Missions

We are looking for a motivated postdoctoral researcher to join the AI for Genome Interpretation (AI4GI) group at the IGMM (CNRS, Montpellier) for 18 months. The project is a collaboration between IGMM and IMAG, at the interface of genetics, bioinformatics, statistics, machine learning and deep learning.
The project
Motivation: Interpreting the genome means modeling the relationship between genotype and phenotype, which is the fundamental goal of biology. Achieving this could revolutionize genetics, medicine, and agricultural technology, leading for example to the development of better crops, able to face the challenges posed by global warming.

Objectives: This project is an interdisciplinary effort at the frontier between Biology (Genetics, Genomics), Bioinformatics, Artificial Intelligence (Neural Networks) and Statistics (LMMs). The aim is to join the Bioinformatics expertise of Dr. Raimondi on the development of GI NN methods and their application to relevant biological problems with the expertise of Dr. Bry and Dr. Trottier on the statistical inference of Linear Mixed Models (LMMs).
The project's goal is to develop a new breed of Mixed Effects Neural Networks (MENN) for Genome InterpretationI that take the best from both worlds, merging the flexibility and power of NNs with the ability of LMMs to robustly learn from structured and noisy (non i.i.d.) data, applying them on the prediction of both plants and human phenotypes.

These models will combine the flexibility of neural networks with the statistical robustness of linear mixed models to tackle one of biology's most fundamental questions: how do genetic variants determine phenotypes?

Activités

The postdoc will:
- Start by familiarizing with existing research and methods for genome interpretation (GI NNs, LMMs, GWAS).
- Familiarize with the sequencing data
- Develop and benchmark MENN prototypes on sequencing datasets (WES/WGS), starting first from model organisms and then working on disease risk prediction in humans.

Compétences

We are looking for a motivated and curious candidate, with a strong passion for science and for scientific discovery through the use and creation of new neural networks and machine learning methods.
Bioinformatics and Genome Interpretation are multi-disciplinary and rapidly evolving fields. Therefore, the candidate is expected to 1) be eager to continuously learn new skills, methods and concepts, and 2) to enjoy finding new solutions in the face of new and unforeseen difficulties.
The ideal candidate has very good 1) python programming skills, 2) understanding of the mathematical foundations and principles of Machine Learning, Linear Algebra (vectorial and matricial operations, optimization), with a particular focus on Neural Networks, 3) problem solving skills, 4) familiarity with GNU/Linux environment.
A good understanding of the basic concepts of Bioinformatics is not necessary but welcome. The project will consist in developing un-orthodox Neural Network models with Pytorch.

At least the B2 level of English is required.

Skills required:
- Strong background in neural networks, machine learning, linear algebra and an understanding of statistics.
- Solid programming skills in Python and in scientific computing (PyTorch, scikit-learn, numpy, etc).
- Familiarity with GNU/Linux.
- Problem solving skills.
- Good communication and teamwork skills.
- Knowledge of linear/mixed models is a plus.
- Familiarity with GWAS, population genetics, or bioinformatics pipelines are a plus.
- Experience with the processing of genomic biological data (whole exome or genome sequencing) is a plus

Contexte de travail

The successful candidate will join the new AI research team led by Daniele Raimondi at the Montpellier Institute of Molecular Genetics (IGMM, UMR5535 CNRS/University of Montpellier) for a 18-month project (initial contract of 13 months).
IGMM is a multidisciplinary institute with a global scientific impact, both fundamental and applied, in molecular and cellular biology (www.igmm.cnrs.fr
). The institute gathers over 200 people – researchers, engineers, technicians, and students – organized into 18 research teams, and benefits from shared services with other CNRS units on campus as well as state-of-the-art technological and scientific platforms.

Informations complémentaires

Location: IGMM, Montpellier (co-supervision at IMAG).
Duration: 18 months (initial contract: 13 months).
Start Date: Flexible; candidate selection before the end of 2025.