3D Genomics for a better synthetic biology and gene therapy.

While genome sequencing has led to significant increases in the amount of genetic information available, we are still far from a comprehensive understanding of how genomes work. Recent experiments have shown that DNA looping and folding are essential mechanisms in the switching of genes between their on and off states [1]. This has led to the idea that genetic information is also encoded through DNA topology and highlights the importance of studying the physical properties of DNA [2-4]. This project aims to predict DNA topology for improving genetic devices and genomes for utilisation in synthetic biology and gene therapy. Theoretical predictions will be compared with experiments done at the group of Mark Leake. Your project will allow you to:
1) Describe DNA loops with a physics-based computational methdology. Small loops are good models for understanding the essentials of gene regulation and also they are excellent gene-therapy vectors for introducing external genetic material in our cells. You will learn the most advanced techniques on molecular modelling
2) Develop a software for structural prediction at the genomic scale. The details learnt from small loops will be used for predicting the 3D architecture of genomes and improved them in the field of synthetic biology or biology engineering, absolutely critical for the production of biofuels, drugs or food additives. You will be trained in data analysis and bioinformatics as well as be familiar on the fields of biotechnology and synthetic biology