The Faculty


Computational analysis and method development in human genetics and genomics


University of Science and Technology of China, B.S. in Biology, 1999

Loyola University of Chicago, M.S. in Computer Science, 2003

University of Illinois at Urbana-Champaign, Ph.D. in Computer Science, 2009

University of California at San Francisco, Postdoc Scholar, 2009-2011

Carnegie Mellon University, Lane Fellow of Computational Biology, 2011-2014

University of Chicago, Assistant Professor, 2014-present

Courses Taught

HGEN 471: Introductory Statistical Genetics

HGEN 488: Fundamentals of Computational Biology: Algorithms and Applications

Selected Publications

Evolution of transcript modification by N6-methyladenosine in primates.

Lijia Ma, Boxuan Zhao, Kai Chen, Amber Thomas, Jigyasa H. Tuteja, Xin He, Chuan He and Kevin P. White

Genome Res. 2017 Mar;27(3):385-392


Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci.

Sanders S, He X, Willsey J, Ercan-Sencicek G, Samocha K, et al.

Neuron, 2015 Sep 23;87(6):1215-33


Synaptic, transcriptional, and chromatin genes disrupted in autism.

De Rubeis S, He X, Goldberg A, Poultney C, Samocha K, et al.

Nature, 2014 Nov 13;515(7526):209


Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.

He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.

PLoS Genetics, 2013 Aug;9(8):e1003671


Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS.

He X, Fuller CK, Song Y, Meng Q, Zhang B, Yang X, Li H.

Am J Hum Genet, 2013 May 2;92(5):667-80


Evolutionary Origins of Transcription Factor Binding Site Clusters.

He X, Duque TS, Sinha S

Mol Biol Evol, 2012, 29(3):1059-70


Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.

He X, Samee MA, Blatti C, Sinha S.

PLoS Comput Biol, 2010 Sep 16;6(9). pii: e1000935


Alignment and prediction of regulatory sequences based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol, 2009 Mar;5(3):e1000299


Evolution of regulatory sequences in 12 Drosophila species.

Kim J*, He X*, Sinha S.

PLoS Genet, 2009 Jan;5(1):e1000330

BPHYS Students

Alan Selewa

Yifan Zhou