Xiaoyu Shi
Assistant Professor, Developmental & Cell Biology
School of Biological Sciences
School of Biological Sciences
Assistant Professor, Chemistry
School of Physical Sciences
School of Physical Sciences
Ph.D., University of Californian, Davis, 2012, Physical Chemistry
University of California, Irvine
1216 Natural Sciences 1
Mail Code: 2300
Irvine, Ca 92697
1216 Natural Sciences 1
Mail Code: 2300
Irvine, Ca 92697
Research Interests
Structural Biology, Super-Resolution Microscopy, Cell Biology, Systems Biology, Single-cell spatial Multiomics, Cell Signaling, Cilia Biology, Bioimaging, Biophysics
Websites
Appointments
Postdoc, University of California, San Francisco
Research Abstract
Cells are the essential building blocks of life. They participate in the development and function of organs at all spatial scales – from molecular signaling to tissue patterning. The mission of Shi’s lab is to elucidate how cells drive developmental mechanisms across all scales using novel imaging and omics methods.
Awards and Honors
NIH Pathway to Independence Award
NIH Director's New Innovator Award
Frontiers of Imaging Award, Chan Zuckergerg Initiative
Hellman Fellow
NIH Director's New Innovator Award
Frontiers of Imaging Award, Chan Zuckergerg Initiative
Hellman Fellow
Short Biography
Xiaoyu Shi is an Assistant Professor in the Department of Developmental and Cell Biology and the Department of Chemistry at the University of California, Irvine. Her research group uses optical and chemical approaches to develop super-resolution microscopy and spatial multiomics methods. She uses these cutting-edge technologies to study the molecular and cellular mechanisms of aging and cancers. Prior to UC Irvine, she received training in super-resolution microscopy and nonlinear optics during her postdoctoral research with Dr. Bo Huang at UCSF and her Ph.D. studies with Dr. Cheuk-Yiu Ng at UC Davis. Professor Shi is the recipient of the NIH Director’s New Innovator Award (DP2), the NIH Pathway to Independence Award (K99/R00), Chan Zuckerberg Initiative Frontiers of Imaging Award, and the Hellman Fellow.
Publications
1. X. Shi * #, Q Li *, Z. Dai, A.A.Tran, S. Feng, A.D. Ramirez, Z. Lin, X. Wang, T.T. Chow, J. Chen, D. Kumar, A.R. McColloch, J.F. Reiter, E.J. Huang, I.B. Seiple #, B. Huang #, Label-Retention Expansion Microscopy, J. Cell Biol. 220, e202105067, 2021.
2. X. Zhao, J.Q. Garcia, K. Tong, X. Chen, B. Yang, Q. Li, Z. Dai, X. Shi, I.B. Seiple, B. Huang, S. Guo, Polarized endosome dynamics engage cytoplasmic Par-3 that recruits dynein during asymmetric cell division, Science Advance 7, eabg1244, 2021
3. D. Kumar, A. Rains, V. Herranz-Pérez, Q. Lu, X. Shi, D.L. Swaney, E. Stevenson, N.J. Krogan, B. Huang, C. Westlake, J.M. Garcia-Verdugo, B. Yoder, J.F. Reiter, A ciliopathy complex builds distal appendages to initiate ciliogenesis. J. Cell Biol. 220, e202011133, 2021.
4. A. Tulpule*, J. Guan*, D.S. Neel*, H.R. Allegakoen, Y.P. Lin, A. Heslin, D. Brown, Y.-T. Chou, A. Heslin, N. Chatterjee, S. Perati, S. Menon, T.A. Nguyen, J. Debnath, A.D. Ramirez, X. Shi, B. Yang, S. Feng, S. Makhija, D. Brown, B. Huang#, T.G. Bivona#, Cytoplasmic protein granules organize kinase-mediated RAS signaling. Cell 184, 2649, 2021.
5. J. Zhang, D. Velmeshev, K. Hashimoto, Y.-H. Huang, J. W. Hofmann, X. Shi, J. Chen, A. M. Leidal, J. G. Dishart, M. K. Cahill, K. W. Kelley, S. A. Liddelow, W. W. Seeley, B. L. Miller, T. C. Walther, R. V. Farese Jr., J. P. Taylor, E. M. Ullian, B. Huang, J. Debnath, T. Wittmann, A. R. Kriegstein, E. J. Huang, Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency, Nature 588, 459, 2020.
