Discovering the Hidden World: High-throughput Discovery of Microbial Community Structure and Interactions
Recent advances in DNA sequencing have revealed that microbes are tightly coupled to our immune system and nutrient supply. They also regulate the planetary carbon and oxygen cycles that are vital to life and are found in almost every cranny on earth. However, these microbes do not act in isolation but in communities, in sometimes mutualistic, parasitic, and competitive relationships. In my talk, I will survey mathematical and computational techniques to understand what microbes compose a community and how they may interact with the host environment and each other. I will show my lab's expertise in accelerating taxonomic classification using bayesian and compressive sensing (which speeds up analysis from 10-1000x depending on the data structure). I will also demonstrate our recent computational advances to understand how "configurations of species" and particular genes/metabolic pathways relate to environmental pressures. Also, we are beginning to develop methods that can discover features at multiple scales that can simultaneously learn microbiome content and DNA sequence-level changes which relate to overall microbiome functions. In each case, I'll demonstrate the use of these methods to understand our microbiome's impact on aging, disease, and other microbial systems.
Gail Rosen received a B.S., M.S., and Ph.D. from the Georgia Institute of Technology. She is a recipient of an NSF CAREER award, a Drexel Faculty Career Development award, and a Louis and Bessie Stein Fellowship award. She serves on the editorial board of the BMC Microbiome journal and has attended two NSF-NIH BD2K Innovation Labs on Quantitative Approaches to Biomedical Data Science. She heads the Ecological and Evolutionary Signal-processing and Informatics (EESI) lab, organizes the Center for Biological Discovery from Big Data, and is the chair of the University Research Computing Facility at Drexel. In 2015-2016, she spent a year as a visiting scholar at Weill Cornell Medicine, improving taxonomic classification and analyzing the ambulance microbiome. Her interests are in machine learning and evolution.
Host: Professor Alex Wyglinski
* Please note - this seminar can be used as a make-up for ECE 596 seminar students. Please fill out a seminar make-up form, have it signed by the faculty member in charge of this lecture, and return the completed form to Colleen in the ECE office.