Missions

As part of Louis-Félix Nothias's ANR project, the ANR SNF MetaboLinkAI project, and in collaboration with the Wimmics team (INRIA Sophia Antipolis), the HolobiomicsLab is recruiting a postdoctoral researcher (M/F) to develop generic and open artificial intelligence tools dedicated to omics sciences, with a preferred application to marine holobiont systems. This project aims to revolutionize access to multi-omics knowledge by combining semantic knowledge graphs and large language models (LLMs) in an international collaborative framework.
The postdoctoral researcher will contribute to developing an ecosystem of open-source tools enabling integrated analysis of metabolomics, proteomics, and genomics data in the context of host-microbiome interactions in marine organisms. These tools represent experimental information from mass spectrometry data and other omics techniques in a standardized framework (RDF), enable advanced data mining queries (SPARQL), and provide natural language interfaces for efficiently querying multi-omics knowledge graphs.
The main objective is to develop a suite of generic and modular tools, while exploring new knowledge graph representations (ArangoDB, GraphRAG, ...) and hybrid agent architectures to support complex molecular analyses of holobionts. The position includes responsibilities for scientific co-supervision of doctoral students and research engineers.

Activités

As part of Louis-Félix Nothias's ANR project, the ANR SNF MetaboLinkAI project, and in collaboration with the Wimmics team (INRIA Sophia Antipolis), the HolobiomicsLab is recruiting a postdoctoral researcher (M/F) to develop generic and open artificial intelligence tools dedicated to omics sciences, with a preferred application to marine holobiont systems. This project aims to revolutionize access to multi-omics knowledge by combining semantic knowledge graphs and large language models (LLMs) in an international collaborative framework.
The postdoctoral researcher will contribute to developing an ecosystem of open-source tools enabling integrated analysis of metabolomics, proteomics, and genomics data in the context of host-microbiome interactions in marine organisms. These tools represent experimental information from mass spectrometry data and other omics techniques in a standardized framework (RDF), enable advanced data mining queries (SPARQL), and provide natural language interfaces for efficiently querying multi-omics knowledge graphs.
The main objective is to develop a suite of generic and modular tools, while exploring new knowledge graph representations (ArangoDB, GraphRAG, ...) and hybrid agent architectures to support complex molecular analyses of holobionts. The position includes responsibilities for scientific co-supervision of doctoral students and research engineers.

Compétences

Technical Skills
Education: PhD in computer science, artificial intelligence, bioinformatics, or related field with expertise in AI and/or omics sciences.
Programming: Advanced proficiency in Python, experience with AI application development and LLM APIs.
Knowledge graphs: Expertise in semantic web technologies (RDF, OWL, SPARQL), Linked Data, and openness to graph-oriented databases (ArangoDB, Neo4j, GraphDB).
Artificial intelligence: Solid understanding of large language models, machine learning techniques, conversational architectures, GraphRAG, and hybrid agents.
Omics sciences: Experience with data processing related to chemistry and metabolomics.
Software development: Experience in software engineering, version control (Git), open-source collaborative development, and modular architectures.
Supervision: Experience or interest in scientific supervision of young researchers and training in emerging technologies.
Cross-cutting Skills
Interdisciplinary collaboration: Ability to work effectively with multidisciplinary teams (computer scientists, chemists, biologists).
Scientific communication: Excellent skills in scientific writing and presentation (publications, international conferences).
Autonomy and leadership: Ability to conduct research projects autonomously and propose innovative solutions.
Languages: Proficiency in scientific English (written and oral), French appreciated.
Adaptability: Ability to adapt to rapid developments in AI technologies and the needs of scientific users.

Contexte de travail

The Institute of Chemistry of Nice (ICN), UMR 7272 CNRS, located on the Valrose scientific campus, offers a cutting-edge research environment in analytical chemistry and metabolomics applied to marine ecosystems. The postdoctoral researcher will join the HolobiomicsLab led by Dr. Louis-Félix Nothias, in close collaboration with the Wimmics team (Dr. Fabien Gandon, INRIA Sophia Antipolis) in a resolutely collaborative and interdisciplinary work framework.
This position is part of the MetaboLinkAI project, a Franco-Swiss initiative aimed at developing artificial intelligence dedicated to metabolomic and multi-omics analysis. The candidate will benefit from privileged access to high-performance computing infrastructures, cutting-edge mass spectrometry equipment, and multi-omics analysis platforms dedicated to marine organisms.
The work environment is resolutely international and interdisciplinary, fostering exchanges with experts in AI, bioinformatics, analytical chemistry, marine ecology, and metabolomics. Regular interactions with Swiss partners and other European collaborators will enrich the research experience. The position offers scientific supervision responsibilities with the supervision of doctoral students and research engineers, as well as participation in training activities in AI applied to omics sciences and holobiont ecosystems.
The laboratory's philosophy emphasizes open-source development and collaborative approaches, with a strong orientation toward sharing tools and methodologies developed with the international scientific community.

Contraintes et risques

Technological complexity: Development on rapidly evolving AI technologies requiring constant technological monitoring and continuous adaptation of methods.
System integration: Work on complex software architectures integrating multiple components (LLMs, databases, web interfaces) requiring exemplary rigor in design and testing.
International collaboration: Coordination with remote teams (France-Switzerland) involving regular virtual meetings and efficient asynchronous communication.
Research deliverables: Pressure to produce high-quality scientific results within allocated timeframes, with publication in competitive international venues.
Digital ergonomics: Intensive screen work requiring adherence to good ergonomic practices and management of risks related to prolonged digital work.
Computer security: Handling of sensitive data and integration of external APIs requiring strict compliance with laboratory computer security protocols.