Effective analysis and experimental design for CRISPR screens with scRNA-seq readout

Understanding how cell fate decisions are regulated is a key question in molecular biology. Exciting new technologies have enabled investigation of how mutating a specific gene in a single cell affects the cell's function in a variety of different conditions. However, current computational methods do not fully exploit this potential: new methods are needed to improve the analysis of the data and to optimise the experimental setup. I will develop these new statistical methods and develop and make publicly available a comprehensive suite of tools. By enabling improved data analysis and experimental setup, my methods will contribute to improved understanding of how genes regulate other genes, of how this varies across individuals, and of how to best differentiate stem cells into more specialised cells, an experimental protocol with important consequences for cell therapy.