Zhuang Research Lab

Perturb-multimodal: a platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue
 R. A. Saunders, W. E. Allen, X. Pan, J. Sandhu, J. Lu, T. K. Lau, K. Smolyar, Z. A. Sullivan, C. Dulac, J. S. Weissman, X. Zhuang
Cell
188(17)
4790-4809 (2025)

The membrane skeleton is constitutively remodeled in neurons by calcium signaling
 E. Heller, N. Kurup, X. Zhuang
Science
389(6760)
eadn6712 (2025)

Cell type-specific 3D-genome organization and transcription regulation in the brain
 S. Liu, C. Y. Wang, P. Zheng, B. B. Jia, N. R. Zemke, P. Ren, H. L. Park, B. Ren, X. Zhuang
Science Advances
11(9)
eadv2067 (2025)

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
 J. Klughammer, D. L. Abravanel, Å. Segerstolpe, T. R. Blosser, Y. Goltsev, Y. Cui, D. R. Goodwin, A. Sinha, O. Ashenberg, M. Slyper, S. Vigneau, J. Jané-Valbuena, S. Alon, C. Caraccio, J. Chen, O. Cohen, N. Cullen, L. K. DelloStritto, D. Dionne, J. Files, A. Frangieh, K. Helvie, M. E. Hughes, S. Inga, A. Kanodia, A. Lako, C. MacKichan, S. Mages, N. Moriel, E. Murray, S. Napolitano, K. Nguyen, M. Nitzan, R. Ortiz, M. Patel, K. L. Pfaff, C. B. M. Porter, A. Rotem, S. Strauss, R. Strasser, A. R. Thorner, M. Turner, I. Wakiro, J. Waldman, J. Wu, J. Gómez Tejeda Zañudo, D. Zhang, N. U. Lin, S. M. Tolaney, E. P. Winer, E. S. Boyden, F. Chen, G. P. Nolan, S. J. Rodig, X. Zhuang, O. Rozenblatt-Rosen, B. E. Johnson, A. Regev, N. Wagle
Nature Medicine
30(11)
3236-3249 (2024)

The commitment of the human cell atlas to humanity
 I. Amit, K. Ardlie, F. Arzuaga, G. Awandare, G. Bader, A. Bernier, P. Carninci, S. Donnelly, R. Eils, A. R. R. Forrest, H. T. Greely, R. Guigo, N. Hacohen, M. Haniffa, E. S. Kirby, B. M. Knoppers, A. Kriegstein, E. S. Lein, S. Linnarsson, P. P. Majumder, M. Merad, K. Meyer, M. M. Mhlanga, G. Nolan, N. A. B. Ntusi, D. Pe'er, S. Prabhakar, M. Raven-Adams, A. Regev, O. Rozenblatt-Rosen, S. Saha, A. Saltzman, A. K. Shalek, J. W. Shin, H. Stunnenberg, S. A. Teichmann, T. Tickle, A.-C. Villani, C. Wells, B. Wold, H. Yang, X. Zhuang
Nature Communications
15(1)
10019 (2024)

Three-dimensional single-cell transcriptome imaging of thick tissues
 R. Fang, A. Halpern, M. Rahman, Z. Huang, Z. Lei, S. J. Hell, C. Dulac, X. Zhuang
eLife
12
RP90029 (2024)

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
 Z. Yao, C. T. J. van Velthoven, M. Kunst, M. Zhang, D. McMillen, C. Lee, W. Jung, J. Goldy, A. Abdelhak, M. Aitken, K. Baker, P. Baker, E. Barkan, D. Bertagnolli, A. Bhandiwad, C. Bielstein, P. Bishwakarma, J. Campos, D. Carey, T. Casper, A. B. Chakka, R. Chakrabarty, S. Chavan, M. Chen, M. Clark, J. Close, K. Crichton, S. Daniel, P. DiValentin, T. Dolbeare, L. Ellingwood, E. Fiabane, T. Fliss, J. Gee, J. Gerstenberger, A. Glandon, J. Gloe, J. Gould, J. Gray, N. Guilford, J. Guzman, D. Hirschstein, W. Ho, M. Hooper, M. Huang, M. Hupp, K. Jin, M. Kroll, K. Lathia, A. Leon, S. Li, B. Long, Z. Madigan, J. Malloy, J. Malone, Z. Maltzer, N. Martin, R. McCue, R. McGinty, N. Mei, J. Melchor, E. Meyerdierks, T. Mollenkopf, S. Moonsman, T. N. Nguyen, S. Otto, T. Pham, C. Rimorin, A. Ruiz, R. Sanchez, L. Sawyer, N. Shapovalova, N. Shepard, C. Slaughterbeck, J. Sulc, M. Tieu, A. Torkelson, H. Tung, N. Valera Cuevas, S. Vance, K. Wadhwani, K. Ward, B. Levi, C. Farrell, R. Young, B. Staats, M.-Q. M. Wang, C. L. Thompson, S. Mufti, C. M. Pagan, L. Kruse, N. Dee, S. M. Sunkin, L. Esposito, M. J. Hawrylycz, J. Waters, L. Ng, K. Smith, B. Tasic, X. Zhuang, H. Zeng
Nature
624
317-332 (2023)

