Zhuang Research Lab
Principal investigator
Group members
Directions to the lab
Positions available
Protocols & software
last updated 08/28/14


  1. W.L. Hwang, S. Deindl, B.T. Harada, X. Zhuang, "Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA" Nature 512, 213-217 (2014)
  2. A. Blunk, Y. Akbergenova, R. Cho, J. Lee, U. Walldorf, K. Xu, G. Zhong, X. Zhuang, J. Littleton, "Postsynaptic actin regulates active zone spacing and glutamate receptor apposition at the Drosophila neuromuscular junction" Mol. Cell. Neurosci. 61, 241-254 (2014)
  3. S. Wang, J. Moffitt, G. Dempsey, X. Xie, X. Zhuang, "Characterization and development of photoactivatable fluorescent proteins for single molecule based superresolution imaging" Proc. Natl. Acad. Sci. USA 111, 8452-8457 (2014)
  4. J. Chung, S. Shim, R. Everley, S. Gygi, X. Zhuang, D. Clapham, "Structurally distinct Ca2+ signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility", Cell 157, 808-822 (2014)
  5. S. Jia, J. Vaughan, X. Zhuang, "Isotropic three-dimensional super-resolution imaging with a self-bending point spread function", Nature Photonics 8, 302-306 (2014)
  6. A. Avalos, A. Bilate, M. Witte, A. Tai, J. He, M. Frushicheva, P. Thill, F. Meyer-Wentrup, C. Theile, A. Chakraborty, X. Zhuang, H. Ploegh, "Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells", JEM 211, 365-379 (2014)
  7. K. Xu, G. Zhong, X. Zhuang, "Actin, spectrin and associated proteins form a periodic cytoskeleton structure in axons", Science 339, 452-456 (2013)
  8. Y. Doksani, J. Wu, T. de Lange, X. Zhuang, "Super-resolution fluorescence imaging reveals TRF2-dependent t-loop formation", Cell 155, 345-356 (2013)
  9. H. Babcock, J. Moffitt, Y. Cao, X. Zhuang, "Fast compressed sensing analysis for super-resolution imaging using L1-homotopy", Optics Express 21, 28583-28596 (2013)
  10. S. Deindl, W.L. Hwang, S.K. Hota, T.R. Blosser, P. Prasad, B. Bartholomew, X. Zhuang, "ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps", Cell 152, 442-452 (2013)
  11. J. He, E. Sun, M.B. Bujny, D. Kim, M.W. Davidson, X. Zhuang, "Dual function of CD81 in influenza uncoating and budding", PLOS Pathogens, (2013)
  12. S. Hota, S. Bhardwaj, S. Deindl, Y. Lin, X. Zhuang, B. Bartholomew, "Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains", Nature Structural and Molecular Biology 20, 222-229 (2013)
  13. J.C. Vaughan, G.T. Dempsey, E. Sun, X. Zhuang, "Phospine Quenching of Cyanin Dyes as a Versatile Tool for Fluorescence Microscopy", JACS 135, 1197-1200 (2013)
  14. E. Sun, J, He, X. Zhuang, "Live cell imaging of viral entry", Current Opinion in Virology 3, 34-43 (2013)
  15. A. Alivisatos, A. Andrews, E. Boyden, M. Chun, G. Church, K. Deisseroth, J. Donoghue, S. Fraser, J. Lippincott-Schwartz, L. Looger, S. Masmanidis, P. McEuen, A. Nurmikko, H. Park, D. Peterka, C. Reid, M. Roukes, A. Scherer, M. Schnitzer, T. Sejnowski, K. Shepard, D. Tsao, G. Turrigiano, P. Weiss, C. Xu, R. Yuste, X. Zhuang, "Nanotools for neuroscience and brain activity mapping", ACS Nano 7, 1850-1866 (2013)
  16. E. Sun, J. He, X. Zhuang, "Dissecting the role of COPI complexes in influenza virus infection", Journal of Virology 87, 2673-2685 (2013)
  17. I. Kim, W. Pan, S. Jones, Y. Zhang, X. Zhuang, D. Wu, "Clathrin and AP2 are required for Ptdlns(4,5)P2-mediated formation of LRP6 signalosomes", JCB 200, 419-428 (2013)
  18. J. Vaughan, S. Jia, X. Zhuang, "Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging", Nature Methods 9, 1181-1184 (2012)