6. X. Huang, X. Shi, M.E. Hansen, C.L. Nemeth, A. Ceili, B. Huang, T. Mauro, M. Koval, T.A. Desai, Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes, ACS Nano 14, 13192, 2020.
7. X. Shi, G. Garcia, Y. Wang, J. Reiter, B. Huang, Alignment of super-resolution images for semi-flexible structures in 3D, PLoS One 0212735, 2019.
8. X. Shi, H. Gao, Q.-Z. Yin, Y.-C. Chang, R. C. Wiens, W. M. Jackson, C. Y. Ng, Branching ratio measurements of the predissociation of 12C16O by time-slice velocity-map ion imaging in the energy region from 106,250 to 107,800 cm-1, J. Phys. Chem. A 122, 8136, 2018.
Cover article
9. T. Chow, X. Shi, J.H. Wei, J. Guan, G. Stadler, B. Huang, E. Blackburn, Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection,
Nat. Commun. 9, 3583, 2018.
10. X. Shi *, G. Garcia *, J. C. Van De Weghe, R. McGorty, G. J. Pazour, D. Doherty, B. Huang, J. F. Reiter, Super-resolution microscopy reveals that disruption of ciliary transition zone architecture is a cause of Joubert syndrome, Nat. Cell Biol. 19, 1178, 2017.
Cover article
11. X. Shi, Q.-Z. Yin, H. Gao, Y. C. Chang, W. M. Jackson, R. Wiens and C. Y. Ng, A Predissociation Branching Ratio Comparison of CO and N2: Implications for Oxygen Nitrogen Isotope Evolution in the Early Solar System, Astrophys. J. 850, 48, 2017.
12. J. Guan, H. Liu, X. Shi, S. Feng, B. Huang, Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH, Biophys. J. 112,1077, 2017.
Highlighted as New and Notable
13. H. Huang, H. Wang, Z. Luo, X. Shi, Y.-C. Chang, C. Y. Ng. A High-Resolution Vacuum Ultraviolet Laser Photoionization and Photoelectron Study of the Co Atom, Astrophys. J. 833, 205, 2016.
14. H. Gao, Y. Song, Y.-C. Chang, X. Shi, Q.-Z. Yin, R. C. Wiens, W. M. Jackson, C. Y. Ng, Branching Ratio Measurements for Vacuum Ultraviolet Photodissociation of 12C16O, J. Phys. Chem. A 117, 6185, 2013.
15. H. Huang, Y.-C. Chang, Z. Luo, X. Shi, C.-S. Lam, K.-C. Lau, and C. Y. Ng, Rovibronically selected and resolved two-color laser photoionization and photoelectron study of cobalt carbide cation, J. Chem. Phys. 138, 094301, 2013.
16. K.-C. Lau, Y. Pan, C.-S. Lam, H. Huang, Y.-C. Chang, Z. Luo, X. Shi, and C. Y. Ng, High-level ab initio predictions for the ionization energy, bond dissociation energies and heats of formation of cobalt carbide (CoC) and its cation (CoC+), J. Chem. Phys. 138, 094302, 2013.
17. X. Shi, H. Huang, B. Jacobson, Y. C. Chang, Q.-Z. Yin, and C. Y. Ng, A High-Resolution Photoionization and Photoelectron Study of 58Ni using a Vacuum Ultraviolet Laser, Astrophys. J. 747, 20, 2012.
18. H. Gao, Y. Song, L. Yang, X. Shi, Q.-Z. Yin, C. Y. Ng, and W. M. Jackson, Branching Ratio measurements of the Predissociation of 12C16O by Time-Slice Velocity-Map Ion Imaging in the Vacuum Ultraviolet region from 108 000 to 110 500 cm-1, J. Chem. Phys. 137, 034305, 2012.
19. H. Gao, Y. Song, L. Yang, X. Shi, Q.-Z. Yin, C. Y. Ng, and W. M. Jackson, Communication: Branching Ratio measurements in the Predissociation of 12C16O by Time-Slice Velocity-Map Ion Imaging in the Vacuum Ultraviolet region, J. Chem. Phys. 135, 221101, 2011.
20. Y. C. Chang, X. Shi, K-C Lau, Q.-Z. Yin, H. T. Liou, and C. Y. Ng, Rovibronically Selected and Resolved Two-color Laser Photoionization and Photoelectron study of Nickel Carbide Cation, J. Chem. Phys. 133, 054310, 2010.
