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Journal Articles & Preprint


Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics
Jean Morrison, Nicholas Knoblauch, Joseph Marcus, Matthew Stephens*, Xin He*
bioRxiv, 2019.

Detailed modeling of positive selection improves detection of cancer driver genes.
Siming Zhao, Jun Liu, Pranav Nanga, Yuwen Liu, Ercument Cicek, Nicholas Knoblauch, Chuan He, Matthew Stephens*, Xin He*.
Nature Communications, 2019 Jul 30;10(1):3399
New story from UChicago Medicine

Jump-Seq: Genome-Wide Capture and Amplification of 5hmC Sites.
Lulu Hu, Yuwen Liu, Shengtong Han, Lei Yang, Xiaolong Cui, Yawei Gao, Qing Dai, Xingyu Lu, Xiaochen Kou, Yanhong Zhao, Wenhui Sheng, Shaorong Gao, Xin He* and Chuan He*.
Journal of American Chemical Society, 2019 May 22

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice.
Xinxin Ke, Alesia Walker, Sven-Bastiaan Haange, Ilias Lagkouvardos, Yuwen Liu,Philippe Schmitt-Kopplin, Martin von Bergen, Nico Jehmlich, Xin He, Thomas Clavel, Peter C.K. Cheun.
Molecular Metabolism. 2019 Apr;22:96


A statistical framework for mapping risk genes from de novo mutations in whole-genome sequencing studies.
Yuwen Liu, Yanyu Liang, Ercument Cicek, Zhongshan Li, Jinchen Li, Rebecca Muhle,, Martina Krenzer, Yue Mei, Yan Wang, Nicholas Knoblauch, Jean Morrison, Siming Zhao, Yi Jiang, Evan Geller, Iuliana Ionita-Laza,  Jinyu Wu, Kun Xia, James Noonan, Zhong Sheng Sun and Xin He*
Am J Hum Genet, 2018 Jun 7;102(6):1031-1047

A comparative study of the genetic components of three subcategories of autism spectrum disorder
Jinchen Li, Shanshan Hu, Kun Zhang, Leisheng Shi, Yi Zhang, Tingting Zhao, Lin Wang, Xin He, Kun Xia, Chunyu Liu and Zhongsheng Sun.
Molecular Psychiatry. 2018 Jun 6.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.
Werling DM,  Brand H, ..., He X, ..., Sanders SJ
Nat Genet. 2018 May;50(5):727


Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders.
Hoang T. Nguyen, Julien Bryois, April Kim, Amanda Dobbyn, Laura M. Huckins, Ana B. Munoz-Manchado, Douglas M. Ruderfer, Giulio Genovese, Menachem Fromer, Xinyi Xu, Dalila Pinto, Sten Linnarsson, Matthijs Verhage, August B. Smit, Jens Hjerling-Leffler, Joseph D. Buxbaum, Christina Hultman, Pamela Sklar, Shaun M. Purcell, Kasper Lage, Xin He, Patrick F. Sullivan and Eli A. Stahl
Genome Med. 2017 Dec 20;9(1):114
Media: SFARI news

Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders
Jinchen Li, Lin Wang, Hui Guo, Leisheng Shi, Kun Zhang, Meina Tang, Shanshan Hu, Shanshan Dong, Yanling Liu, Tianyun Wang, Ping Yu, Xin He, Zhengmao Hu, Jinping Zhao, Chunyu Liu, Zhong Sheng Sun & Kun Xia
Mol Psychiatry. 2017 Sep;22(9):1282-1290

Comment on: An Expanded View of Complex Traits: From Polygenic to Omnigenic
Xin He
Journal of Psychiatry and Brain Science 2017; 2(5):S2

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
Cover story of Genome Res.


Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.
Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, Xia K, Liu C, Sun ZS, Wu J.
Mol Psychiatry, 2016 Feb;21(2):290-7


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
Recommended by Faculty of 1000, rated Exceptional.