  19. V. Berk, J.C.N. Fong, G.T. Dempsey, O.N. Develioglu, X. Zhuang, J. Liphardt, F.H. Yildiz, S. Chu "Molecular Architecture and Assembly Principles of Vibrio Cholerae Biofilms", Science 13, 236-239 (2012)
  20. S-H. Shim, C. Xia, G. Zhong, H.P. Babcock, J.C. Vaughan, B. Huang, X. Wang, C. Xu, G-Q. Bi, X. Zhuang "Super-resolution Fluorescence Imaging of Organelles in Live Cells with Photoswitchable Membrane Probes", Proc. Natl. Acad. Sci. 109, 13978-13983 (2012)
  21. S. Deindl, X. Zhuang, "Monitoring Conformational Dynamics with Single-Molecule Fluorescence Resonance Energy Transfer: Application in Nucleosome Remodeling", Methods Enzymology 513, 59-86 (2012)
  22. H. P. Babcock, Y. Sigal, X. Zhuang, "A High-Density 3D Localization Algorithm for Stochastic Optical Reconstruction Microscopy", Optical Nanoscopy 1, 6 (2012)
  23. E. A. Mukamel, H. P. Babcock, X. Zhuang, "Statistical Deconvolution for Super-resolution Fluorescence Microscopy", Biophysical Journal 102, 2391-2400 (2012)
  24. K. Xu, H. Babcock, X. Zhuang, "Dual-objective STORM Reveals Three-dimensional Filament Organization in the Actin Cytoskeleton", Nature Methods 9, 185-188 (2012)
  25. M. Lakadamyali, H. Babcock, M. Bates X. Zhuang, J. Lichtman, "3D Multicolor Super-Resolution Imaging Offers Improved Accuracy in Neuron Tracing", PLoS One 7, e30826 (2012)
  26. M. Bates, G. T. Dempsey, K. H. Chen, X. Zhuang, "Multicolor Super-resolution Fluorescence Imaging Via Multi-parameter Fluorophore Detection", Chemphyschem 13, 99-107 (2012)
  27. G. Dempsey, J. Vaughan, K. Chen, M. Bates, X. Zhuang, "Evaluation of Fluorophores for Optimal Performance in Localization-based Super-resolution Imaging", Nature Methods 8, 1027-1036 (2011)
  28. J. Vaughan, X. Zhuang, "New Fluorescent Probes for Super-resolution Imaging", Nature Biotechnology 29, 880-881 (2011)
  29. W. Wang, G. Li, C. Chen, X. Xie, X. Zhuang, "Chromosome Organization by a Nucleoid Associated Protein", Science 333, 1445-1449 (2011)
  30. E. Garner, R. Bernard, W. Wang, X. Zhuang, D. Rudner, T. Mitchison, "Coupled, Circumferential Motions of the Cell Wall Synthesis Machinery and MreB Filaments in B. subtilis", Science 333, 222-225 (2011)
  31. S. Jones, S-H. Shim, J. He, X. Zhuang, "Fast, three-dimensional super-resolution imaging of live cells", Nature Methods 8, 499-505 (2011)
  32. M. Mihalusova, J.Y. Wu, X. Zhuang, "Functional importance of telomerase pseudoknot revealed by single-molecule analysis", Proc. Natl. Acad. Sci. , (2011)
  33. B. Huang, H. Babcock, X. Zhuang, "Breaking the diffraction barrier: Super-resolution imaging of cells", Cell 143, 1047-1058 (2010)
  34. S. Liu, B.T. Harada, J.T. Miller, S.F.J. Le Grice, X. Zhuang, "Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription", Nature Struct. Mol. Biol. 17, 1453-1460 (2010)
  35. A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang, "Super-resolution imaging of chemical synapses in the brain", Neuron 68, 843-856 (2010)
  36. M. Wu, B. Huang, M. Graham, A. Raimondi, J.E. Heuser, X. Zhuang, P. De Camilli, "Coupling between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free system", Nature Cell Biology 12, 902-908 (2010)
  37. S. Chung, M. Wendeler, J.W. Rausch, G. Beilhartz, M. Gotte, B.R. O'Keefe, A. Bermingham, J.A. Beutler, S. Liu, X. Zhuang, S.F.J. Le Grice, "Structure-Activity Analysis of Vinylogous Urea Inhibitors of Human Immunodeficiency Virus-Encoded Ribonuclease H", Antimicrob Agents Chemother 54, 3913-3921 (2010)
  38. E. Schuman, X. Zhuang, "New technologies, editorial overview", Current Opinion in Neurobiology 20, 608-609 (2010)
