MIT Stochastics & Statistics Seminar Series: Jun Liu
November 13, 2015 | 11:00am-12:00pm | 32-141

Title: Expansion of Biological Pathways by Integrative Genomics

Abstract: The number of publicly available gene expression datasets has been growing dramatically. Various methods had been proposed to predict gene co-expression by integrating the publicly available datasets. These methods assume that the genes in the query gene set are homogeneously correlated and consider no gene-specific correlation tendencies, no background intra-experimental correlations, and no quality variations of different experiments. We propose a two-step algorithm called CLIC (CLustering by Inferred Co-expression) based on a coherent Bayesian model to overcome these limitations.  CLIC first employs a Bayesian partition model with feature selection to partition the gene set into disjoint co-expression modules (CEMs), simultaneously assigning posterior probability of selection to each dataset. In the second step, CLIC expands each CEM by scanning the whole reference genome for candidate genes that were not in the input gene set but co-expressed with the genes in this CEM. CLIC is capable of integrating over thousands of gene expression datasets to achieve much higher co-expression prediction accuracy compared to traditional co-expression methods. Application of CLIC to ~1000 annotated human pathways and ~6000 poorly characterized human genes reveals new components of some well-studied pathways and provides strong functional predictions for some poorly characterized genes. We validated the predicted association between protein C7orf55 and ATP synthase assembly using CRISPR knock-out assays.

Based on the joint work with Yang Li and the Vamsi Mootha lab.

Bio: Jun Liu is a professor of statistics at Harvard University. Prof. Liu has provided consulting to leading multinational pharmaceutical manufacturers and has served as a principal investigator in numerous National Science Foundation (NSF) and National Institutes of Health (NIH) programs. Prof. Liu is the author of the book Monte Carlo Strategies in Scientific Computing. He has published more than 150 research articles in leading scientific journals and is an Institute for Scientific Information highly-cited mathematician. In 2000 he received the Mitchell Award for the best Bayesian statistics application paper. In 2002, he received the prestigious COPSS Presidents’ Award given annually to an individual under age 40. In 2010 he received the Morningside Gold Medal in Applied Mathematics presented every three years to an individual of Chinese descent under age 45. He was selected as a Medallion Lecturer by the Institute of Mathematical Statistics (IMS) in 2002, as a Bernoulli lecturer in 2004, and as a Kuwait Lecturer in 2008 by Cambridge University. He was elected to fellow of the IMS in 2004 and fellow of the American Statistical Association in 2005. He is co-editor of the Journal of the American Statistical Association.

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