Ye Zheng

Associate Professor

NOMIS Center for Immunobiology and Microbial Pathogenesis

Salk Institute for Biological Studies - Publications

all Publications


Hang, S., Paik, D., Yao, L., Kim, E., Jamma, T., Lu, J., Ha, S., Nelson, B.N., Kelly, S.P., Wu, L., Zheng, Y., Longman, R.S., Rastinejad, F., Devlin, A.S., Krout, M.R., Fischbach, M.A., Littman, D.R., Huh, J.R. Bile acid metabolites control T17 and T cell differentiation. (2019) Nature. DOI: 10.1038/s41586-019-1785-z

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Bapat, S.P., Liang, Y., Zheng, Y. Characterization of Immune Cells from Adipose Tissue. (2019) Current Protocols in Immunology. 126(1):e86. DOI: 10.1002/cpim.86

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Chang, C., Loo, C.S., Zhao, X., Solt, L.A., Liang, Y., Bapat, S.P., Cho, H., Kamenecka, T.M., Leblanc, M., Atkins, A.R., Yu, R.T., Downes, M., Burris, T.P., Evans, R.M., Zheng, Y. The nuclear receptor REV-ERBα modulates Th17 cell-mediated autoimmune disease. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116(37):18528-18536. DOI: 10.1073/pnas.1907563116

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Zheng, B., Nimmerjahn, A. Editorial for "In vivo spinal cord imaging in health, injury and disease". (2019) Exp. Neurol. 322:113038. DOI: 10.1016/j.expneurol.2019.113038


Owen, D.L., Mahmud, S.A., Sjaastad, L.E., Williams, J.B., Spanier, J.A., Simeonov, D.R., Ruscher, R., Huang, W., Proekt, I., Miller, C.N., Hekim, C., Jeschke, J.C., Aggarwal, P., Broeckel, U., LaRue, R.S., Henzler, C.M., Alegre, M.L., Anderson, M.S., August, A., Marson, A., Zheng, Y., Williams, C.B., Farrar, M.A. Thymic regulatory T cells arise via two distinct developmental programs. (2019) Nature Immunology. DOI: 10.1038/s41590-018-0289-6

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Zhang, L.J., Chen, S.X., Guerrero-Juarez, C.F., Li, F., Tong, Y., Liang, Y., Liggins, M., Chen, X., Chen, H., Li, M., Hata, T., Zheng, Y., Plikus, M.V., Gallo, R.L. Age-Related Loss of Innate Immune Antimicrobial Function of Dermal Fat Is Mediated by Transforming Growth Factor Beta. (2018) Immunity. DOI: 10.1016/j.immuni.2018.11.003

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Klann, J.E., Kim, S.H., Remedios, K.A., He, Z., Metz, P.J., Lopez, J., Tysl, T., Olvera, J.G., Ablack, J.N., Cantor, J.M., Boland, B.S., Yeo, G., Zheng, Y., Lu, L.F., Bui, J.D., Ginsberg, M.H., Petrich, B.G., Chang, J.T. Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. (2018) Journal of Immunology. 200(12):4012-4023. DOI: 10.4049/jimmunol.1800112

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Cao, Q., Zhao, X., Bai, J., Gery, S., Sun, H., Lin, D.C., Chen, Q., Chen, Z., Mack, L., Yang, H., Deng, R., Shi, X., Chong, L.W., Cho, H., Xie, J., Li, Q.Z., Müschen, M., Atkins, A.R., Liddle, C., Yu, R.T., Alkan, S., Said, J.W., Zheng, Y., Downes, M., Evans, R.M., Koeffler, H.P. Circadian clock cryptochrome proteins regulate autoimmunity. (2017) Proceedings of the National Academy of Sciences of the United States of America. 114(47):12548-12553. DOI: 10.1073/pnas.1619119114

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He, N., Fan, W., Henriquez, B., Yu, R.T., Atkins, A.R., Liddle, C., Zheng, Y., Downes, M., Evans, R.M. Metabolic control of regulatory T cell (Treg) survival and function by Lkb1. (2017) Proc. Natl. Acad. Sci. U.S.A. 114(47):12542-12547. DOI: 10.1073/pnas.1715363114

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Wang, J., He, N., Zhang, N., Quan, D., Zhang, S., Zhang, C., Yu, R.T., Atkins, A.R., Zhu, R., Yang, C., Cui, Y., Liddle, C., Downes, M., Xiao, H., Zheng, Y., Auwerx, J., Evans, R.M., Leng, Q. NCoR1 restrains thymic negative selection by repressing Bim expression to spare thymocytes undergoing positive selection. (2017) Nature Communications. 8(1):959. DOI: 10.1038/s41467-017-00931-8

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Zheng, Y. A Rogue Foxp3 Mutant Undermines Treg Cell Function. (2017) Immunity. 47(2):211-214. DOI: 10.1016/j.immuni.2017.07.024

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Klann, J.E., Remedios, K.A., Kim, S.H., Metz, P.J., Lopez, J., Mack, L.A., Zheng, Y., Ginsberg, M.H., Petrich, B.G., Chang, J.T. Talin Plays a Critical Role in the Maintenance of the Regulatory T Cell Pool. (2017) Journal of Immunology. 198(12):4639-4651. DOI: 10.4049/jimmunol.1601165