  39. M. Bates, S.A. Jones, X. Zhuang, "Stochastic Optical Reconstruction Micrscopy (STORM) -- A Method for Superresolution Fluorescence Imaging", Imaging: A Laboratory Manual, Rafael Yuste (Ed.) Cold Spring Harbor Laboratory Press (2010)
  40. T. Blosser, J. Yang, M. Stone, G. Narlikar, X. Zhuang, "Dynamics of Nucleosome Remodeling by Individual ACF Complexes", Nature 462, 1022-1027 (2009)
  41. G. Dempsey, M. Bates, W. Kowtoniuk, D. Liu, R. Tsien, X. Zhuang, "Photoswitching Mechanism of Cyanine Dyes", J. Am. Chem. Soc. 131 131, 18192-18193 (2009)
  42. M. Bates, B. Huang, M. Rust, G. Dempsey, W. Wang, X. Zhuang, "Sub-diffraction-limit Imaging with Stochastic Optical Reconstruction Micrscopy (STORM)", Nobel Volume on Single Molecule Spectroscopy in Chemistry, Springer (2009)
  43. G. Dempsey, W. Wang, X. Zhuang, "Fluorescence imaging at sub-diffraction limit resolution with stochastic optical reconstruction microscopy", Handbook of Single-Molecule Biophysics, Springer (2009)
  44. J. Wu, M. Stone, X. Zhuang, "A Single-molecule Assay for Telomerase Structural-function Analysis", Nucleic Acid Research, doi:10.1093/nar/gkp1033
  45. J. Vaughan, B. Brandenburg, J. Hogle, X. Zhuang, "Rapid Actin-dependent Viral Motility in Live Cells", Biophysical Journal 97, 1647-1656 (2009)
  46. X. Zhuang, "Nano-imaging with STORM", Nature Photonics 3, 365-367 (2009)
  47. B. Huang, M. Bates, X. Zhuang, "Super-resolution Fluorescence Microscopy", Annual Review Biochemistry 78, 993-1016 (2009)
  48. E. Abbondanzieri, X. Zhuang, "Concealed Enzyme Coordination", Nature 457, 392-393 (2009)
  49. H.M. van der Schaar, M.J. Rust, C. Chen, H. van der Ende-Metselaar, J. Wilschut, X. Zhuang, J.M. Smit, "Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells", PLOS Pathogens 4, e1000244 (2008)
  50. B. Huang, S.A. Jones, B. Brandenburg, X. Zhuang, "Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution", Nature Methods 5, 1047-1052 (2008)
  51. S. Liu, E. Abbondanzieri, J. W. Rausch, S. F. J. Le Grice, X. Zhuang, "Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates", Science 322, 1092-1097 (2008)
  52. M. Bates, B. Huang, X. Zhuang, "Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes", Curr. Opin. Chem. Biol. 12, 505-514 (2008)
  53. E. Abbondanzieri, G. Bokinsky, J. W. Rausch, J. X. Zhang, S. F. J. Le Grice, X. Zhuang, "Dynamic binding orientations direct activity of HIV reverse transcriptase", Nature 453, 184-189 (2008)
  54. C. Chen, X. Zhuang, "Epsin1 is a cargo specific adaptor for the clathrin-mediated endocytosis of influenza virus", Proc. Natl. Acad. Sci. USA 105, 11790-11795 (2008)
  55. J. Zheng, Y. Ding, B. Tian, Z. Wang, X. Zhuang, "Luminescent and Raman active silver nanoparticles with polycrystalline structure", J. Am. Chem. Soc. 130, 10472-10473 (2008)
  56. B. Huang, W. Wang, M. Bates, X. Zhuang, "Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy", Science 319, 810-813 (2008)
  57. M. Rust, M. Lakadamyali, B. Brandenburg, X. Zhuang, "Single-virus tracking in live cells.", Single Molecule Techniques: A Laboratory Manual, P.R. Selvin, T. Ha (Eds), Cold Spring Harbor Laboratory Press (2008)
  58. M. Bates, B. Huang, G. T. Dempsey, X. Zhuang, "Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes", Science 317, 1749-1753 (2007)
  59. S. Liu, G. Bokinsky, N. G. Walter, X. Zhuang, "Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic fingerprinting", Proc. Natl. Acad. Sci. USA 104, 12634-12639 (2007)
  60. B. Brandenburg, L. Y. Lee, M. Lakadamyali, M. J. Rust, X. Zhuang, J. M. Hogle, "Imaging poliovirus entry in live cells", PLoS Biol. 5, e183, 1543-1555 (2007)