A molecularly defined and spatially resolved cell atlas of the whole mouse brain
 M. Zhang, X. Pan, W. Jung, A. Halpern, S. W. Eichhorn, Z. Lei, L. Cohen, K. A. Smith, B. Tasic, Z. Yao, H. Zeng, X. Zhuang
Nature
624
343-354 (2023)

Molecular and spatial signatures of mouse brain aging at single cell resolution
 W. E. Allen, T. R. Blosser, Z. A. Sullivan, C. Dulac, X. Zhuang
Cell
186
194-208 (2023)

Spatially resolved epigenomic profiling of single cells in complex tissues
 T. Lu, C. E. Ang, X. Zhuang
Cell
185
4448-4464 (2022)

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
 R. Fang, C. Xia, J. L. Close, M. Zhang, J. He, Z. Huang, A. R. Halpern, B. Long, J. A. Miller, E. S. Lein, X. Zhuang
Science
377
56-62 (2022)

A Preoptic neuronal population controls fever and appetite during sickness
 J. A. Osterhout, V. Kapoor, S. W. Eichhorn, E. Vaughn, J. D. Moore, D. Liu, D. Lee, L. A. DeNardo, L. Luo, X. Zhuang, C. Dulac
Nature
606
937-944 (2022)

Three-dimensional interrogation of cell types and instinctive behavior in periaqueductal gray
 E. Vaughn, S. Eichhorn, W. Jung, X. Zhuang, C. Dulac
bioRxiv
(https://doi.org/10.1101/2022.06.27.497769) (2022)

Proteomic and functional analyses of the periodic membrane skeleton in neurons
 R. Zhou, B. Han, R. Nowak, Y. Lu, E. Heller, C. Xia, A. H. Chishti, V. M. Fowler, X. Zhuang
Nature Communications
13
3196 (2022)

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
 M. Zhang, S. W. Eichhorn, B. Zingg, Z. Yao, K. Cotter, H. Zeng, H. Dong, X. Zhuang
Nature
598
137-143 (2021)

A multimodal cell census and atlas of the mammalian primary motor cortex
 BRAIN Initiative Cell Census Network (BICCN)
Nature
598
86-102 (2021)

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
 T. Biancalani, G. Scalia, L. Buffoni, R. Avasthi, Z. Lu, A. Sanger, N. Tokcan, C. R. Vanderburg, Å. Segerstolpe, M. Zhang, I. Avraham-Davidi, S. Vickovic, M. Nitzan S. Ma, A. Subramanian, M. Lipinski, J. Buenrostro, N. B. Brown, D. Fanelli, X. Zhuang, E. Z. Macosko, A. Regev
Nature Methods
18
1352-1362 (2021)

Decoding molecular and cellular heterogeneity of mouse nucleus accumbens
 R. Chen, T. R. Blosser, M. N. Djekidel, J. Hao, A. Bhattacherjee, W. Chen, L. M. Tuesta, X. Zhuang, Y. Zhang
Nature Neuroscience
24
1757-1771 (2021)

Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy
 H. Lee, C. -C. Yu, E. S. Boyden, X. Zhuang, P. Kosuri
Scientific Reports
11
16944 (2021)

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
 B. F. Miller, D. Bambah-Mukku, C. Dulac, X. Zhuang, J. Fan
Genome Research
31
1843-1855 (2021)