21. K.-C. Lau, Y. C. Chang, X. Shi, C. Y. Ng, High-level ab initio predictions for the ionization energy, bond dissociation energies and heats of formations of Nickel carbide (NiC) and its cation (NiC+), J. Chem. Phys. 133, 114304, 2010.
22. Q.-Z. Yin, X. Shi, C. Chang, C. Y. Ng, Comment on ''Experimental test of self-shielding in vacuum ultraviolet photodissociation of CO'', Science 324, 1516, 2009.
23. W. M. Jackson, X. Yang, X. Shi, and A. L. Cochran, The temporal changes in the emission spectrum of Comet 9P/ Tempel 1 after Deep Impact, Astrophys. J. 698, 1609, 2009.
24. Y. Zhu, M. Tang, X. Shi, Y. Zhao, Quantum chemical study of cyclic dipeptides, Int. J. Quantum Chem. 3, 745, 2007.
2. X. Zhao, J.Q. Garcia, K. Tong, X. Chen, B. Yang, Q. Li, Z. Dai, X. Shi, I.B. Seiple, B. Huang, S. Guo, Polarized endosome dynamics engage cytoplasmic Par-3 that recruits dynein during asymmetric cell division, Science Advance 7, eabg1244, 2021
3. D. Kumar, A. Rains, V. Herranz-Pérez, Q. Lu, X. Shi, D.L. Swaney, E. Stevenson, N.J. Krogan, B. Huang, C. Westlake, J.M. Garcia-Verdugo, B. Yoder, J.F. Reiter, A ciliopathy complex builds distal appendages to initiate ciliogenesis. J. Cell Biol. 220, e202011133, 2021.
4. A. Tulpule*, J. Guan*, D.S. Neel*, H.R. Allegakoen, Y.P. Lin, A. Heslin, D. Brown, Y.-T. Chou, A. Heslin, N. Chatterjee, S. Perati, S. Menon, T.A. Nguyen, J. Debnath, A.D. Ramirez, X. Shi, B. Yang, S. Feng, S. Makhija, D. Brown, B. Huang#, T.G. Bivona#, Cytoplasmic protein granules organize kinase-mediated RAS signaling. Cell 184, 2649, 2021.
5. J. Zhang, D. Velmeshev, K. Hashimoto, Y.-H. Huang, J. W. Hofmann, X. Shi, J. Chen, A. M. Leidal, J. G. Dishart, M. K. Cahill, K. W. Kelley, S. A. Liddelow, W. W. Seeley, B. L. Miller, T. C. Walther, R. V. Farese Jr., J. P. Taylor, E. M. Ullian, B. Huang, J. Debnath, T. Wittmann, A. R. Kriegstein, E. J. Huang, Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency, Nature 588, 459, 2020.
6. X. Huang, X. Shi, M.E. Hansen, C.L. Nemeth, A. Ceili, B. Huang, T. Mauro, M. Koval, T.A. Desai, Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes, ACS Nano 14, 13192, 2020.
7. X. Shi, G. Garcia, Y. Wang, J. Reiter, B. Huang, Alignment of super-resolution images for semi-flexible structures in 3D, PLoS One 0212735, 2019.
8. X. Shi, H. Gao, Q.-Z. Yin, Y.-C. Chang, R. C. Wiens, W. M. Jackson, C. Y. Ng, Branching ratio measurements of the predissociation of 12C16O by time-slice velocity-map ion imaging in the energy region from 106,250 to 107,800 cm-1, J. Phys. Chem. A 122, 8136, 2018.
Cover article
9. T. Chow, X. Shi, J.H. Wei, J. Guan, G. Stadler, B. Huang, E. Blackburn, Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection,
Nat. Commun. 9, 3583, 2018.
10. X. Shi *, G. Garcia *, J. C. Van De Weghe, R. McGorty, G. J. Pazour, D. Doherty, B. Huang, J. F. Reiter, Super-resolution microscopy reveals that disruption of ciliary transition zone architecture is a cause of Joubert syndrome, Nat. Cell Biol. 19, 1178, 2017.
Cover article
11. X. Shi, Q.-Z. Yin, H. Gao, Y. C. Chang, W. M. Jackson, R. Wiens and C. Y. Ng, A Predissociation Branching Ratio Comparison of CO and N2: Implications for Oxygen Nitrogen Isotope Evolution in the Early Solar System, Astrophys. J. 850, 48, 2017.
12. J. Guan, H. Liu, X. Shi, S. Feng, B. Huang, Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH, Biophys. J. 112,1077, 2017.
