Xiaowei Zhuang
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Title |
Howard Hughes Medical Institute Investigator |
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Institute |
Harvard University |
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Fax |
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Website |
Education
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1987-1991 |
B.S., Physics, University of Science and Technology of China |
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1991-1996 |
Ph.D., Physics, University of California, Berkeley |
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1997-2001 |
Chodorow Postdoctoral Fellow, Stanford University |
Positions
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2014- |
David B. Arnold Jr. Professor of Science, Harvard University |
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2006- |
Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University |
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2005- |
Investigator, Howard Hughes Medical Institute |
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2005 |
Associate Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University |
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2001-2005 |
Assistant Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University |
Honors
Selected awards and elected membership
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2015 |
National Academy of Sciences Award in Molecular Biology |
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2014 |
Chinese Institute of Engineers USA Distinguished Achievement Award |
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2013 |
Member, American Academy of Arts and Sciences |
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2012 |
Member, National Academy of Sciences |
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2012 |
Fellow, American Physical Society |
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2012 |
Fellow, American Association of the Advancement of Science |
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2011 |
Raymond & Beverly Sackler International Prize in Biophysics |
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2010 |
Max Delbruck Prize in Biological Physics |
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2008 |
HHMI collaborative Innovation Award |
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2008 |
Coblentz Award |
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2006 |
Pure Chemistry Award |
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2005 |
Camille Dreyfus Teacher-Scholar Award |
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2004 |
Sloan Research Fellowship |
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2004 |
Technology Review Worlds Top 100 Young Innovators Award |
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2003 |
MacArthur Fellowship |
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2003 |
Packard Fellowship for Science and Engineering |
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2003 |
CAREER award, National Science Foundation |
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2003 |
Searle Scholar |
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2003 |
Beckman Young Investigator Award |
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2002 |
Young Investigator Award, Office of Naval Research |
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1997 |
Chodorow Postdoctoral Fellowship, Stanford University |
Distinguished lectureship
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2014 |
Krimm Lecture, University of Michigan |
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Harvey Lecture, Harvey Society |
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Huck Distinguished Lecture, Penn State University |
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Laureate Lecture, University of Pittsburg |
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McLean Lecture, Baylor College |
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Caspar Lecture, Florida State University |
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2013 |
Dow Lecture, University of British Columbia |
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Global Lecture, Peking University |
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2012 |
Danny Thomas Lecture, St Jude Research Hospital |
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Sproul Lecture, Cornell University |
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Wang Ying-Lai Lecture, University of Texas Medical Branch |
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Leica Scientific Forum Lectures, California (UCSF, UCLA, UCSD) |
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2011 |
Leica Scientific Forum Lectures, Germany (Munich, Heidelberg, Berlin) |
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Greenfield Lecture, Case Western University |
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Fredric Fay Lecture, University of Massachusetts School of Medicine |