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains
 H. Huang, Q. Zhu, A. Jussila, Y. Han, B. Bintu, C. Kern, M. Conte, Y. Zhang, S. Bianco, A. M. Chiariello, M. Yu, R. Hu, M. Tastemel, I. Juric, M. Hu, M. Nicodemi, X. Zhuang, B. Ren
Nature Genetics
53
1064-1074 (2021)

Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma
 T. Hara, R. Chanoch-Myers, N. D. Mathewson, C. Myskiw, L. Atta, L. Bussema, S. W. Eichhorn, A. C. Greenwald, G. S. Kinker, C. Rodman, L. N. G. Castro, H. Wakimoto, O. Rozenblatt-Rosen, X. Zhuang, J. Fan, T. Hunter, I. M.Verma, K. W. Wucherpfennig, A. Regev, M. L. Suvà, I. Tirosh
Cancer Cell
39
779-792 (2021)

Spatially-resolved single-cell genomics and transcriptomics by imaging
 X. Zhuang.
Nature Methods
18
18-22 (2021)

Spatial organization of the transcriptome in individual neurons
 G. Wang, C.-E. Ang, J. Fan, A. Wang, J. R. Moffitt, X. Zhuang.
bioRxiv
(https://doi.org/10.1101/2020.12.07.414060) (2020)

A multimodal cell census and atlas of the mammalian 1 primary motor cortex
 BRAIN Initiative Cell Census Network (BICCN).
bioRxiv
(https://doi.org/10.1101/2020.10.19.343129) (2020)

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics
 M. Zhang, S. W. Eichhorn, B. Zingg, Z. Yao, H. Zeng, H. Dong, X. Zhuang
bioRxiv
(https://doi.org/10.1101/2020.06.04.105700) (2020)

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
 J. -H. Su, P. Zheng, S. S. Kinrot, B. Bintu, X. Zhuang
Cell
182
1641-1659 (2020)

m6A-binding YTHDF proteins promote stress granule formation
 Y. Fu, X. Zhuang
Nature Chemical Biology
16
955-963 (2020)

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
 C. Xia, J. Fan, G. Emanuel, J. Hao, X. Zhuang
PNAS
116
19490-19499 (2019)

Membrane-associated periodic skeleton is a signaling platform for RTK transactivation in neurons
 R. Zhou, B. Han, C. Xia, X. Zhuang
Science
365
929-934 (2019)

Rotation tracking of genome-processing enzymes using DNA origami rotors
 P. Kosuri, B.D. Altheimer, M. Dai, P. Yin, X. Zhuang
Nature
7767
136-140 (2019)

Synaptic neurexin-1 assembles into dynamically regulated active zone nanoclusters
 J.H. Trotter, J. Hao, S. Maxeiner, T. Tsetsenis, Z. Liu, X. Zhuang, T.C. Sudhof
JCB
218 (8)
2677-2698 (2019)

beta II-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport
 D.N. Lorenzo, A. Badea, R. Zhou, P.J. Mohler, X. Zhuang, V. Bennett
PNAS
116
15686-15695 (2019)

Multiplexed detection of RNA using MERFISH and branched DNA amplification
 C. Xia, H.P. Babcock, J.R. Moffitt, X. Zhuang
Sci Rep.
9
7721 (2019)

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization
 C. Wang, T. Lu, G. Emanuel, H.P. Babcock, X. Zhuang
PNAS
116
10842-10851 (2019)

Structural plasticity of actin-spectrin membrane skeleton and functional role of actin and spectrin in axon degeneration
 G. Wang, D.J. Simon, Z. Wu, D.M. Belsky, E. Heller, M.K. O'Rourke, N.T. Hertz, H. Molina, G. Zhong, M. Tessier-Lavigne, X. Zhuang
eLife
8
e38730 (2019)

Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling
 A. Sabantsev, R.F. Levendosky, X. Zhuang, G.D. Bowman, S. Deindl
Nat. Commun.
10
1720 (2019)

Structural maturation of cortical perineuronal nets and their perforating synapses revealed by superresolution imaging
 Y.M. Sigal, H. Bae, L.J. Bogart, T.K. Hensch, X. Zhuang
PNAS
116
7071-7076 (2019)

Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria
 C.Y. Chan, A.M. Pedley, D. Kim, C. Xia, X. Zhuang, S.J. Benkovic
PNAS
115
13009-13014 (2018)

Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region
 J. Moffitt, D. Bambah-Mukku, S. Eichhorn, E. Vaughn, K. Shekhar, N. Rubinstein, J. Hao, A. Regev, C. Dulac, X. Zhuang
Science
363
eaau5324 (2018)

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
 B. Bintu, L. Mateo, J. Su, N. Sinnott-Armstrong, M. Parker, S. Kinrot, K. Yamaya, A. Boettiger, X. Zhuang
Science
362
eaau1783 (2018)

Visualizing and discovering cellular structures with super-resolution microscopy
 Y.M. Sigal, R. Zhou, X. Zhuang
Science
361
880-887 (2018)

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy
 G. Wang, J.R. Moffitt, X. Zhuang
Sci. Rep
8
4847 (2018)

High-throughput, image-based screening of pooled genetic-variant libraries
 G. Emanuel, J.R. Moffitt, X. Zhuang
Nat. Methods
14
1159-1162 (2017)

In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT
 B.J. Beliveau, A.N. Boettiger, G. Nir, B. Bintu, P. Yin, X. Zhuang, C.T. Wu
Methods Mol. Biol.
1663
231-252 (2017)

Structural organization of the actin-spectrin-based membrane skeleton in dendrites and soma of neurons
 B. Han, R. Zhou, C. Xia, X. Zhuang
PNAS
114
E6678-E6685 (2017)

The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction
 L.A. Timashev, H. Babcock, X. Zhuang, T. de Lange
Genes Dev.
31
578-589 (2017)

Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines
 H.P. Babcock, X. Zhuang
Sci. Rep.
7
552 (2017)

CatSper-zeta regulates the structural continuity of sperm Ca2+ signaling domains and is required for normal fertility
 J. Chung, K. Miki, D. Kim, S. Shim, H.F. Shi, J.Y. Hwang, X. Cai, Y. Iseri, X. Zhuang, D.E. Clapham
eLife
6
e23082 (2017)

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing
 J.R. Moffitt, J. Hao, D. Bambah-Mukkua, T. Lu, C. Dulac, X. Zhuang
PNAS
113
14456 (2016)

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
 J.R. Moffitt, J. Hao, G. Wang, K.H. Chen, H.P. Babcock, X. Zhuang
PNAS
113
11046 (2016)

Spatial organization of chromatin domains and compartments in single chromosomes
 S. Wang, J.H. Su, B.J. Beliveau, J.R. Moffitt, C.T. Wu, X. Zhuang
Science
353
598 (2016)

Chapter One - RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)
 J.R. Moffitt, X. Zhuang
Methods in Enzymology
572
1 (2016)

An RNA-aptamer-based two-color CRISPR labeling system
 S. Wang, J.H. Su, F. Zhang, X. Zhuang
Sci. Rep.
6
26857 (2016)

Spatial organization shapes the turnover of a bacterial transcriptome
 J.R. Moffitt, S. Pandey, A.N. Boettiger, S. Wang, X. Zhuang
eLife
5
e13065 (2016)

Prevalent presence of periodic actin-spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species
 J. He, R. Zhou, Z. Wu, M.A. Carrasco, P.T. Kurshan, J.E. Farley, D.J. Simon, G. Wang, B. Han, J. Hao, E. Heller, M.R. Freeman, K. Shen, T. Maniatis, M. Tessier-Lavigne, X. Zhuang
PNAS
113
6029-6034 (2016)

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells
 C. Wang, B. Han, R. Zhou, X. Zhuang
Cell
165
990-1001 (2016)

Spatial colocalization and functional link of purinosomes with mitochondria
 J.B. French, S.A. Jones, H. Deng, A.M. Pedley, D. Kim, C.Y. Chan, H. Hu, R.J. Pugh, H. Zhao, Y. Zhang, T.J. Huang, Y. Fang, X. Zhuang, S.J. Benkovic
Science
351
733-737 (2016)

Stepwise nucleosome translocation by RSC remodeling complexes
 B.T. Harada, W.L. Hwang, S. Deindl, N. Chatterjee, B. Bartholomew, X. Zhuang
eLife
5
e10051 (2016)