  61. M. D. Stone, M. Mihalusova, C. M. O'Connor, R. Prathapam, K. Collins, X. Zhuang, "Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein", Nature 446, 458-461 (2007)
  62. B. Brandenburg, X. Zhuang, "Virus trafficking - learning from single-virus tracking", Nat. Rev. Microbiology 5, 197-208 (2007)
  63. Y. Zhou, X. Zhuang, "Kinetic analysis of sequential multi-step reactions", J. Phys. Chem. B 111, 13600-13610, (2007)
  64. H. M. van der Shaar, M. J. Rust, B. Waarts, H. van der Ende Metselaar, R. J. Kuhn, J. Wilschut, X. Zhuang, J. M. Smit, "Characterization of the early events in Dengue virus cell entry by biochemical assays and single-virus tracking", J. Virol. 81, 12019-12028 (2007)
  65. C. K. Payne, S. Jones, C. Chen, X. Zhuang, "Internalization and trafficking of cell surface proteoglycans and proteoglycan binding ligands", Traffic 8, 389-401 (2007)
  66. Y. Zhou, X. Zhuang, "Robust reconstruction of the rate constant distribution using the phase function method", Biophysical Journal 91, 4045-4053 (2006)
  67. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)", Nature Methods 3, 793-795 (2006)
  68. G. Bokinsky, L. G. Nivon, S. Liu, G. Chai, M. Hong, K. M. Weeks, X. Zhuang, "Two distinct binding modes of a protein cofactor with its target RNA", J. Mol. Biol. 361, 771-784 (2006)
  69. M. Lakadamyali, M. J. Rust, X. Zhuang, "Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes", Cell 124, 997-1009 (2006)
  70. G. Bokinsky, X. Zhuang, "Single-molecule RNA folding", Acc. Chem. Res. 38, 566-573 (2005)
  71. X. Zhuang, "Single-molecule RNA Science", Annu. Rev. Biophys. Biomol. Struct. 34, 399-414 (2005)
  72. M. Bates, T. R. Blosser, X. Zhuang, "Short-range spectroscopic ruler based on a single-molecule optical switch", Phys. Rev. Lett. 94, 108101 (2005)
  73. X. Zhuang, "Unraveling DNA condensation by optical tweezers", Science 305 , 188-190 (2004)
  74. M. J. Rust, M. Lakadamyali, F. Zhang, X. Zhuang, "Assembly of endocytic machinery around individual influenza viruses during viral entry", Nature Struct. Mol. Biol. 11 , 567-573 (2004)
  75. M. Lakadamyali, M. J. Rust, X. Zhuang, "Endocytosis of influenza viruses", Micro. Infection 6, 929-936 (2004)
  76. F. Patolsky, G. Zheng, O. Hayden, M. Lakadamyali, X. Zhuang, C. M. Lieber, "Electrical detection of single viruses", Proc. Natl. Acad. Sci. USA 101, 14017-14022 (2004)
  77. H. P. Babcock, C. Chen, X. Zhuang, "Using single particle-tracking to study nuclear trafficking of viral genes", Biophys. J. 87, 2749-2758 (2004)
  78. D. Rueda, G. Bokinsky, M. M. Rhodes, M. J. Rust, X. Zhuang, N. G. Walter, "Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance", Proc. Natl. Acad. Sci. USA 101, 10066-10071 (2004)
  79. M. Lakadamyali, M. J. Rust, H P. Babcock, X. Zhuang, "Visualizing infection of individual influenza viruses", Proc. Natl. Acad. Sci. USA 100, 9280-9285 (2003)
  80. G. Bokinsky, D. Rueda, V. K. Misra, A. Gordus, M. M. Rhodes, H. P. Babcock, N. G. Walter, X. Zhuang, "Single-molecule transition-state analysis of RNA folding", Proc. Natl. Acad. Sci. USA 100 , 9302-9307 (2003)
  81. X. Zhuang and M. Rief, "Single-molecule folding", Curr. Opin. Struct. Biol. 13 , 88-97 (2003)
  82. L. E. Bartley, X. Zhuang, R. Das, S. Chu, D. Herschlag, "Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA", J. Mol. Biol. 328 , 1011-1026 (2003)
  83. X. Zhuang, H. Kim, M. Pereira, H. Babcock, N. Walter, S. Chu, "Correlating structural dynamics and function in single ribozyme molecules", Science 296 , 1473-1476 (2002)
  84. R. Russell, X. Zhuang, H. Babcock, I. S. Millett, S. Doniach, S. Chu, D. Herschlag, "Exploring the folding landscape of a structured RNA", Proc. Natl. Acad. Sci. USA 99 , 155-160 (2002)
