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From Genetics to CRISPR Gene Editing with Machine Learning

Seminar: Seminars of interest | March 9 | 4-5 p.m. | 306 Soda Hall


Jennifer Listgarten, Senior Researcher, Microsoft Research New England

Electrical Engineering and Computer Sciences (EECS)


Molecular biology, healthcare and medicine have been slowly morphing into large-scale, data driven sciences dependent on machine learning and applied statistics. In this talk I will start by explaining some of the modelling challenges in finding the genetic underpinnings of disease, which is important for screening, treatment, drug development, and basic biological insight. Genome and epigenome-wide associations, wherein individual or sets of (epi)genetic markers are systematically scanned for association with disease are one window into disease processes. Naively, these associations can be found by use of a simple statistical test. However, a wide variety of structure and confounders lie hidden in the data, leading to both spurious and missed associations if not properly addressed. Much of this talk will focus on how to model these types of data. Once we uncover genetic causes, genome editing—which is about deleting or changing parts of the genetic code—will one day let us fix the genome in a bespoke manner. Editing will also help us to understand mechanisms of disease, enable precision medicine and drug development, to name just a few more important applications. I will close by discussing how we developed machine learning approaches to enable more effective CRISPR gene editing.

Bio:

Jennifer Listgarten is a Senior Researcher at Microsoft Research New England, located in Cambridge, MA. She took a long and winding road to find her current area of interest in computational biology, starting off with an undergraduate degree in Physics, followed by a Master’s in Computer Vision before completing a Ph.D. in Machine Learning at the University of Toronto. Her current focus is in machine learning and applied statistics with application to problems in biology. She works on both methods development and applications enabling new insights into basic biology and medicine. Particular areas of focus have included CRISPR guide design, statistical genetics, immunoinformatics, liquid-chromatography proteomics, and microarray analysis.


510-643-6618