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
 A.N. Boettiger, B. Bintu, J.R. Moffitt, S. Wang, B.J. Beliveau, G. Fudenberg, M. Imakaev, L.A. Mirny, C.T. Wu, X. Zhuang
Nature
529
418-422 (2016)

Chromatin topology is coupled to Polycomb group protein subnuclear organization
 A.H. Wani, A.N. Boettiger, P. Schorderet, A. Ergun, C. Muenger, R.I. Sadreyev, X. Zhuang, R.E. Kingston, N.J. Francis
Nat Commun.
7
10291 (2016)

Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging
 Y.M. Sigal, C.M. Speer, H.P. Babcock, X. Zhuang
Cell
163
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
Science
348
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
12
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
6
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
10
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
PNAS
112
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
eLife
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
PNAS
111
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
207
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
Nature
512
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.
61
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
111
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
Cell
157
808-822 (2014)

Isotropic three-dimensional super-resolution imaging with a self-bending point spread function
 S. Jia, J. Vaughan, X. Zhuang
Nature Photonics
8
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
JEM
211
365-379 (2014)

Actin, spectrin and associated proteins form a periodic cytoskeleton structure in axons
 K. Xu, G. Zhong, X. Zhuang
Science
339
452-456 (2013)

Super-resolution fluorescence imaging reveals TRF2-dependent t-loop formation
 Y. Doksani, J. Wu, T. de Lange, X. Zhuang
Cell
155
345-356 (2013)

Fast compressed sensing analysis for super-resolution imaging using L1-homotopy
 H. Babcock, J. Moffitt, Y. Cao, X. Zhuang
Optics Express
21
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
Cell
152
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
9
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
20
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
JACS
135
1197-1200 (2013)

Live cell imaging of viral entry
 E. Sun, J, He, X. Zhuang
Current Opinion in Virology
3
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
7
1850-1866 (2013)

Dissecting the role of COPI complexes in influenza virus infection
 E. Sun, J. He, X. Zhuang
Journal of Virology
87
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
JCB
200
419-428 (2013)

Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging
 J. Vaughan, S. Jia, X. Zhuang
Nature Methods
9
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
Science
13
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.
109
13978-13983 (2012)

Monitoring Conformational Dynamics with Single-Molecule Fluorescence Resonance Energy Transfer: Application in Nucleosome Remodeling
 S. Deindl, X. Zhuang
Methods Enzymology
513
59-86 (2012)

A High-Density 3D Localization Algorithm for Stochastic Optical Reconstruction Microscopy
 H. P. Babcock, Y. Sigal, X. Zhuang
Optical Nanoscopy
1
6 (2012)

Statistical Deconvolution for Super-resolution Fluorescence Microscopy
 E. A. Mukamel, H. P. Babcock, X. Zhuang
Biophysical Journal
102
2391-2400 (2012)

Dual-objective STORM Reveals Three-dimensional Filament Organization in the Actin Cytoskeleton
 K. Xu, H. Babcock, X. Zhuang
Nature Methods
9
185-188 (2012)

3D Multicolor Super-Resolution Imaging Offers Improved Accuracy in Neuron Tracing
 M. Lakadamyali, H. Babcock, M. Bates X. Zhuang, J. Lichtman
PLoS One
7
e30826 (2012)

Multicolor Super-resolution Fluorescence Imaging Via Multi-parameter Fluorophore Detection
 M. Bates, G. T. Dempsey, K. H. Chen, X. Zhuang
Chemphyschem
13
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
8
1027-1036 (2011)

New Fluorescent Probes for Super-resolution Imaging
 J. Vaughan, X. Zhuang
Nature Biotechnology
29
880-881 (2011)

Chromosome Organization by a Nucleoid Associated Protein
 W. Wang, G. Li, C. Chen, X. Xie, X. Zhuang
Science
333
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
Science
333
222-225 (2011)

Fast, three-dimensional super-resolution imaging of live cells
 S. Jones, S-H. Shim, J. He, X. Zhuang
Nature Methods
8
499-505 (2011)

Functional importance of telomerase pseudoknot revealed by single-molecule analysis
 M. Mihalusova, J.Y. Wu, X. Zhuang
Proc. Natl. Acad. Sci.
108
20339-20344 (2011)

Breaking the diffraction barrier: Super-resolution imaging of cells
 B. Huang, H. Babcock, X. Zhuang
Cell
143
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.
17
1453-1460 (2010)