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Closs Lecture, University of Chicago |
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Maggie & Nick DeWolf Public Lecture, Aspen Center for Physics |
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2010 |
Director’s WALS Lecture, National Institutes of Health |
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Magomedov-Shcherbinina Memorial Prize Lecture, University of Rochester |
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2008 |
ST Huang Memorial Lecture, Hong Kong University |
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Brockman Lecture, University of Michigan |
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Morrison Lecture, Cornell University |
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2006 |
Seymour Rothchild Lecture, University of Rochester |
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2004 |
Gunnar and Gunnel Kallén Memorial Lecture, Lund University, Sweden |
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Jean-Francois Lefèvre Lecture in Biophysics, Ecole Supérieure de Biotechnologie de Strasbourg, France |
Editorial Board Positions
Cell (editorial advisory board)
eLife (reviewing editorial board)
Annual Review on Biophysics (Editorial board, associate editor)
Optical Nanoscopy (editorial advisory board)
Chemical Physics Letter (editorial advisory board)
ACS Central Science (editorial advisory board)
ACS Photonics (editorial advisory board)
Partial List of Professional Services
Co-Chair, Cold Spring Harbor Conference on "New Advances in Optical Imaging of Live Cells and
Organisms" (2011, 2013)
Chair, American Society of Cell Biology Meeting, Symposium on “Breaking the diffraction barrier”
(2009)
Co-Chair, 355 th Xiangshan Science Conference, “Single-Molecule Imaging, Spectroscopy and
Manipulation of Biological Systems,” Beijing, 2009
Co-chair, Gordon Research Conference on “Single Molecule Approaches to Biology” (2008)
Co-chair, American Chemical Society National Meeting, Symposium on “Single-molecule imaging,
spectroscopy, and manipulation of biomolecular systems” (2007)
Co-vice chair, Gordon Research Conference on “Single Molecule Approaches to Biology” (2006)
Member, NIH College of CSR Reviewers (2010-present)
NIH Study Section: Review Panel of the NIH Director’s Pioneer Award (2012, 2014), Review panel
on Nanomedicine Development Centers for the NIH Roadmap Nanomedicine Initiative (2008),
Interview panel of the NIH Director’s Pioneer Award (2007), Study section on Molecular
Structure and Function C (2007), Study section on Cell Structure and Function (2006), Study
section on Nanomedicine Development Centers for the NIH Roadmap Nanomedicine Initiative
(2005), Study section on Bioanalytical, Engineering, and Chemistry Emphasis (2003)
External advisory Board, NSF Center for the Physics of Living Cells (CPLC), UIUC
Scientific Advisory Board, School of Life Sciences, University of Science of Technology of China
Scientific Advisory Board, ICFO – Institute of Photonics Science, Barcelona, Spain
Pew Scholars National Advisory Committee
Scientific Advisory Board, Welch Foundation
Publications
G. Zhong, J. He, R. Zhou, D. Lorenzo, H. P. Babcock, V. Bennett, X. Zhuang. Developmental
mechanism of the periodic membrane skeleton in axons. eLife (DOI: 10.7554/eLife.04581)
C. Y. Chan, H. Zhao, R. J. Pugh, A. M. Pedley, J. French, S. A. Jones, X. Zhuang, H. Jinnah, T. J.
Huang, S. J Benkovic. Purinosome formation as a function of the cell cycle. Proc. Natl. Acad.
Sci. USA (in press)
T. Shemesh, R. W. Klemm, F. B. Romano, S. Wang, J. C. Vaughan, X. Zhuang, M. M. Kozlov, T.
A. Rapoport. A model for the generation and interconversion of ER morphologies. Proc. Natl.
Acad. Sci. USA (in press, DOI: 10.1073/pnas.1419997111)
D. N. Lorenzo, A. Badea, J. Q. Davis, J. Hostettler, J. He, G. Zhong, X. Zhuang,V. Bennett. A
PIK3C3–Ankyrin-B–Dynactin pathway promotes axonal growth and multiorganelle transport. J.
Cell Biol 207, 735-752 (2014).
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).
A D. Blunk, Y. Akbergenova, R. W. Cho, J. Lee, U. Walldorf, K. Xu, G. Zhong, X. Zhuang and J. T.
Littleton. Postsynaptic actin regulates active zone spacing and glutamate receptor apposition
at the Drosophila neuromuscular junction. Mol. Cell. Neurosci 61, 241-254 (2014).
S. Wang, J. R. Moffit, G. T. Dempsey, X. S. 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).
J. -J. Chung, S. -H. Shim, R. A. Everley, S. P. Gygi, X. Zhuang, D. E. Clapham. Structurally
Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and
Motility. Cell 157, 808–822 (2014)
S. Jia, J. C. Vaughan, X. Zhuang. Isotropic 3D super-resolution imaging with a self-bending point-
spread function. Nat. Photonics 8, 302-306 (2014)
A. M. Avalos, A. M. Bilate, M.D. Witte, A. K. Tai, J. He, M. P. Frushicheva, P. D. Thill, F. Meyer-
Wentrup, C. S. Theile, A. K. Chakraborty, X. Zhuang, H. L. Ploegh. Monovalent engagement
of the BCR activates ovalbumin-specific transnuclear B cells. J. Exp. Med. 211, 365-79 (2014)
K. Xu, G. Zhong, X. Zhuang. Actin, spectrin and associated proteins form a periodic cytoskeleton
structure in axons. Science 339, 452-456 (2013).
