XinHeXin He0.000000000000000.000000000000003083He, XinStatistical geneticsComputational biologyPsychiatric geneticsCancer genomicsGene regulationMy 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.Associate Professorplugins:TwitterTwitterprns:coAuthorOfcoauthor ofprns:emailEncryptedemail addressprns:endDateend dateFaculty Rankprns:fullNamefull nameprns:grantAwardedBygrant awarded byprns:hasAuthorListauthor listprns:hasFacultyRankhas faculty rankprns:hasNetworkhas networkprns:hasPublicationVenuepublished inprns:informationResourceReferenceinformation resource referenceprns:isPrimaryPositionis primary positionprns:latitudelatitudeprns:longitudelongitudeprns:mainImagephotoprns:maxWeightmaximum weightprns:medlineTAjournal title abbreviationprns:meshDescriptorUIMeSH DescriptorUIprns:meshSemanticGroupNameMeSH semantic group nameprns:minWeightminimum weightprns:numberOfAuthorsnumber of authorsprns:numberOfConnectionsnumber of connectionsprns:numberOfPublicationsnumber of publicationsprns:personIdPerson IDprns:personInPrimaryPositionperson in primary positionprns:physicalNeighborOfphysical neighborprns:pluginSearchableDataProfilesRNS Plugin Searchable Dataprns:positionInDepartmentposition in departmentprns:predicateNodepredicate nodeprns:principalInvestigatorNameprincipal investigator nameprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:startDatestart dateprns:trainingAtOrganizationeducational organizationprns:trainingLocationtraining locationprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provinceAgreementvivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipvivo:degreeEarneddegree earnedDepartmentvivo:educationalTrainingeducation and trainingEducational Trainingvivo:freetextKeywordkeywordsGrantvivo:hasResearchArearesearch areasvivo:hasResearcherRoleresearch activitiesvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:majorFieldmajor field of degreevivo:orcidIdORCID idvivo:overviewoverviewvivo:personInPositionpositionsPositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleResearcher Rolevivo:researcherRoleOfresearcher role ofRolevivo:roleContributesTocontributes tovivo:sponsorAwardIdsponsor award idURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPersonD001686Phenomena330.993921Biological PhenomenaAuthorship 1069402Authorship 106941226402605Sanders 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, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW, Autism Sequencing Consortium, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MWNeuronInsights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron. 2015 Sep 23; 87(6):1215-1233.Neuron2015-09-23T00:00:002015Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.25363760De 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, Lehtimäki T, 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, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, 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 JDNatureSynaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014 Nov 13; 515(7526):209-15.Nature2014-10-29T00:00:002014Synaptic, transcriptional and chromatin genes disrupted in autism.09/2009University of IllinoisUrbana-ChampaignUniversity of Illinois, Computer SciencePhDComputer Science07/2011University of CaliforniaSan FranciscoUniversity of California, Statistical geneticsPostdocStatistical genetics08/2014Carnegie Mellon UniversityPittsburghCarnegie Mellon University, Computational BiologyPostdocComputational BiologyXiaochangZhangXiaochang Zhang41.7886000000000087.598699999999993579Zhang, XiaochangAssistant ProfessorMedicine-Genetic MedicineAuthorship 1084962029754769Liu 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 XAmerican journal of human geneticsA 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.Am J Hum Genet2018-05-10T00:00:002018A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.D009857Genes & Molecular Sequences65880.965304Oncogenes31363082Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He XNature communicationsDetailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399.Nat Commun2019-07-30T00:00:002019Detailed modeling of positive selection improves detection of cancer driver genes.32451458Morrison J, Knoblauch N, Marcus JH, Stephens M, He XNature geneticsMendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nat Genet. 2020 07; 52(7):740-747.Nat Genet2020-05-25T00:00:002020Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.Authorship 1384239Authorship 138424532601472Zhang 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 CNature geneticsGenetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet. 2020 09; 52(9):939-949.Nat Genet2020-06-29T00:00:002020Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability.32732423Zhang 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 JScience (New York, N.Y.)Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants. Science. 