence (IDEX) UCA JEDI Initiative d'Excellence (IDEX) of the Université Côte d'Azur. He contributes to the development of an AI-framework for knowledge graph for omics research.

An IT Engineer specialized in Artificial Intelligence, graduated from Polytech Sophia-Antipolis, France, with academic and professional background in artificial neural networks and semantic knowledge integration and development in the fields of biology and chemistry. He has the join the HolobiomicsLab since October 2024, supported by funding from the Université Côte d'Azur JEDI Initiative d'Excellence (IDEX). His work focuses on the development of a method at the intersection between metabolomics / knowledge graph and artificial intelligence, contributing to the integration and analysis of metabolomics data for biological research.

Join our team as a Research Engineer (M/F) to design and develop an innovative AI research assistant for metabolomics. Over a 48-month, you will harness advanced language models, multi-agent systems, and knowledge graphs to create a state-of-the-art tool for exploring and analyzing metabolomic data.

In addition to technical development, you will contribute to project-wide operations, ensuring seamless collaboration among international partners and overseeing collective code repositories. This role is part of the Franco-Swiss MetaboLinkAI consortium (ANR-24-CE93-0012-01), in close cooperation with leading research teams in France and Switzerland. We are looking for candidates with strong expertise in Python, AI-driven development, and project management, combined with a passion for interdisciplinary scientific research.

We are looking for a skilled postdoctoral researcher with a strong background in liquid chromatography & mass spectrometry method development. This is a two-year postdoc position in the frame of the ANR POPS "DeciPhering the rOle of PolyamineS in Bacterial Virulence" project (ANR-24-CE44-1190) to investigats how polyamines modulate bacterial virulence in Pseudomonas aeruginosa and Staphylococcus aureus 🦠. By combining controlled modifications of polyamine biosynthetic pathways with integrated omics approaches, we aim to uncover the molecular mechanisms driving pathogenicity. The HolobiomicsLab is developing advanced metabolomics approaches for profiling and interpreting the metabolome of Staphylococcus aureus when exposed to polyamines.studying the metabolites involved in Pseudomonas aeruginosa's virulence and its interaction with Staphylococcus aureus, where we will use advanced experimental and computational metabolomics from multi-modal metabolomics analysis collected with state-of-art equipement. The expected starting date is late 2025. Candidate can contact L-F Nothias.

We are looking for a very talented master student with training in chemoinformatics / bioinformatics / omics. This is an exciting three-year PhD position funded by the CIFRE program with the clinical deeptech TECHiNCARE.

The PhD projects aims at designing an AI-medical assistant that can navigate multi-omics clinical data for precision medecine. A very ambitious project with high potential thanks to the advanced molecular technics being used, and the unique clinical datasets, as well as an exceptional work environment (Valrose & Hopital Lenval - with offices facing the Mediterranean sea). The start is expected at the end of 2025. Candidate can contact L-F Nothias.

Emma Tysinger has a BSc in Bioinformatics from the MIT and joined the lab in July 2023 with the support of the MIT-France program. Emma successfully implemented the first prototype of the KGBot agent during her research stay (2 months). She is now pursuing a graduate PhD program in Bioinformatics at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). See her Google Scholar.