Société Française de Bioinformatique

Mots-Clés

Deep learning L1 Retrotransposon Genomics Genetics Bioinformatics

Description

Project Overview

The TAGC / TGML INSERM U1090 laboratory (Aix‑Marseille Université) invites applications for a ANR‑funded PhD dedicated to the development of predictive models that estimate the impact of new L1 retrotransposon insertions on gene expression.
The project is supervised by Aitor González (MCF‑HDR, Aix‑Marseille Université) and is carried out in close collaboration with Gaël Cristofari (DR1, Inserm) at IRCAN (Nice, France), a world‑leading expert on L1 biology.
Our laboratory brings together bioinformaticians and experimentalists to uncover the functional architecture of the genome using state‑of‑the‑art genomics and bioinformatics approaches.

Scientific Goals

• Build and benchmark machine‑learning and deep‑learning models that predict how novel L1 insertions influence transcriptional activity.
• Leverage both public genomic resources and in‑house functional data.
• Analyze model features (e.g., through SHAP, in‑silico mutagenesis) so that predictions can generate testable hypotheses about L1‑driven regulatory mechanisms.

Candidate Profile

We are looking for a highly motivated candidate holding a Master’s degree in bioinformatics (or a closely related field) with a strong interest in machine and deep learning, genomics, and genetics.

Application Details

• Contact for application and informal inquiries: aitor.gonzalez@univ-amu.fr
• Application materials: cover letter, curriculum vitae, and contact information for at least two reference letters.
• Application period: Ongoing until the position is filled with an appropriate candidate.

Useful Links

• https://tagc.univ-amu.fr/en/directory/gonzalez-aitor
• https://tagc.univ-amu.fr/
• https://univ-cotedazur.fr/m-gael-cristofari
• https://www.ircan.org/research/teams/gael-cristofari