Y. Doksani, J. Wu, T. de Lange, X. Zhuang. Super-resolution fluorescence imaging reveals TRF2-
dependent t-loop formation. Cell 155, 345-356 (2013).
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).
H. Babcock, J. Moffitt, Y. Zhao, X. Zhuang. Fast compressed sensing analysis for super-resolution
imaging using L1-homotopy. Optics Express 21, 28583-28596 (2013).
J. He, E. Sun, M. B. Bujny, D. Kim, M. W. Davidson, X. Zhuang. Dual function of CD81 in
influenza uncoating and budding. PLoS Pathogen 9, e1003701 (2013).
S. K. Hota, S. K. Bhardwaj, S. Deindl, Y. C. Lin, X. Zhuang, B. Bartholomew. Nucleosome
mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat.
Struct. Mol. Biol. 152, 442-452 (2013).
J.C. Vaughan, G.T. Dempsey, E. Sun, X. Zhuang. Phospine Quenching of Cyanin Dyes as a
Versatile Tool for Fluorescence Microscopy. J. Am. Chem. Soc. 135, 1197-1200 (2013).
E. Sun, J. He, X. Zhuang, Live cell imaging of viral entry. Curr Opin Virol. 3, 34-43 (2013).
A. P. Alivisatos, A. M. Andrews, E. S. Boyden, M. Chun, G. M. Church, K. Deisseroth, J. P.
Donoghue, S. E. Fraser, J. Lippincott-Schwartz, L. L. Looger, S. Masmanidis, P. L. McEuen,
A. V. Nurmikko, H. Park, D. S. Peterka, C. Reid, M. L. Roukes, A. Scherer, M. Schnitzer, T. J.
Sejnowski, K. L. Shepard, D. Tsao, G. Turrigiano, P. S Weiss, C. Xu, R. Yuste, X. Zhuang.
Nanotools for neuroscience and brain activity mapping. ACS nano 7, 1850-1866 (2013)
E. Sun, J. He, X. Zhuang. Dissecting the role of COPI complexes on influenza virus infection. J.
Virol. 87, 2673-2685(2013)
I. Kim, W. Pan, S. A. Jones, Y. Zhang, X. Zhuang, D. Wu. Clathrin and AP2 are required for
PtdIns(4,5)P2-mediated formation of LRP6 signalosomes. J. Cell Biol. 200, 419-428 (2013).
J. Vaughan, S. Jia, X. Zhuang. Ultra-bright Photoactivatable Fluorophores Created by Reductive
Caging. Nat. Methods 9, 1181-1184 (2012).
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
337, 236-239 (2012).
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. USA 109, 13978–13983 (2012).
S. Deindl, X. Zhuang. Monitoring conformational dynamics with single-molecule fluorescence
resonance energy transfer: Application in Nucleosome Remodeling. Methods Enzymol 513,
59–86 (2012)
H. Babcock, Y. Sigal, X. Zhuang. A high-density 3D localization algorithm for stochastic optical
reconstruction microscopy. Nanoscopy 1: 6 (2012).
E. A. Mukamel, H. P. Babcock, X. Zhuang. Statistical deconvolution for super-resolution
fluorescence Microscopy. Biophys. J. 102, 2391-2400 (2012)
K. Xu, H. P. Babcock, X. Zhuang. Dual-objective STORM reveals three-dimensional filament
organization in the actin cytoskeleton. Nat. Methods 9, 185-188 (2012).