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Chinen, T., Kannan, A.K., Levine, A.G., Fan, X., Klein, U., Zheng, Y., Gasteiger, G., Feng, Y., Fontenot, J.D., Rudensky, A.Y. An essential role for the IL-2 receptor in Treg cell function. (2016) Nature Immunology. 17(11):1322-1333. DOI: 10.1038/ni.3540

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Liu, W.H., Kang, S.G., Huang, Z., Wu, C.J., Jin, H.Y., Maine, C.J., Liu, Y., Shepherd, J., Sabouri-Ghomi, M., Gonzalez-Martin, A., Xu, S., Hoffmann, A., Zheng, Y., Lu, L.F., Xiao, N., Fu, G., Xiao, C. A miR-155-Peli1-c-Rel pathway controls the generation and function of T follicular helper cells. (2016) Journal of Experimental Medicine. 213(9):1901-19. DOI: 10.1084/jem.20160204

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Bapat, S.P., Myoung Suh, J., Fang, S., Liu, S., Zhang, Y., Cheng, A., Zhou, C., Liang, Y., LeBlanc, M., Liddle, C., Atkins, A.R., Yu, R.T., Downes, M., Evans, R.M., Zheng, Y. Depletion of fat-resident Treg cells prevents age-associated insulin resistance. (2015) Nature. 528(7580):137-41. DOI: 10.1038/nature16151

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Hernandez, J.B., Chang, C., LeBlanc, M., Grimm, D., Le Lay, J., Kaestner, K.H., Zheng, Y., Montminy, M. The CREB/CRTC2 pathway modulates autoimmune disease by promoting Th17 differentiation. (2015) Nature Communications. 6:7216. DOI: 10.1038/ncomms8216

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Li, X., Zheng, Y. Regulatory T cell identity: formation and maintenance. (2015) Trends in Immunology. 36(6):344-53. DOI: 10.1016/j.it.2015.04.006

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Li, X., Liang, Y., LeBlanc, M., Benner, C., Zheng, Y. Function of a Foxp3 cis-element in protecting regulatory T cell identity. (2014) Cell. 158(4):734-48. DOI: 10.1016/j.cell.2014.07.030

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Zheng, Y. ChIP-on-chip for FoxP3. (2011) Methods in Molecular Biology. 707:71-82. DOI: 10.1007/978-1-61737-979-6_6

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Zheng, Y., Josefowicz, S., Chaudhry, A., Peng, X.P., Forbush, K., Rudensky, A.Y. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. (2010) Nature. 463(7282):808-12. DOI: 10.1038/nature08750

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Zheng, Y., Chaudhry, A., Kas, A., deRoos, P., Kim, J.M., Chu, T.T., Corcoran, L., Treuting, P., Klein, U., Rudensky, A.Y. Regulatory T-cell suppressor program co-opts transcription factor IRF4 to control T(H)2 responses. (2009) Nature. 458(7236):351-6. DOI: 10.1038/nature07674

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Wang, J., Wang, X., Hussain, S., Zheng, Y., Sanjabi, S., Ouaaz, F., Beg, A.A. Distinct roles of different NF-kappa B subunits in regulating inflammatory and T cell stimulatory gene expression in dendritic cells. (2007) Journal of Immunology. 178(11):6777-88.

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Zheng, Y., Rudensky, A.Y. Foxp3 in control of the regulatory T cell lineage. (2007) Nature Immunology. 8(5):457-62. DOI: 10.1038/ni1455

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Zheng, Y., Josefowicz, S.Z., Kas, A., Chu, T.T., Gavin, M.A., Rudensky, A.Y. Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. (2007) Nature. 445(7130):936-40. DOI: 10.1038/nature05563

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Hsieh, C.S., Zheng, Y., Liang, Y., Fontenot, J.D., Rudensky, A.Y. An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires. (2006) Nature Immunology. 7(4):401-10. DOI: 10.1038/ni1318

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Prendes, M., Zheng, Y., Beg, A.A. Regulation of developing B cell survival by RelA-containing NF-kappa B complexes. (2003) Journal of Immunology. 171(8):3963-9.

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Qu, J., Li, X., Novitch, B.G., Zheng, Y., Kohn, M., Xie, J.M., Kozinn, S., Bronson, R., Beg, A.A., Minden, A. PAK4 kinase is essential for embryonic viability and for proper neuronal development. (2003) Molecular and Cellular Biology. 23(20):7122-33.

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Tao, X., Xu, Y., Zheng, Y., Beg, A.A., Tong, L. An extensively associated dimer in the structure of the C713S mutant of the TIR domain of human TLR2. (2002) Biochemical and Biophysical Research Communications. 299(2):216-21. DOI: 10.1016/s0006-291x(02)02581-0

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Ouaaz, F., Arron, J., Zheng, Y., Choi, Y., Beg, A.A. Dendritic cell development and survival require distinct NF-kappaB subunits. (2002) Immunity. 16(2):257-70.

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Education

BS, Peking University, Beijing, China
PhD, Columbia University, New York, NY
Postdoctoral Fellow, University of Washington, Seattle, WA
Research Scholar, Memorial Sloan-Kettering Cancer Center, New York, NY


Awards & Honors

  • 2010-2015 Rita Allen Scholar Award
  • 2005-2008 Cancer Research Institute postdoctoral fellowship