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Zhuzhu Zhang

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    My research lies at the intersection of genomics, neuroscience, and bioinformatics. Our lab delves into the complexities of epigenomic regulation in the brain, influenced by both inherent genetic factors and life experiences. Developing and utilizing innovative single-cell multi-omics and spatial genomics methodologies, along with neural circuit analysis and integrative computational approaches, we interrogate dynamic epigenomic and gene regulation at the levels of individual cell types, brain regions, and neural circuits. Additionally, we aim to elucidate how life experiences interplay with individuals' genetics to leave enduring imprints on epigenetic regulation, thereby affecting behavior and the propensity for brain disorders.

    Collapse Biography 
    Collapse education and training
    The Salk Institute for Biological Studies, La JollaPostdoctoral Fellow10/2022Epigenomics and Neuroscience
    The University of North Carolina at Chapel Hill, Chapel HillPhD06/2014Bioinformatics and Computational Biology
    The University of North Carolina at Chapel Hill, Chapel HillMS06/2014Statistics
    Purdue University, West LafayetteMS06/2008Developmental Biology

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Zhou J, Zhang Z, Wu M, Liu H, Pang Y, Bartlett A, Peng Z, Ding W, Rivkin A, Lagos WN, Williams E, Lee CT, Miyazaki PA, Aldridge A, Zeng Q, Salinda JLA, Claffey N, Liem M, Fitzpatrick C, Boggeman L, Yao Z, Smith KA, Tasic B, Altshul J, Kenworthy MA, Valadon C, Nery JR, Castanon RG, Patne NS, Vu M, Rashid M, Jacobs M, Ito T, Osteen J, Emerson N, Lee J, Cho S, Rink J, Huang HH, Pinto-Duartec A, Dominguez B, Smith JB, O'Connor C, Zeng H, Chen S, Lee KF, Mukamel EA, Jin X, Margarita Behrens M, Ecker JR, Callaway EM. Brain-wide correspondence of neuronal epigenomics and distant projections. Nature. 2023 Dec; 624(7991):355-365. PMID: 38092919; PMCID: PMC10719087.
      Citations: 1     Fields:    Translation:AnimalsCells
    2. Fu X, Yang X, Zhang N, Zhang R, Zhang Z, Jin A, Ye R, Zhang H. Bearing surface defect detection based on improved convolutional neural network. Math Biosci Eng. 2023 May 22; 20(7):12341-12359. PMID: 37501445.
      Citations:    Fields:    
    3. Wanamaker SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2023 Mar; 20(3):469. PMID: 36690743.
      Citations:    Fields:    
    4. Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2022 Mar 09; 2(3). PMID: 35419551; PMCID: PMC9004682.
      Citations: 35     
    5. Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs MW, Ito-Cole T, O'Connor C, Pinto-Duartec A, Dominguez B, Smith JB, Niu SY, Lee KF, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM. Epigenomic diversity of cortical projection neurons in the mouse brain. Nature. 2021 10; 598(7879):167-173. PMID: 34616065; PMCID: PMC8494636.
      Citations: 26     Fields:    Translation:AnimalsCells
    6. Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, Poirion OB, Preissl S, Pinto-Duarte A, O'Connor C, Boggeman L, Fitzpatrick C, Nunn M, Mukamel EA, Zhang Z, Callaway EM, Ren B, Dixon JR, Behrens MM, Ecker JR. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 2021 10; 598(7879):120-128. PMID: 34616061; PMCID: PMC8494641.
      Citations: 70     Fields:    Translation:AnimalsCells
    7. Kim EJ, Zhang Z, Huang L, Ito-Cole T, Jacobs MW, Juavinett AL, Senturk G, Hu M, Ku M, Ecker JR, Callaway EM. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. Neuron. 2020 07 22; 107(2):274-282.e6. PMID: 32396852; PMCID: PMC7381365.
      Citations: 48     Fields:    Translation:AnimalsCells
    8. Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, Schmitz RJ, Lewsey MG, Chory J, Ecker JR. Epigenetic silencing of a multifunctional plant stress regulator. Elife. 2019 08 16; 8. PMID: 31418686; PMCID: PMC6739875.
      Citations: 8     Fields:    Translation:AnimalsCells
    9. Wanamaker SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 08; 14(8):819-825. PMID: 28650476; PMCID: PMC5564216.
      Citations: 64     Fields:    Translation:Animals
    10. Ma H, O'Neil RC, Marti Gutierrez N, Hariharan M, Zhang ZZ, He Y, Cinnioglu C, Kayali R, Kang E, Lee Y, Hayama T, Koski A, Nery J, Castanon R, Tippner-Hedges R, Ahmed R, Van Dyken C, Li Y, Olson S, Battaglia D, Lee DM, Wu DH, Amato P, Wolf DP, Ecker JR, Mitalipov S. Functional Human Oocytes Generated by Transfer of Polar Body Genomes. Cell Stem Cell. 2017 01 05; 20(1):112-119. PMID: 27840020; PMCID: PMC5218919.
      Citations: 34     Fields:    Translation:HumansCells
    11. Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R. Molecular Criteria for Defining the Naive Human Pluripotent State. Cell Stem Cell. 2016 10 06; 19(4):502-515. PMID: 27424783; PMCID: PMC5065525.
      Citations: 239     Fields:    Translation:HumansAnimalsCells
    12. Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T. Histone modifications predispose genome regions to breakage and translocation. Genes Dev. 2015 Jul 01; 29(13):1393-402. PMID: 26104467; PMCID: PMC4511214.
      Citations: 27     Fields:    Translation:HumansCells
    13. Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21; 521(7552):316-21. PMID: 25945737; PMCID: PMC5278765.
      Citations: 109     Fields:    Translation:HumansAnimalsCells
    14. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 06; 489(7414):75-82. PMID: 22955617; PMCID: PMC3721348.
      Citations: 1493     Fields:    Translation:HumansCells
    15. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS, Gräf S. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011 Oct; 21(10):1757-67. PMID: 21750106; PMCID: PMC3202292.
      Citations: 298     Fields:    Translation:HumansCells
    16. Guo J, Zhang Z, Bi Y, Yang W, Xu Y, Zhang L. Decreased stability of photosystem I in dgd1 mutant of Arabidopsis thaliana. FEBS Lett. 2005 Jul 04; 579(17):3619-24. PMID: 15961080.
      Citations: 16     Fields:    Translation:AnimalsCells
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