Zhuang Research Lab

Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging
Y.M. Sigal, C.M. Speer, H.P. Babcock, X. Zhuang
493-505 (2015)

Spatially resolved, highly multiplexed RNA profiling in single cells
K.H. Chen, A.N. Boettiger, J.R. Moffitt, S. Wang, X. Zhuang
aaa6090 (2015)

High-performance probes for light and electron microscopy
S. Viswanathan, M.E. Williams, E.B. Bloss, T.J. Stasevich, C.M. Speer, A. Nern, B.D. Pfeiffer, B.M. Hooks, W-P. Li, B.P. English, T. Tian, G.L. Henry, J.J. Macklin, R. Patel, C.R. Gerfen, X. Zhuang, Y. Wang, G.M. Rubin, L.L. Looger
Nature Methods
568-576 (2015)

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
B. Beliveau, A. Boettiger, M. Avendano, R. Jungmann, R. McCole, E. Joyce, C. Kim-Kiselak, F. Bantignies, C. Fonseka, J. Erceg, M. Hannan, H. Hoang, D. Colognori, J. Lee, W. Shih, P. Yin, X. Zhuang, C.T. Wu
Nature Communications
7147 (2015)

Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy
D. Kim, T.J. Deerinck, Y.M. Sigal, H.P. Babcock, M.H. Ellisman, X. Zhuang
PLoS One
e0124581 (2015)

Purinosome formation as a function of the cell cycle
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
1368-1373 (2015)

Developmental mechanism of the periodic membrane skeleton in axons
G. Zhong, J. He, R. Zhou, D. Lorenzo, H.P. Babcock, V. Bennett, X. Zhuang
DOI:10.7554/eLife.04581 (2014)

A model for the generation and interconversion of ER morphologies
T. Shemesh, R.W. Klemm, F.B. Romano, S. Wang, J.C. Vaughan, X. Zhuang, H. Tukachinsky, M.M. Kozlov, T.A. Rapoport
E5243-E5251 (2014)

A PIK3C3-Ankryin-B-Dynactin pathway promotes axonal growth and multiorganelle transport
D.N. Lorenzo, A. Badea, J. Davis, J. Hostettler, J. He, G. Zhong, X. Zhuang, V. Bennett
J. Cell Biol
735-752 (2014)

Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
W.L. Hwang, S. Deindl, B.T. Harada, X. Zhuang
213-217 (2014)

Postsynaptic actin regulates active zone spacing and glutamate receptor apposition at the Drosophila neuromuscular junction
A. Blunk, Y. Akbergenova, R. Cho, J. Lee, U. Walldorf, K. Xu, G. Zhong, X. Zhuang, J. Littleton
Mol. Cell. Neurosci.
241-254 (2014)

Characterization and development of photoactivatable fluorescent proteins for single molecule based superresolution imaging
S. Wang, J. Moffitt, G. Dempsey, X. Xie, X. Zhuang
Proc. Natl. Acad. Sci. USA
8452-8457 (2014)

Structurally distinct Ca2+ signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility
J. Chung, S. Shim, R. Everley, S. Gygi, X. Zhuang, D. Clapham
808-822 (2014)

Isotropic three-dimensional super-resolution imaging with a self-bending point spread function
S. Jia, J. Vaughan, X. Zhuang
Nature Photonics
302-306 (2014)

Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells
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
365-379 (2014)

Super-resolution fluorescence imaging reveals TRF2-dependent t-loop formation
Y. Doksani, J. Wu, T. de Lange, X. Zhuang
345-356 (2013)

Fast compressed sensing analysis for super-resolution imaging using L1-homotopy
H. Babcock, J. Moffitt, Y. Cao, X. Zhuang
Optics Express
28583-28596 (2013)

ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps
S. Deindl, W.L. Hwang, S.K. Hota, T.R. Blosser, P. Prasad, B. Bartholomew, X. Zhuang
442-452 (2013)

Dual function of CD81 in influenza uncoating and budding
J. He, E. Sun, M.B. Bujny, D. Kim, M.W. Davidson, X. Zhuang
PLOS Pathogens
e1003701 (2013)

Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains
S. Hota, S. Bhardwaj, S. Deindl, Y. Lin, X. Zhuang, B. Bartholomew
Nature Structural and Molecular Biology
222-229 (2013)

Phospine Quenching of Cyanin Dyes as a Versatile Tool for Fluorescence Microscopy
J.C. Vaughan, G.T. Dempsey, E. Sun, X. Zhuang
1197-1200 (2013)

Live cell imaging of viral entry
E. Sun, J, He, X. Zhuang
Current Opinion in Virology
34-43 (2013)

Nanotools for neuroscience and brain activity mapping
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
ACS Nano
1850-1866 (2013)

Dissecting the role of COPI complexes in influenza virus infection
E. Sun, J. He, X. Zhuang
Journal of Virology
2673-2685 (2013)

Clathrin and AP2 are required for Ptdlns(4,5)P2-mediated formation of LRP6 signalosomes
I. Kim, W. Pan, S. Jones, Y. Zhang, X. Zhuang, D. Wu
419-428 (2013)

Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging
J. Vaughan, S. Jia, X. Zhuang
Nature Methods
1181-1184 (2012)

Molecular Architecture and Assembly Principles of Vibrio Cholerae Biofilms
V. Berk, J.C.N. Fong, G.T. Dempsey, O.N. Develioglu, X. Zhuang, J. Liphardt, F.H. Yildiz, S. Chu
236-239 (2012)

Super-resolution Fluorescence Imaging of Organelles in Live Cells with Photoswitchable Membrane Probes
S-H. Shim, C. Xia, G. Zhong, H.P. Babcock, J.C. Vaughan, B. Huang, X. Wang, C. Xu, G-Q. Bi, X. Zhuang
Proc. Natl. Acad. Sci.
13978-13983 (2012)

A High-Density 3D Localization Algorithm for Stochastic Optical Reconstruction Microscopy
H. P. Babcock, Y. Sigal, X. Zhuang
Optical Nanoscopy
6 (2012)

Statistical Deconvolution for Super-resolution Fluorescence Microscopy
E. A. Mukamel, H. P. Babcock, X. Zhuang
Biophysical Journal
2391-2400 (2012)

3D Multicolor Super-Resolution Imaging Offers Improved Accuracy in Neuron Tracing
M. Lakadamyali, H. Babcock, M. Bates X. Zhuang, J. Lichtman
PLoS One
e30826 (2012)

Multicolor Super-resolution Fluorescence Imaging Via Multi-parameter Fluorophore Detection
M. Bates, G. T. Dempsey, K. H. Chen, X. Zhuang
99-107 (2012)

Evaluation of Fluorophores for Optimal Performance in Localization-based Super-resolution Imaging
G. Dempsey, J. Vaughan, K. Chen, M. Bates, X. Zhuang
Nature Methods
1027-1036 (2011)

New Fluorescent Probes for Super-resolution Imaging
J. Vaughan, X. Zhuang
Nature Biotechnology
880-881 (2011)

Chromosome Organization by a Nucleoid Associated Protein
W. Wang, G. Li, C. Chen, X. Xie, X. Zhuang
1445-1449 (2011)

Coupled, Circumferential Motions of the Cell Wall Synthesis Machinery and MreB Filaments in B. subtilis
E. Garner, R. Bernard, W. Wang, X. Zhuang, D. Rudner, T. Mitchison
222-225 (2011)

Fast, three-dimensional super-resolution imaging of live cells
S. Jones, S-H. Shim, J. He, X. Zhuang
Nature Methods
499-505 (2011)

Functional importance of telomerase pseudoknot revealed by single-molecule analysis
M. Mihalusova, J.Y. Wu, X. Zhuang
Proc. Natl. Acad. Sci.
20339-20344 (2011)

Breaking the diffraction barrier: Super-resolution imaging of cells
B. Huang, H. Babcock, X. Zhuang
1047-1058 (2010)

Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription
S. Liu, B.T. Harada, J.T. Miller, S.F.J. Le Grice, X. Zhuang
Nature Struct. Mol. Biol.
1453-1460 (2010)

Super-resolution imaging of chemical synapses in the brain
A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang
843-856 (2010)

