I have moved to Department of Human Genetics at University of Chicago. Here is my new homepage.

I am a Lane fellow at Lane Center of Computational Biology at Carnegie Mellon University. I work with Drs. Kathryn Roeder and Ziv Bar-Joseph. My research is focused on developing computational and statistical methods for better understanding of genetic basis of complex diseases. Dramatic improvement in sequencing technology has enabled generation of a huge amount of data, yet to translate data into biological insights remains a key challenge. I believe the best way to address this challange is integrated analysis of multiple genetic and genomic datasets. The integrated approach would allow researchers to combine signals in different datasets to increase the power of studies. More importantly, by putting DNA sequence variations in the cellular context of gene interaction and regulatory networks, it is possible to better understand the mechanism linking genetic changes to phenotypes.

I have also been interested in computational approaches to address these fundamental biological problems:

  1. What is the cis-regulatory "code" that guides precise spatial-temporal patterns of gene expression?
  2. How were complex, in particular, novel biological systems evolved?

My Biography

I obtained a Bachelor degree in Biochemistry in China and started graduate study in US at a Ph.D. program in Biology. Hoping to better use my quantitative skills, I switched program after two years and eventually obtained a Ph.D. in Computer Science from University of Illinois at Urbana-Champaign in 2009. In my thesis work with Dr. Saurabh Sinha, I developed quantitative models of how regulatory sequences drive spatial gene expression patterns, and how these sequences evolve during evolution. My first postdoc is with Dr. Hao Li's at UC San Francisco. During this period, I became interested in the genetics of human diseases, and invented a novel method to use gene expression QTL to extract insights from genetic association data. For family reasons, I moved to Pittsburgh in 2011 to start my current position. With Dr. Kathryn Roeder, I developed a method for analyzing exome sequencing data from family and case-control studies, and this method was particularly useful for mapping the genetics of autism. With Dr. Ziv Bar-Joseph, I have worked on several different topics, from constructing transcriptional regulatory networks to network design principles.

Contact Information

Lane Center of Computational Biology
School of Computer Science
Carnegie Mellon University
GHC 7409
5000 Forbes Ave
Pittsburgh, PA 15213
Email: xinhe2@gmail.com