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Computational methods for mining microbiome data

Yuzhen Ye, Ph.D.

Friday, November 3 at 12:30 p.m. in IT 252

Abstract

Advances of experimental and computational techniques have enabled the study of microbiomes (communities of microorganisms) that are related to almost every aspect of human beings. We have been developing new algorithms and computational tools for microbiome research, to address arising computational demands and challenges, and to make new use of microbiome data. In this talk, I will focus on our recently developed subtractive approaches for detecting consistent microbial marker genes that are associated with diseases such as type II diabetes and liver cirrhosis. In addition, I will share our research on the CRISPR–Cas systems (the bacterial defense systems that have been repurposed and become the most powerful tools for genome engineering), focusing on the tools we developed for discovery and characterization of CRISPR–Cas systems using microbiome data.

About Yuzhen Ye

Dr. Yuzhen Ye is an associate professor at the Computer Science department in the School of Informatics and Computing, Indiana University, Bloomington. Her group has been supported by the NIH and NSF since 2008, focusing on the development of new algorithms and tools for microbiome data analysis. She was first a post-doc and then a research assistant professor in the Burnham Institute for Medical Research before she joined IU. She completed her Ph.D. in Computational Biology at Shanghai Institute of Biochemistry, Chinese Academy of Sciences in 2001.