2020 07 31; 369(6503):561-565.Science2020-07-31T00:00:002020Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants.Authorship 14126715Authorship 14126820PriyaMoorjaniPriya Moorjani0.000000000000000.000000000000002924Moorjani, PriyaPost Doctoral ScholarWilliamDobynsWilliam B. Dobyns0.000000000000000.000000000000002964Dobyns, WilliamPROFESSOR 33268355Sakabe 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 MAScience advancesTranscriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Sci Adv. 2020 12; 6(49).Sci Adv2020-12-02T00:00:002020Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.Medicine-Hematology and OncologyAuthorship 14898028Principal InvestigatorPrincipal InvestigatorCo-Investigator2024-05-31NIHHE, XIN2017-05-17Integrative Approaches to Understanding Genetic Basis of Neuropsychiatric DiseasesR01MH1105312024-01-31NIHALEXANDROV, BOIAN STOIANOV;DUAN, JUBAO ;HE, XIN2019-04-08Integrating epigenomics with DNA breathing dynamics for human non-coding disease variantsR01MH1162812024-06-30NIHHE, XIN ;NOVEMBRE, JOHN2020-09-01Refining mutation rates and measures of purifying selection with an application to understanding the impact of non-coding variation on neuropsychiatric diseasesR01HG010773D058685Genes & Molecular SequencesPhysiology19240.977788Genetic Pleiotropy35576194Lai B, Qian S, Zhang H, Zhang S, Kozlova A, Duan J, Xu J, He XPLoS computational biologyAnnotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning. PLoS Comput Biol. 2022 05; 18(5):e1010011.PLoS Comput Biol2022-05-16T00:00:002022Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning.Chicago60637IL0.9599960.022335978research areas0.4206510.04849411coauthor of22.40152.3023960similar to1112selected publicationsAuthorship 1578318D057182Procedures18430.965302Mendelian Randomization AnalysisChuanHe1Gp8Cq8dHMzMknJtY0fp/Cv/+94=Chuan He0.000000000000000.000000000000003123He, ChuanProfessorD064112Chemicals & DrugsGenes & Molecular Sequences19220.968984Clustered Regularly Interspaced Short Palindromic Repeatshttps://cgh.uchicago.edu/page/leadershipGlobal Healthhttps://zhanglaboratory.org/Zhang Labhttps://www.uchicagomedicine.org/find-a-physician/physician/olufunmilayo-i-olopadeUChicago Medicinehttp://ober.bsd.uchicago.edu/My Lab Sitehttps://www.northshore.org/research-institute/investigators/jubao-duan-phd/NorthShore Labhttps://xinhelab.org/Lab websitehttp://jnpopgen.orgNovembre Lab Sitehttps://cancerbio.uchicago.edu/program/faculty/olufunmilayo-olopadeCancer Biologyhttps://www.uchicagomedicine.org/conditions-services/cancer/cancer-risk-preventionCancer Risk and Preventionhttp://he-group.uchicago.eduMy Lab Sitehttp://stephenslab.uchicago.edu/lab websitehttps://psychiatry.uchicago.edu/research-0Psychiatric Researchhttps://genes.uchicago.edu/faculty/xiaochang-zhang-phdHuman Geneticshttps://pott-lab.uchicago.edu/Pott Labhttps://github.com/stephenslabgithub pagehttps://psychiatry.uchicago.edu/center-psychiatric-genetics-cpg-northshore-university-healthsystemCenter for Psychiatric Geneticsjnovembremstephens999jubao9812SebastianPottxHJmH7U1DO/RmHllZ0mg9mHvSebastian Pott0.000000000000000.000000000000003142Pott, Sebastian0000-0002-4118-6150Assistant ProfessorMatthewStephensMatthew Stephens0.000000000000000.000000000000003155Stephens, MatthewProfessorChemistryHuman GeneticsMedicineUniversity of ChicagoNancy JeanCox2WFmE4EXCuiXhHlsaUXv9Gq0+s+oNancy Jean Cox41.78927490000000-87.601250000000001011Cox, Nancy JeanEmeritus/Emerita37591828Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott SNature communicationsSingle-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun. 2023 08 17; 14(1):4999.Nat Commun2023-08-17T00:00:002023Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation.CaroleOber1G1rDrM1DO/RmHllZ0mg9mHvCarole Ober41.78927490000000-87.601250000000001623Ober, CaroleProfessorOlufunmilayoOlopade321vBIF1GuTQkntjbwjr93A=Olufunmilayo Olopade41.78927490000000-87.601250000000001960Olopade, OlufunmilayoProfessor37889749Yang Y, Yang R, Kang B, Qian S, He X, Zhang XCell reportsSingle-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons. Cell Rep. 2023 11 28; 42(11):113335.Cell Rep2023-10-26T00:00:002023Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons.Authorship 1674235Authorship 1674245Authorship 1674251037770710Zhou Y, Luo K, Liang L, Chen M, He XNature methodsA 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.Nat Methods2023-09-28T00:00:002023A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening.YusukeNakamuraYusuke Nakamura41.78927490000000-87.60125000000000582Nakamura, YusukeEmeritus/Emerita, ProfessorJubaoDuanJubao Duan41.78927490000000-87.60125000000000801Duan, JubaoProfessor, Part-Timetrue1ProfessorProfessortrue1Postdoctoral FellowPostdoctoral Fellowtrue1Assistant ProfessorAssistant Professortrue1ProfessorProfessortrue1Postdoctoral ScholarPostdoctoral Scholartrue1ProfessorProfessortrue1Post Doctoral ScholarPost Doctoral Scholartrue1Associate ProfessorAssociate Professortrue1PROFESSOR PROFESSOR true1Emeritus/Emerita, ProfessorEmeritus/Emerita, Professortrue1Emeritus/EmeritaEmeritus/Emeritatrue1Assistant ProfessorAssistant Professortrue1ProfessorProfessortrue1Professor, Part-TimeProfessor, Part-Timetrue1ProfessorProfessor1010Psychiatry & Behav. NeurosciStatistics RaphaelMouradRaphael Mourad0.000000000000000.000000000000002792Mourad, RaphaelPostdoctoral ScholarJohnNovembreJohn Novembre0.000000000000000.000000000000002807Novembre, JohnProfessorYairFieldYair Field0.000000000000000.000000000000002823Field, YairPostdoctoral Fellow