Bioinformatics Engineer (F/M) for ERC GeneMotors Program

The laboratory

The successful candidate will join the team led by Leonid Mirny at Institut Curie, affiliated with both Institut Curie UMR 3664 (Paris) and the Massachusetts Institute of Technology (MIT). The team studies the physical principles of genome organization and their impact on cellular function, combining theoretical modeling, computational approaches, and close interaction with experimental collaborators.

A large part of our current research focuses on understanding how cohesin-mediated loop extrusion and chromatin folding regulate enhancer–promoter communication.

The project

This position is part of a newly funded ERC-supported project aimed at understanding the mechanistic principles by which cohesin-mediated loop extrusion controls long-range gene regulation.

The central question of ERC Project GeneMotors is:

How does DNA loop extrusion by cohesin enable enhancer–promoter communication across large genomic distances, and how do regulatory “control knobs” such as CTCF positioning, motor processivity, and directionality shape transcriptional output?

The project aims to develop a predictive, quantitative framework that connects:

-         The molecular properties of cohesin (speed, processivity, directionality, bypassing rules)

-         The folding of chromatin into loops and topologically associating domains (TADs)

-         The probability and stability of enhancer–promoter contacts

-         The resulting transcriptional activity

The project combines:

-        Development of a quantitative 1D mechanistic model of enhancer–promoter communication driven by loop extrusion

-         Polymer-based 3D chromatin simulations linking loop extrusion dynamics to spatial genome folding

-        Iterative integration with experimental data from imaging, genomics, and synthetic perturbation systems within the GeneMotors consortium

Expectations / Role

 The candidate will play a central role in developing quantitative and predictive models of genome regulation within the GeneMotors program. The position involves building mechanistic frameworks that link cohesin-mediated loop extrusion dynamics to chromatin folding and transcriptional output.

Responsibilities include:

-        Develop and extend mechanistic models of enhancer–promoter communication driven by loop extrusion

-        Implement and analyze large-scale 1D stochastic models and 3D polymer simulations of chromatin organization

-        Quantitatively analyze genomic, transcriptional, and imaging datasets to confront model predictions with experimental observations

-        Work in close interaction with experimental collaborators to iteratively refine theoretical predictions

-        Contribute to scientific publications and presentations within an international collaborative consortium