M. Lakadamyali, H. Babcock, M. Bates, X. Zhuang, J. Lichtman. 3D Multicolor Super-Resolution
Imaging Offers Improved Accuracy in NeuronTracing. PLoS One 7: e30826 (2012)
M. Bates, G. T. Dempsey, K. H. Chen, X. Zhuang. Multicolor super-resolution fluorescence
imaging through via multi-parameter fluorophore detection. Chemphyschem 13, 99-107
(2012)
G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, X. Zhuang. Evaluation of fluorophores for
optimal performance in localization-based super-resolution imaging. Nat. Methods 8, 1027-
1036 (2011).
J. C. Vaughan, X. Zhuang. New fluorescent probes for Super-resolution imaging. Nat.
Biotechnol. 29, 880-881 (2011)
W. Wang, G.W. Li, C. Chen, X. S. Xie, X. Zhuang. Chromosome organization by a nucleoid
associated protein. Science 333, 1445-1449 (2011).
E. C. Garner, R. Bernard, W. Wang, X. Zhuang, D. Z. Rudner, T. Mitchison. Circumferential
Motions of the Cell Wall Synthesis Machinery Drive Cytoskeletal Dynamics in B. subtilis.
Science 333, 222-225 (2011).
S. Jones, S.-H. Shim, J. He, X. Zhuang. Fast three-dimensional super-resolution imaging of live
cells. Nat. Methods 8, 499-505 (2011).
M. Mihalusova, J. Y. Wu, X. Zhuang. Functional importance of telomerase pseudoknot revealed
by single-molecule analysis. Proc. Natl. Acad. Sci. USA 108, 20339-20344 (2011).
B. Huang, H. Babcock, X. Zhuang, Breaking the diffraction barrier: Super-resolution imaging of
cells. Cell 143, 1047-1058 (2010).
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. Nat. Struct. Mol.
Biol. 17, 1453-1460 (2010)
A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang. Super-resolution imaging of chemical
synapses in the brain. Neuron 68, 843-856 (2010)
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. Nat. Cell Biol. 12, 902-908 (2010)
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)
E. Schuman, X. Zhuang. New technologies, Editorial overview. Curr Opin Neurobiology 20, 608-
690 (2010)
M. Bates, S. A. Jones, X. Zhuang. Stochastic Optical Reconstruction Microscopy (STORM) -- A
Method for Superresolution Fluorescence Imaging. Chapter 35 in Imaging: A Laboratory
Manual. Ed. Rafael Yuste. Cold Spring Harbor Laboratory Press (2010)
G. Dempsey, W. Wang, X. Zhuang, Fluorescence Imaging at Sub–Diffraction-Limit Resolution with
Stochastic Optical Reconstruction Microscopy. Pp. 95-127 in Handbook of Single-molecule
Biophysics (ed. Hinterdorfer P, van Oijen AM), Springer Science and Business Media, New
York.
T. Blosser, J. Yang, M. Stone, G. Narlikar, X. Zhuang, Dynamics of nucleosome remodeling by
individual ACF complexes. Nature 462, 1022-1027 (2009)
G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, X. Zhuang. Photoswitching
mechanism of cyanine dyes. J. Am. Chem. Soc. 131, 18192-18193 (2009)
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 Publishing (2009).
J. Wu, M. Stone, X. Zhuang. A Single-molecule assay for telomerase structural-function analysis.
Nucleic Acid Res. doi:10.1093/nar/gkp1033 (2009)
J. Vaughan, B. Brandenburg, J. Hogle, X. Zhuang. Rapid actin-dependent viral motility in live cells.
Biophysical Journal 97, 1647-1656 (2009)
X. Zhuang. Nano-imaging with STORM. Nat. Photon. 3, 365-367 (2009)
Huang, M. Bates, X. Zhuang. Super-resolution fluorescence microscopy. Annu. Rev. Biochem.
78, 993 – 1016 (2009)
E. Abbondanzieri, X. Zhuang. Concealed enzyme coordination. Nature 457, 392-393 (2009).
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 single Dengue virus particles in living cells. PLoS
Pathogen 4, e1000244 (2009)
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 substrate. Science 322, 1092-1097
(2008).