Super-resolution imaging of chemical synapses in the brain
 A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang
Neuron
68
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
12
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
54
3913-3921 (2010)

New technologies, editorial overview
 E. Schuman, X. Zhuang
Current Opinion in Neurobiology
20
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
Nature
462
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
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
96
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
38
e16 (2010)

Rapid Actin-dependent Viral Motility in Live Cells
 J. Vaughan, B. Brandenburg, J. Hogle, X. Zhuang
Biophysical Journal
97
1647-1656 (2009)

Nano-imaging with STORM
 X. Zhuang
Nature Photonics
3
365-367 (2009)

Super-resolution Fluorescence Microscopy
 B. Huang, M. Bates, X. Zhuang
Annual Review Biochemistry
78
993-1016 (2009)

Concealed Enzyme Coordination
 E. Abbondanzieri, X. Zhuang
Nature
457
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
4
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
5
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
Science
322
1092-1097 (2008)

Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes
 M. Bates, B. Huang, X. Zhuang
Curr. Opin. Chem. Biol.
12
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
Nature
453
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
105
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.
130
10472-10473 (2008)

Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy
 B. Huang, W. Wang, M. Bates, X. Zhuang
Science
319
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
Science
317
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
104
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.
5
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
Nature
446
458-461 (2007)

Virus trafficking - learning from single-virus tracking
 B. Brandenburg, X. Zhuang
Nat. Rev. Microbiology
5
197-208 (2007)

Kinetic analysis of sequential multi-step reactions
 Y. Zhou, X. Zhuang
J. Phys. Chem. B
111
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.
81
12019-12028 (2007)

Internalization and trafficking of cell surface proteoglycans and proteoglycan binding ligands
 C. K. Payne, S. Jones, C. Chen, X. Zhuang
Traffic
8
389-401 (2007)

Robust reconstruction of the rate constant distribution using the phase function method
 Y. Zhou, X. Zhuang
Biophysical Journal
91
4045-4053 (2006)

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
 M. J. Rust, M. Bates, X. Zhuang
Nature Methods
3
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.
361
771-784 (2006)

Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes
 M. Lakadamyali, M. J. Rust, X. Zhuang
Cell
124
997-1009 (2006)

Single-molecule RNA folding
 G. Bokinsky, X. Zhuang
Acc. Chem. Res.
38
566-573 (2005)

Single-molecule RNA Science
 X. Zhuang
Annu. Rev. Biophys. Biomol. Struct.
34
399-414 (2005)

Short-range spectroscopic ruler based on a single-molecule optical switch
 M. Bates, T. R. Blosser, X. Zhuang
Phys. Rev. Lett.
94
108101 (2005)

Unraveling DNA condensation by optical tweezers
 X. Zhuang
Science
305
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.
11
567-573 (2004)

Endocytosis of influenza viruses
 M. Lakadamyali, M. J. Rust, X. Zhuang
Micro. Infection
6
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
101
14017-14022 (2004)

Using single particle-tracking to study nuclear trafficking of viral genes
 H. P. Babcock, C. Chen, X. Zhuang
Biophys. J.
87
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
101
10066-10071 (2004)

Visualizing infection of individual influenza viruses
 M. Lakadamyali, M. J. Rust, H P. Babcock, X. Zhuang
Proc. Natl. Acad. Sci. USA
100
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
100
9302-9307 (2003)

Single-molecule folding
 X. Zhuang and M. Rief
Curr. Opin. Struct. Biol.
13
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.
328
1011-1026 (2003)

Correlating structural dynamics and function in single ribozyme molecules
 X. Zhuang, H. Kim, M. Pereira, H. Babcock, N. Walter, S. Chu
Science
296
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
99
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
Science
288
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
97
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
96
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
63
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.
123
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.
358
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
62
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.
82
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
59
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
59
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.
321
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.
19
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.
78
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.
258
620-625 (1996)

The application of nonlinear optics to the study of polymers at interfaces
X. Zhuang and Y. R. Shen
Trends Polym. Sci.
4
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.
246
279-284 (1995)

Orientation of amphiphilic molecules on polar substrates
 X. Zhuang, D. Wilk, L. Marrucci, and Y. R. Shen
Phys. Rev. Lett.
75
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.
262
35-43 (1995)

last updated 10/20/2025