De Novo ChIP-Seq analysis.
He X, Cicek E, Wang Y, Schulz M, Le H, Bar-Joseph Z.
Genome Biol, 2015 Sep 23;16:205


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
This large whole exome sequencing study of autism is powered by the statistical method I developed (TADA).
Media: Time, CNN, NPR, NBCUS News & World ReportWashington Post, Newsweek, CBS News, SFARI News

Topological properties of robust biological and computational networks
Navlakha S, He X, Faloutsos C, Bar-Joseph Z.
J R Soc Interface, 2014 Apr 30;11(96)
Media: Science Daily

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics.
Liu L, Lei J, Sanders SJ, Willsey AJ, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma'ayan A, Noonan JP, Sestan N, McFadden KA, State MW, Buxbaum JD, Devlin B, Roeder K.
Mol Autism, 2014 Mar 6;5(1):22.


Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.
Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW.
Cell, 2013 Nov 21;155(5):997-1007

Predicting tissue specific transcription factor binding sites.
Zhong S*, He X*, Bar-Joseph Z.
BMC Genomics, 2013 Nov 15;14(1):796 (Highly accessed)

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
Media: SFARI News (Simons Foundation Autism Research Initiative).
Recommended by Faculty of 1000 Genomics & Genetics.

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
Featured by Am. J Hum. Genet. and Genetics.


Evolutionary Origins of Transcription Factor Binding Site Clusters.
He X, Duque TS, Sinha S
Mol Biol Evol, 2012, 29(3):1059-70


Towards an evolutionary model of transcription networks.
Xie D*, Chen CC*, He X, Cao X, Zhong S
PLoS Comput Biol, 2011 Jun;7(6):e1002064

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.
Sen Sarma M, Arcoleo D, Khetani RS, Chee B, Ling X, He X, Jiang J, Mei Q, Zhai C, Schatz B
Nucleic Acids Res, 2011 Jul;39 W462-9


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

BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects.
He X, Li Y, Khetani R, Sanders B, Lu Y, Ling X, Zhai C, Schatz B.
Nucleic Acids Res, 2010 Jul 1;38 W175-81.

Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.
He X, Sarma MS, Ling X, Chee B, Zhai C, Schatz B.
BMC Bioinformatics, 2010 May 20;11:272.


A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.
PLoS ONE, 2009 Dec 1;4(12):e8155. (accepted by RECOMB Regulatory Genomics)

Detecting gene clusters under evolutionary constraint in a large number of genomes.
Ling X, He X, Xin D.
Bioinformatics, 2009 Mar 1;25(5):571-7

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 (*Equal contribution).
PLoS Genet, 2009 Jan;5(1):e1000330

Before 2008

Efficiently identifying max-gap clusters in pairwise genome comparison
Ling X, He X, Xin D, Han J.
J Comput Biol, 2008 Jul-Aug;15(6):593-609.

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.
Sinha S, He X
PLoS Comput Biol, 2007 Nov;3(11):e216

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses.
Li L, Zhu Q, He X, Sinha S, Halfon MS.
Genome Biol, 2007;8(6):R101 (Highly accessed)

Cross-species microarray analysis with the OSCAR system suggests an INSR-Pax6-NQO1 neuro-protective pathway in aging and Alzheimer's disease.
Lu Y, He X, Zhong S.
Nucleic Acid Research, 2007 Jul;35:W105-14

Generating gene summaries from biomedical literature: a study of semi-structured summarization.
Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B
Information Processing and Management, 43, 2007, 1777-1791

Identifying conserved gene clusters in the presence of homology families.
He X, Goldwasser M.
J Comput Biol, RECOMB Special Issue, 2005 Jul-Aug;12(6):638-56

Reviews and Book Chapters


ChIPs and regulatory bits.
He X, Sinha S.
Nat Biotechnol, 2010 Feb;28(2):142-3

Evolution of cis-regulatory sequences in Drosophila.
He X, Sinha S
Computational Biology of Transcription Factor Binding: Methods Mol Biol. Ed: Istvan Ladunga. Humana Press, 2010