Navigating the human genome is currently a 1-dimensional (1D) search: we can find a gene of interest by its coordinates on the linear sequence, along with its annotations and metadata. Graphs are typically used to represent gene associations, for example regulatory interactions, and a large body of research is devoted to reconstruct and analyse such networks in order infer unknown associations. However, 1D genome navigation and association networks typically lack the spatial context in which the underlying biological processes take place. Recent advances in molecular methods have made it possible to capture physical interactions between genomic fragments, opening the way to reconstruct 3-dimensional (3D) genome maps and spatial networks. In this talk I will present key approaches for inferring 3D conformations from high-throughput molecular data, spanning probabilistic and spectral methods, as well as the computational challenges on the journey towards 3D and 4D (spatio-temporal) genome navigation.
Yoli Shavit is a PhD student at the Computer Laboratory, University of Cambridge and a recipient of the Cambridge International Trust scholarship. She studied Computer Science and Life Sciences at Tel Aviv University, earning a joint BSc. After graduating in 2009, Yoli moved to Imperial College London where she received her MSc in Bioinformatics and Theoretical Systems Biology. Subsequently, she held a position as a software engineer at Algotec, a company specializing in medical image processing and analysis. In 2012, Yoli started her PhD at the Artificial Intelligence Group of the Computer Laboratory, under the supervision of Dr Pietro Lio’. Her current research focuses on developing algorithms and tools for integration and calibration of nucleomic data with the aim of reconstructing 3-dimensional (3D) genome maps at different resolutions and over time (4D). In addition to her ongoing research, Yoli has interned at the Computational Biology group at Microsoft Research (Cambridge), where she has developed methods for modelling gene regulatory networks. She is also the current chair of women@CL, an organization promoting women engagement and leadership in Computer Science.