Highlighted as New and Notable
13. H. Huang, H. Wang, Z. Luo, X. Shi, Y.-C. Chang, C. Y. Ng. A High-Resolution Vacuum Ultraviolet Laser Photoionization and Photoelectron Study of the Co Atom, Astrophys. J. 833, 205, 2016.
14. H. Gao, Y. Song, Y.-C. Chang, X. Shi, Q.-Z. Yin, R. C. Wiens, W. M. Jackson, C. Y. Ng, Branching Ratio Measurements for Vacuum Ultraviolet Photodissociation of 12C16O, J. Phys. Chem. A 117, 6185, 2013.
15. H. Huang, Y.-C. Chang, Z. Luo, X. Shi, C.-S. Lam, K.-C. Lau, and C. Y. Ng, Rovibronically selected and resolved two-color laser photoionization and photoelectron study of cobalt carbide cation, J. Chem. Phys. 138, 094301, 2013.
16. K.-C. Lau, Y. Pan, C.-S. Lam, H. Huang, Y.-C. Chang, Z. Luo, X. Shi, and C. Y. Ng, High-level ab initio predictions for the ionization energy, bond dissociation energies and heats of formation of cobalt carbide (CoC) and its cation (CoC+), J. Chem. Phys. 138, 094302, 2013.
17. X. Shi, H. Huang, B. Jacobson, Y. C. Chang, Q.-Z. Yin, and C. Y. Ng, A High-Resolution Photoionization and Photoelectron Study of 58Ni using a Vacuum Ultraviolet Laser, Astrophys. J. 747, 20, 2012.
18. H. Gao, Y. Song, L. Yang, X. Shi, Q.-Z. Yin, C. Y. Ng, and W. M. Jackson, Branching Ratio measurements of the Predissociation of 12C16O by Time-Slice Velocity-Map Ion Imaging in the Vacuum Ultraviolet region from 108 000 to 110 500 cm-1, J. Chem. Phys. 137, 034305, 2012.
19. H. Gao, Y. Song, L. Yang, X. Shi, Q.-Z. Yin, C. Y. Ng, and W. M. Jackson, Communication: Branching Ratio measurements in the Predissociation of 12C16O by Time-Slice Velocity-Map Ion Imaging in the Vacuum Ultraviolet region, J. Chem. Phys. 135, 221101, 2011.
20. Y. C. Chang, X. Shi, K-C Lau, Q.-Z. Yin, H. T. Liou, and C. Y. Ng, Rovibronically Selected and Resolved Two-color Laser Photoionization and Photoelectron study of Nickel Carbide Cation, J. Chem. Phys. 133, 054310, 2010.
21. K.-C. Lau, Y. C. Chang, X. Shi, C. Y. Ng, High-level ab initio predictions for the ionization energy, bond dissociation energies and heats of formations of Nickel carbide (NiC) and its cation (NiC+), J. Chem. Phys. 133, 114304, 2010.
22. Q.-Z. Yin, X. Shi, C. Chang, C. Y. Ng, Comment on ''Experimental test of self-shielding in vacuum ultraviolet photodissociation of CO'', Science 324, 1516, 2009.
23. W. M. Jackson, X. Yang, X. Shi, and A. L. Cochran, The temporal changes in the emission spectrum of Comet 9P/ Tempel 1 after Deep Impact, Astrophys. J. 698, 1609, 2009.
24. Y. Zhu, M. Tang, X. Shi, Y. Zhao, Quantum chemical study of cyclic dipeptides, Int. J. Quantum Chem. 3, 745, 2007.
Grants
NIH Pathway to Independence Award (K99/R00), NIGMS; 2018-2023
NIH Director's New Innovator Award (DP2), 2022-2027
Frontiers of Imaging Award, Chan Zuckergerg Initiative, 2021-2023
Professional Societies
Biophysical Society (BPS)
American Chemical Society (ACS)
American Society for Cell Biology (ASCB)
Other Experience
Postdoc
University of California, San Francisco 2013—2019
University of California, San Francisco 2013—2019
Research Centers
Center for Complex Biological Systems (CCBS)
NSF-Simons Center for Multiscale Cell Fate Research (CMCF)
Chao Family Comprehensive Cancer Center (CFCCC)
Link to this profile
https://faculty.uci.edu/profile/?facultyId=7023
https://faculty.uci.edu/profile/?facultyId=7023
Last updated
11/02/2022
11/02/2022