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Supertree-like Methods for Advancing Evolutionary Genomic Biology
Erin Molloy
IRB 4105
Tuesday, March 3, 2020, 11:00 am-12:00 pm Calendar
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Abstract
 An "unlimited thirst for genome sequencing" is driving research in many domains. Evolutionary genomic biology is no exception, as demonstrated by the 10,000 Plant Genomes Project, the (70,000) Vertebrate Genomes Project, and the Earth BioGenomes Project (which aims to assemble genomes for all living species on Earth). A goal for these ultra-large datasets is to enable researchers to address fundamental questions, such as how do species evolve/adapt to their environments and how is biodiversity created/maintained. But to transform these data into scientific insights, computational advances are needed. Estimating evolutionary trees is a key step in many research studies; however, many of the current leading methods are heuristics for NP-hard optimization problems, and the time required to run such methods on large datasets can be prohibitive. In this talk, I will present my recent work to address this challenge through the development of three new supertree-like methods. All of these methods run in polynomial time, enable provably statistically consistent phylogeny (evolutionary tree) estimation, and achieve similar accuracy to the current leading methods, while dramatically reducing memory usage and running time. I will also address open challenges and future work.

 

Bio

Erin Molloy is a PhD candidate in Computer Science at the University of Illinois, Urbana Champaign. She is motivated by the computational advances required to make sense of (genomic) data, and her work combines discrete optimization, graph algorithms, statistics, and high performance computing for applications in evolution, genomics, and neuroscience. Recently, she was a resident at the Institute for Pure and Applied Math's long program, Science at Extreme Scales---Where Big Data Meets Large Scale Computing. She has co-authored 12 referred papers in computational phylogenetics and 6 referred papers in neuroimaging. Her dissertation research, advised by Tandy Warnow and Bill Gropp, has been supported by the NSF Graduate Research Fellowship and two allocations on the Blue Waters supercomputer. More information can be found on her website (http://erinkmolloy.web.illinois.edu).

This talk is organized by Richa Mathur