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Institut de Recherche pour le Développement

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PhD student in AI for plant gene regulation Institut de recherche pour le développement in France

Degree Level

PhD

Field of study

Computer Science

Funding

Available

Deadline

Dec 4, 2026

Country flag

Country

France

University

Institut de Recherche pour le Développement

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Keywords

Computer Science
Agriculture
Biology
Computational Biology
Genomic
Bioinformatic
ML

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About this position

Research theme: This PhD project focuses on predicting gene expression in plants by combining genomic language models with machine learning on gene regulatory networks.

The thesis is part of the BioLLM-CRE project and is hosted in the DIADE research unit (Diversity, Adaptation and Development of tropical plants), a joint unit involving IRD, CIRAD and the University of Montpellier. The unit works on plant biodiversity, adaptation mechanisms and plant-environment interactions, using approaches that span genome analysis, biochemistry, physiology, microscopy, modelling and data integration.

The doctoral research is strongly interdisciplinary, bringing together bioinformatics, artificial intelligence and root developmental biology. The student will work on plant regulatory genomics and computational modelling, with access to high-performance computing resources and an international research environment in Montpellier.

  • Build a reference dataset linking cis-regulatory elements to spatio-temporal expression profiles in Arabidopsis and rice.
  • Evaluate general-purpose and plant-specific genomic language models for expression prediction.
  • Compare these approaches with classical machine learning methods.
  • Design graph learning models, including GNNs and Graph Transformers, to integrate sequence representations into gene regulatory networks.
  • Interpret the models to identify regulatory modules and test transfer to other cereals.
  • Disseminate results through publications, conferences and the PhD thesis.

The student will also help share the benchmark, code and models as open source and take part in the scientific life of the unit.

Funding details

Available

What's required

Applicants should hold a level 7 degree (Master's or engineering degree) in bioinformatics, computer science (AI, machine learning), or computational biology. Required skills include strong Python programming, a deep learning framework such as PyTorch, knowledge of machine learning and deep learning (including transformers and representation learning), and familiarity with graph learning tools such as PyTorch Geometric or DGL and language models such as Hugging Face. Candidates should also have knowledge of genomics and sequencing data handling (NGS formats, bioinformatics tools), good scientific English in writing and speaking, scientific curiosity, autonomy, rigour, team spirit, good interpersonal skills, ability to synthesise and write, perseverance, and adaptability.

How to apply

Apply through the IRD recruitment website using the advert link provided. Use the application page referenced in the posting and follow the instructions on the platform. The position is a fixed-term doctoral contract.

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