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Xin He

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Overview 
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    My lab uses computational approaches to study the genetics of human diseases. A primary focus of our research is to develop novel tools for mapping risk genes of complex diseases from genome wide association studies (GWAS) and sequencing studies. These tools are often been used in close collaboration with experimental biologists. A key feature of our strategy is the integration of multiple genomic datasets, such as transcriptome data, epigenetic data, and biological networks. This integrated approach could combine signals in different datasets to increase the power of studies, and shed light on the mechanism connecting genetic changes to phenotypes.

    We are also interested in computational questions in regulatory genomics. How do cis-regulatory sequences interpret the information in cellular environments to drive spatial-temporal gene expression patterns? How do variations of regulatory sequences shape phenotypic variation and evolution? We believe a better understanding of these questions will also help the study of human genetics, specifically by improving our ability to interpret variations in non-coding sequences.
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    Collapse Biography 
    Collapse education and training
    University of Illinois, Urbana-ChampaignPhD09/2009Computer Science
    University of California, San FranciscoPostdoc07/2011Statistical genetics
    Carnegie Mellon University, PittsburghPostdoc08/2014Computational Biology

    Collapse Research 
    Collapse research activities and funding
    R01HG010773     (HE, XIN ;NOVEMBRE, JOHN)Sep 1, 2020 - Jun 30, 2024
    NIH
    Refining mutation rates and measures of purifying selection with an application to understanding the impact of non-coding variation on neuropsychiatric diseases
    Role: Principal Investigator
    R01MH116281     (ALEXANDROV, BOIAN STOIANOV;DUAN, JUBAO ;HE, XIN)Apr 8, 2019 - Jan 31, 2024
    NIH
    Integrating epigenomics with DNA breathing dynamics for human non-coding disease variants
    Role: Co-Investigator
    R01MH110531     (HE, XIN)May 17, 2017 - May 31, 2024
    NIH
    Integrative Approaches to Understanding Genetic Basis of Neuropsychiatric Diseases
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Yang Y, Yang R, Kang B, Qian S, He X, Zhang X. Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons. Cell Rep. 2023 11 28; 42(11):113335. PMID: 37889749; PMCID: PMC10842930.
      Citations: 2     Fields:    Translation:HumansCells
    2. Zhou Y, Luo K, Liang L, Chen M, He X. A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening. Nat Methods. 2023 Nov; 20(11):1693-1703. PMID: 37770710; PMCID: PMC10630124.
      Citations: 3     Fields:    Translation:HumansCells
    3. Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun. 2023 08 17; 14(1):4999. PMID: 37591828; PMCID: PMC10435551.
      Citations: 1     Fields:    Translation:HumansCells
    4. Lai B, Qian S, Zhang H, Zhang S, Kozlova A, Duan J, Xu J, He X. Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning. PLoS Comput Biol. 2022 05; 18(5):e1010011. PMID: 35576194; PMCID: PMC9135341.
      Citations: 4     Fields:    
    5. Sakabe NJ, Aneas I, Knoblauch N, Sobreira DR, Clark N, Paz C, Horth C, Ziffra R, Kaur H, Liu X, Anderson R, Morrison J, Cheung VC, Grotegut C, Reddy TE, Jacobsson B, Hallman M, Teramo K, Murtha A, Kessler J, Grobman W, Zhang G, Muglia LJ, Rana S, Lynch VJ, Crawford GE, Ober C, He X, Nóbrega MA. Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Sci Adv. 2020 12; 6(49). PMID: 33268355; PMCID: PMC7710387.
      Citations: 16     Fields:    Translation:HumansCells
    6. Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, Kozlova A, Shi J, Sanders AR, Wang G, Luo K, Sengupta S, West S, Qian S, Streit M, Avramopoulos D, Cowan CA, Chen M, Pang ZP, Gejman PV, He X, Duan J. Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants. Science. 2020 07 31; 369(6503):561-565. PMID: 32732423; PMCID: PMC7773145.
      Citations: 47     Fields:    Translation:HumansCells
    7. Zhang Z, Luo K, Zou Z, Qiu M, Tian J, Sieh L, Shi H, Zou Y, Wang G, Morrison J, Zhu AC, Qiao M, Li Z, Stephens M, He X, He C. Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet. 2020 09; 52(9):939-949. PMID: 32601472; PMCID: PMC7483307.
      Citations: 73     Fields:    Translation:HumansCells
    8. Morrison J, Knoblauch N, Marcus JH, Stephens M, He X. Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nat Genet. 2020 07; 52(7):740-747. PMID: 32451458; PMCID: PMC7343608.
      Citations: 165     Fields:    
    9. Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X. Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399. PMID: 31363082; PMCID: PMC6667447.
      Citations: 34     Fields:    Translation:Humans
    10. Liu Y, Liang Y, Cicek AE, Li Z, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, Zhao S, Jiang Y, Geller E, Ionita-Laza I, Wu J, Xia K, Noonan JP, Sun ZS, He X. A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies. Am J Hum Genet. 2018 06 07; 102(6):1031-1047. PMID: 29754769; PMCID: PMC5992125.
      Citations: 13     Fields:    Translation:HumansCells
    11. Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Walsh CA, Yu TW, Autism Sequencing Consortium, Ledbetter DH, Martin CL, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW, Morrow EM, Talkowski ME, Sutcliffe JS, Cook EH. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron. 2015 Sep 23; 87(6):1215-1233. PMID: 26402605; PMCID: PMC4624267.
      Citations: 679     Fields:    Translation:Humans
    12. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK, DDD Study, Homozygosity Mapping Collaborative for Autism, UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD, Lehtimäki T, Rehnström K, Schulte-Rüther M. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014 Nov 13; 515(7526):209-15. PMID: 25363760; PMCID: PMC4402723.
      Citations: 1330     Fields:    Translation:HumansCells
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