Coupling between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free system
M. Wu, B. Huang, M. Graham, A. Raimondi, J.E. Heuser, X. Zhuang, P. De Camilli
Nature Cell Biology
902-908 (2010)

Structure-Activity Analysis of Vinylogous Urea Inhibitors of Human Immunodeficiency Virus-Encoded Ribonuclease H
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
Antimicrob Agents Chemother
3913-3921 (2010)

New technologies, editorial overview
E. Schuman, X. Zhuang
Current Opinion in Neurobiology
608-609 (2010)

Stochastic Optical Reconstruction Micrscopy (STORM) -- A Method for Superresolution Fluorescence Imaging
M. Bates, S.A. Jones, X. Zhuang
Imaging: A Laboratory Manual
Rafael Yuste (2010)

Dynamics of Nucleosome Remodeling by Individual ACF Complexes
T. Blosser, J. Yang, M. Stone, G. Narlikar, X. Zhuang
1022-1027 (2009)

Photoswitching Mechanism of Cyanine Dyes
G. Dempsey, M. Bates, W. Kowtoniuk, D. Liu, R. Tsien, X. Zhuang
J. Am. Chem. Soc. 131
18192-18193 (2009)

Sub-diffraction-limit Imaging with Stochastic Optical Reconstruction Micrscopy (STORM)
M. Bates, B. Huang, M. Rust, G. Dempsey, W. Wang, X. Zhuang
Nobel Volume on Single Molecule Spectroscopy in Chemistry
399-415 (2009)

Fluorescence imaging at sub-diffraction limit resolution with stochastic optical reconstruction microscopy
G. Dempsey, W. Wang, X. Zhuang
Handbook of Single-Molecule Biophysics
95-127 (2009)

A Single-molecule Assay for Telomerase Structural-function Analysis
J. Wu, M. Stone, X. Zhuang
Nucleic Acid Research
e16 (2010)

Rapid Actin-dependent Viral Motility in Live Cells
J. Vaughan, B. Brandenburg, J. Hogle, X. Zhuang
Biophysical Journal
1647-1656 (2009)

Nano-imaging with STORM
X. Zhuang
Nature Photonics
365-367 (2009)

Super-resolution Fluorescence Microscopy
B. Huang, M. Bates, X. Zhuang
Annual Review Biochemistry
993-1016 (2009)

Concealed Enzyme Coordination
E. Abbondanzieri, X. Zhuang
392-393 (2009)

Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells
H.M. van der Schaar, M.J. Rust, C. Chen, H. van der Ende-Metselaar, J. Wilschut, X. Zhuang, J.M. Smit
PLOS Pathogens
e1000244 (2008)

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution
B. Huang, S.A. Jones, B. Brandenburg, X. Zhuang
Nature Methods
1047-1052 (2008)

Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates
S. Liu, E. Abbondanzieri, J. W. Rausch, S. F. J. Le Grice, X. Zhuang
1092-1097 (2008)

Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes
M. Bates, B. Huang, X. Zhuang
Curr. Opin. Chem. Biol.
505-514 (2008)

Dynamic binding orientations direct activity of HIV reverse transcriptase
E. Abbondanzieri, G. Bokinsky, J. W. Rausch, J. X. Zhang, S. F. J. Le Grice, X. Zhuang
184-189 (2008)

Epsin1 is a cargo specific adaptor for the clathrin-mediated endocytosis of influenza virus
C. Chen, X. Zhuang
Proc. Natl. Acad. Sci. USA
11790-11795 (2008)

Luminescent and Raman active silver nanoparticles with polycrystalline structure
J. Zheng, Y. Ding, B. Tian, Z. Wang, X. Zhuang
J. Am. Chem. Soc.
10472-10473 (2008)

Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy
B. Huang, W. Wang, M. Bates, X. Zhuang
810-813 (2008)

Single-virus tracking in live cells.
M. Rust, M. Lakadamyali, B. Brandenburg, X. Zhuang
Single Molecule Techniques: A Laboratory Manual
P.R. Selvin, T. Ha (2008)

Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes
M. Bates, B. Huang, G. T. Dempsey, X. Zhuang
1749-1753 (2007)

Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic fingerprinting
S. Liu, G. Bokinsky, N. G. Walter, X. Zhuang
Proc. Natl. Acad. Sci. USA
12634-12639 (2007)

Imaging poliovirus entry in live cells
B. Brandenburg, L. Y. Lee, M. Lakadamyali, M. J. Rust, X. Zhuang, J. M. Hogle
PLoS Biol.
1543-1555 (2007)

Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein
M. D. Stone, M. Mihalusova, C. M. O'Connor, R. Prathapam, K. Collins, X. Zhuang
458-461 (2007)

Virus trafficking - learning from single-virus tracking
B. Brandenburg, X. Zhuang
Nat. Rev. Microbiology
197-208 (2007)

Kinetic analysis of sequential multi-step reactions
Y. Zhou, X. Zhuang
J. Phys. Chem. B
13600-13610, (2007)

Characterization of the early events in Dengue virus cell entry by biochemical assays and single-virus tracking
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
J. Virol.
12019-12028 (2007)

Internalization and trafficking of cell surface proteoglycans and proteoglycan binding ligands
C. K. Payne, S. Jones, C. Chen, X. Zhuang
389-401 (2007)

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
M. J. Rust, M. Bates, X. Zhuang
Nature Methods
793-795 (2006)

Two distinct binding modes of a protein cofactor with its target RNA
G. Bokinsky, L. G. Nivon, S. Liu, G. Chai, M. Hong, K. M. Weeks, X. Zhuang
J. Mol. Biol.
771-784 (2006)

Single-molecule RNA folding
G. Bokinsky, X. Zhuang
Acc. Chem. Res.
566-573 (2005)

Single-molecule RNA Science
X. Zhuang
Annu. Rev. Biophys. Biomol. Struct.
399-414 (2005)

Short-range spectroscopic ruler based on a single-molecule optical switch
M. Bates, T. R. Blosser, X. Zhuang
Phys. Rev. Lett.
108101 (2005)

Unraveling DNA condensation by optical tweezers
X. Zhuang
188-190 (2004)

Assembly of endocytic machinery around individual influenza viruses during viral entry
M. J. Rust, M. Lakadamyali, F. Zhang, X. Zhuang
Nature Struct. Mol. Biol.
567-573 (2004)

Endocytosis of influenza viruses
M. Lakadamyali, M. J. Rust, X. Zhuang
Micro. Infection
929-936 (2004)

Electrical detection of single viruses
F. Patolsky, G. Zheng, O. Hayden, M. Lakadamyali, X. Zhuang, C. M. Lieber
Proc. Natl. Acad. Sci. USA
14017-14022 (2004)

Using single particle-tracking to study nuclear trafficking of viral genes
H. P. Babcock, C. Chen, X. Zhuang
Biophys. J.
2749-2758 (2004)

Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance
D. Rueda, G. Bokinsky, M. M. Rhodes, M. J. Rust, X. Zhuang, N. G. Walter
Proc. Natl. Acad. Sci. USA
10066-10071 (2004)

Visualizing infection of individual influenza viruses
M. Lakadamyali, M. J. Rust, H P. Babcock, X. Zhuang
Proc. Natl. Acad. Sci. USA
9280-9285 (2003)

Single-molecule transition-state analysis of RNA folding
G. Bokinsky, D. Rueda, V. K. Misra, A. Gordus, M. M. Rhodes, H. P. Babcock, N. G. Walter, X. Zhuang
Proc. Natl. Acad. Sci. USA
9302-9307 (2003)

Single-molecule folding
X. Zhuang and M. Rief
Curr. Opin. Struct. Biol.
88-97 (2003)

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
L. E. Bartley, X. Zhuang, R. Das, S. Chu, D. Herschlag
J. Mol. Biol.
1011-1026 (2003)

Correlating structural dynamics and function in single ribozyme molecules
X. Zhuang, H. Kim, M. Pereira, H. Babcock, N. Walter, S. Chu
1473-1476 (2002)