  85. X. Zhuang, L. Bartley, H. Babcock, R. Russell, T. Ha, D. Herschlag, S. Chu, "A single-molecule study of RNA catalysis and folding", Science 288 , 2048-2051 (2000)
  86. X. Zhuang, T. Ha, H. Kim, T. Centner, S. Labeit, S. Chu, "Fluorescence quenching: a tool for single-molecule protein-folding study", Proc. Natl. Acad. Sci. USA 97 , 14241-14244 (2000)
  87. T. Ha, X. Zhuang, H. Kim, J. Orr, J. Williamson, S. Chu, "Ligand-induced conformational changes of single RNA molecules", Proc. Natl. Acad. Sci. USA 96 , 9077-9082 (1999)
  88. S.-C. Hong, M. Oh-e, X. Zhuang, Y. R. Shen, J. J. Ge, F. W. Harris, S. Z. D. Cheng, "Orientation of side chains and adsorbed liquid crystal molecules on a rubbed polyimide surface studied by optical harmonic generation", Phys. Rev. E 63 , 0517061-7 (2001)
  89. J. J. Ge, C. Y. Li, G.I. Xue, I. K. Mann, S. Z. D. Cheng, J. Z. Zhang, D. Zhang, S. Wang, F. W. Harris, S.-C. Hong, X. Zhuang, Y. R. Shen, "Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains", J. Am. Chem. Soc. 123 , 5768-5776 (2001)
  90. X. Wei, X. Zhuang, D. Kim, S.-C. Hong, T. Goto, and Y. R. Shen, "Vibrational spectroscopy of rubbed polymer surfaces", Mole. Cryst. Liq. Cryst. 358 , 103-108 (2001)
  91. X. Wei, S. Hong, X. Zhuang, T. Goto, Y. R. Shen, "Nonlinear optical studies of liquid crystal alignment on a rubber polyvinyl alcohol surface", Phys. Rev. E 62 , 5160-5172, (2000)
  92. X. Wei, X. Zhuang, S. Hong, T. Goto, Y. R. Shen, "Sum-Frequency vibrational spectroscopic study of a rubbed polymer surface", Phys. Rev. Lett. 82 , 4256-4259 (1999)
  93. X. Zhuang, P. B. Miranda, D. Kim, Y. R. Shen, "Mapping molecular orientation and conformation at interfaces by surface nonlinear optics", Phys. Rev. B 59 , 12632-12640 (1999)
  94. T. Qian, X. Zhuang, Y. R. Shen, "Surface-monolayer-induced bulk alignment of liquid crystals: from nematic to smectic-a phase", Phys. Rev. E 59 , 1873-1879 (1999)
  95. X. Zhuang, R. Muenster, M. Jarasch, Y. R. Shen, "Dye-induced enhancement of optical nonlinearity in liquid crystals and ordinary liquids", Mole. Cryst. Liq. Cryst. 321 , 165-172 (1998)
  96. J. J. Ge, G.Xue, K. W. McCreight, S. Wang, F. W. Harris, S. Z. D. Cheng, X. Zhuang, S. Hong, Y. R. Shen, "Surface studies of polyimide thin films via surface enhanced Raman scattering and second harmonic generation", Macromol. Rapid Comm. 19 , 619-623 (1998)
  97. R. Muenster, M. Jarasch, X. Zhuang, Y. R. Shen, "Enhanced optical kerr effect of dye-doped isotropic liquid", Phys. Rev. Lett. 78 , 42-45 (1997)
  98. A. Le Calvez, S. Montant, E. Freysz, A. Ducasse, X. Zhuang, Y. R. Shen, "Ultrafast orientation dynamics of liquid crystals in smectic phase", Chem. Phys. Lett. 258 , 620-625 (1996)
  99. X. Zhuang and Y. R. Shen, "The application of nonlinear optics to the study of polymers at interfaces", Trends Polym. Sci. 4 , 258-264 (1996)
  100. X. Zhuang, H. S. Lackritz, and Y. R. Shen, "Photo-isomerization of polymer monolayers and multi-layers on water", Chem. Phys. Lett. 246 , 279-284 (1995)
  101. X. Zhuang, D. Wilk, L. Marrucci, and Y. R. Shen, "Orientation of amphiphilic molecules on polar substrates", Phys. Rev. Lett. 75 , 2144-2147 (1995)
  102. X. Zhuang, L. Marrucci, D. Johannsmann, and Y. R. Shen, "Dependence of liquid crystal bulk alignment on its surface monolayer", Mole. Cryst. Liq. Cryst. 262 , 35-43 (1995)
  103. X. Zhuang, L. Marrucci, and Y. R. Shen, "Surface-monolayer-induced bulk alignment of liquid crystals", Phys. Rev. Lett. 73 , 1513-1516 (1994)