Upcoming Event: Oden Institute & Dept. of Molecular Biosciences

Integrative Models of 3D Nuclear DNA Organization

Anupama Jha, Postdoctoral Scholar, University of Washington

Abstract

My long-term research goal is to study how DNA sequence variations influence the 3D genome organization in humans and across mammalian evolution, how variations in genome organization impact transcriptional and post-transcriptional gene regulation across human tissues, and how this regulatory infrastructure is misregulated in cancer. In this talk, I will cover previous work constructing sequence-to-function models for different steps of gene regulation, including 3D genome architecture, gene expression and alternative splicing. We identified several regulatory elements implicated in gene regulation by interpreting these models using existing and novel techniques. These include transcription factors and G-quadruplexes implicated in trans-contacts and RNA-binding proteins implicated in tissue-specific alternative splicing. Furthermore, we leveraged interpretable machine-learning techniques to find typical transcriptomic signatures of solid tumors in the form of shared protein-coding genes, lncRNAs and splice junctions. I will outline my vision for developing novel computational methods for large-scale multi-omics data analysis.  These methods can potentially yield actionable insights into cell-specific gene regulation in heterogeneous healthy and diseased individuals.

Biography

Anupama Jha is a postdoctoral scholar in the Department of Genome Sciences at the University of Washington, advised by Prof. William Stafford Noble. Dr. Jha obtained her Ph.D. in computer science from the University of Pennsylvania, advised by Prof. Yoseph Barash. Her research interests include developing interpretable models for different steps of gene regulation, including 3D genome architecture, gene expression and alternative splicing using large-scale machine learning methods.