Exploring the folding landscape of a structured RNA
R. Russell, X. Zhuang, H. Babcock, I. S. Millett, S. Doniach, S. Chu, D. Herschlag
Proc. Natl. Acad. Sci. USA
155-160 (2002)

A single-molecule study of RNA catalysis and folding
X. Zhuang, L. Bartley, H. Babcock, R. Russell, T. Ha, D. Herschlag, S. Chu
2048-2051 (2000)

Fluorescence quenching: a tool for single-molecule protein-folding study
X. Zhuang, T. Ha, H. Kim, T. Centner, S. Labeit, S. Chu
Proc. Natl. Acad. Sci. USA
14241-14244 (2000)

Ligand-induced conformational changes of single RNA molecules
T. Ha, X. Zhuang, H. Kim, J. Orr, J. Williamson, S. Chu
Proc. Natl. Acad. Sci. USA
9077-9082 (1999)

Orientation of side chains and adsorbed liquid crystal molecules on a rubbed polyimide surface studied by optical harmonic generation
S.-C. Hong, M. Oh-e, X. Zhuang, Y. R. Shen, J. J. Ge, F. W. Harris, S. Z. D. Cheng
Phys. Rev. E
0517061-7 (2001)

Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains
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
J. Am. Chem. Soc.
5768-5776 (2001)

Vibrational spectroscopy of rubbed polymer surfaces
X. Wei, X. Zhuang, D. Kim, S.-C. Hong, T. Goto, and Y. R. Shen
Mole. Cryst. Liq. Cryst.
103-108 (2001)

Nonlinear optical studies of liquid crystal alignment on a rubber polyvinyl alcohol surface
X. Wei, S. Hong, X. Zhuang, T. Goto, Y. R. Shen
Phys. Rev. E
5160-5172, (2000)

Sum-Frequency vibrational spectroscopic study of a rubbed polymer surface
X. Wei, X. Zhuang, S. Hong, T. Goto, Y. R. Shen
Phys. Rev. Lett.
4256-4259 (1999)

Mapping molecular orientation and conformation at interfaces by surface nonlinear optics
X. Zhuang, P. B. Miranda, D. Kim, Y. R. Shen
Phys. Rev. B
12632-12640 (1999)

Surface-monolayer-induced bulk alignment of liquid crystals: from nematic to smectic-a phase
T. Qian, X. Zhuang, Y. R. Shen
Phys. Rev. E
1873-1879 (1999)

Dye-induced enhancement of optical nonlinearity in liquid crystals and ordinary liquids
X. Zhuang, R. Muenster, M. Jarasch, Y. R. Shen
Mole. Cryst. Liq. Cryst.
165-172 (1998)

Surface studies of polyimide thin films via surface enhanced Raman scattering and second harmonic generation
J. J. Ge, G.Xue, K. W. McCreight, S. Wang, F. W. Harris, S. Z. D. Cheng, X. Zhuang, S. Hong, Y. R. Shen
Macromol. Rapid Comm.
619-623 (1998)

Dye-Induced Enhancement of Optical Nonlinearity in Liquids and Liquid Crystals
R. Muenster, M. Jarasch, X. Zhuang, Y. R. Shen
Phys. Rev. Lett.
42-45 (1997)

Ultrashort orientation dynamics of liquid crystals in the smectic-A phase
A. Le Calvez, S. Montant, E. Freysz, A. Ducasse, X. Zhuang, Y. R. Shen
Chem. Phys. Lett.
620-625 (1996)

The application of nonlinear optics to the study of polymers at interfaces
X. Zhuang and Y. R. Shen
Trends Polym. Sci.
258-264 (1996)

Photo-isomerization of polymer monolayers and multi-layers on water
X. Zhuang, H. S. Lackritz, and Y. R. Shen
Chem. Phys. Lett.
279-284 (1995)

Orientation of amphiphilic molecules on polar substrates
X. Zhuang, D. Wilk, L. Marrucci, and Y. R. Shen
Phys. Rev. Lett.
2144-2147 (1995)

Dependence of liquid crystal bulk alignment on its surface monolayer
X. Zhuang, L. Marrucci, D. Johannsmann, and Y. R. Shen
Mole. Cryst. Liq. Cryst.
35-43 (1995)