B. Huang, S. Jones, B. Brandenburg, X. Zhuang. Whole cell 3D STORM reveals interactions
between cellular structures with nanometer-scale resolution. Nat. Meth. 5, 1047 - 1052 (2008).
M. Bates, B. Huang, X. Zhuang. Super-resolution microscopy by nanoscale localization of photo-
switchable fluorescent probes. Curr. Opin. Chem. Biol. 208, 1-10 (2008)
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)
J. Zheng, X. Zhuang. Luminescent and Raman active silver nanoparticles with polycrystalline
structure. J. Am. Chem. Soc. 130, 10472-10473 (2008)
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).
B. Huang, W. Wang, M. Bates, X. Zhuang. Three-dimensional super-resolution imaging by
stochastic optical reconstruction microscopy. Science 319, 810-813 (2008).
M. Bates, B. Huang, G. Dempsey, X. Zhuang. Multicolor super-resolution imaging with photo-
switchable fluorescent probes. Science 317, 1749-1753 (2007).
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).
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).
B. Brandenburg, L. Y. Lee, M. Lakadamyali, M. J. Rust, X. Zhuang, and J. M. Hogle. Imaging
poliovirus entry in live cells. PLoS Biol. 5, 1543-1555 (2007).
B. Brandenburg, X. Zhuang. Virus trafficking – learning from single-virus tracking. Nat. Rev.
Microbiol. 5, 197-208 (2007).
M. J. Rust, M. Lakadamyali, B. Brandenburg, and X. Zhuang. Single-virus tracking in live cells. In
Single Molecule Techniques Ed. P.S. Selvin and T.Ha (Cold Spring Harbor Laboratory Press).
Y. Zhou, X. Zhuang. Kinetic analysis of sequential multi-step reactions. J. Phys. Chem. B, 111,
13600-13610, 2007 (2007).
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).
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).
Y. Zhou and X. Zhuang. Robust reconstruction of the rate constant distribution using the phase
function method. Biophys. J. 91, 4045-4053 (2006).
M. J. Rust, M. Bates, X. Zhuang. Sub-diffraction-limit imaging by stochastic reconstruction optical
microscopy (STORM). Nat. Meth. 3, 793-795 (2006).
G. Bokinsky, L. G. Nivon, S. Liu, G. Chai., M. Hong, K. M. Weeks, X. Zhuang. Two distinct binding
mode of a protein cofactor with its target RNA. J. Mol. Biol. 361, 771-784 (2006).
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).
X. Zhuang. Single-molecule RNA Science. Annu. Rev. Biophys. Biomol. Struct. 34, 399-414
(2005)
G. Bokinsky, X. Zhuang. Single-molecule RNA folding. Acct. Chem. Res. 38, 566-573 (2005).
M. Bates, T. R. Blosser, X. Zhuang. Short-range spectroscopic ruler based on a single-molecule
optical switch. Phys. Rev. Lett. 94, 108101 (2005).
X. Zhuang. Unraveling DNA condensation by optical tweezers. Science 305, 188-190 (2004).
M. Lakadamyali, M. J. Rust, X. Zhuang. Endocytosis of influenza viruses. Micro. Infect. 6, 929-
936 (2004).
M. J. Rust, M. Lakadamyali, F. Zhang, X. Zhuang. Assembly of endocytic machinery around
individual influenza viruses during viral entry. Nat. Struct. Mol. Biol. 11, 567-573 (2004).
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).
H. P. Babcock, C. Chen, X. Zhuang. Using single particle-tracking to study nuclear trafficking of
viral genes. Biophys. J. 87, 2749-2758 (2004).
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).
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).
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).
X. Zhuang and M. Rief. Single-molecule folding. Curr. Opin. Struct. Biol. 13, 88-97 (2003).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
A. Le Calvez, S. Montant, E. Freysz, A. Ducasse, X. Zhuang, Y. R. Shen. Ultrafast orientation
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