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The folding of chromosomes inside the cell nucleus plays an essential role in the regulation of genome functions. However, the underlying biological and physico-chemical mecanisms are still poorly understood, impeding any reliable quantitative predictions of genome organization and activity changes when subject to environmental, physiological or genetic/genomic perturbations . "3D Genomics" address such questions and now represents a booming field due to the recent development of high-resolution and high-throughput experimental approaches. Since its expansion, this domain of biology has required physical modeling and statistical data analyses due to the inherent complexity of experimental data. During the last decade, spectacular advances in the understanding of the coupling between genome structure and functions have been obtained thanks to the interaction between these different scientific disciplines. This school aims at enhancing such interdisciplinary communication by training researchers to computational approaches: physical modeling (theoretical concepts and numerical simulation of chromosome folding) and to data analysis (theoretical concepts and numerical approaches).
The school will be organized around these three following topics:
- Experimental approaches to characterize the spatial organization of the genome:
The aim here is to introduce the computational community to the the different experimental methods, their specific contribution and their limits, the type of data they generate, the futures issues and challenges to take up, the different technical obstacles to remove in the future.
- Bio-informatical and bio-statistical methods to analyze and interpret experimental data:
We will introduce the theoretical concepts and students will familiarize with the recent numerical tools (filtering/denoising, normalization, model parameter inference, machine learning) during daily numerical practical sessions (Python programming). We will use concrete examples by analyzing experimental data and data obtained from simulations (see next topic).
- Concepts, physical models and numerical approaches for the quantitative description of experiments:
We will introduce the main concepts of the physics of chromosomes; students will familiarize with numerical tools (simulators such as OpeenMM, Lammps or HOOMD-blue) during practical sessions.