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Academic

Xiaowei Zhuang

Academic

RankDistinguished

As of2019 · CV

DepartmentHarvard Chemistry

UniversityHarvard

FieldChemistry

ORCID0000-0002-6034-7853

Scholarprofile

Totals

Publications192

Citations78,992

h-index123 · Scholar

Citations per year in post3,159.7

Years in post25 from the CV positions

Coverage

Works with a count189 of 192

Share98%

Positions

Co-founder, consultant, scientific and techni…2019–

David B. Arnold Professor of Science, Harvard…2014–

Professor, Department of Chemistry and Chemic…2006–

Investigator, Howard Hughes Medical Institute2005–

Associate Professor, Department of Chemistry…2005–2006

Assistant Professor, Department of Chemistry…2001–2005

Chodorow Postdoctoral Fellow, Stanford Univer…1997–2001

Howard Hughes Medical Institute Investigator—

and 1 more

Top venues 63 venues

The 8 holding the most of these works; 55 more hold at least one.

Proceedings of the National Academy of Scienc…23

Science21

Cell12

Nature12

Nature Methods11

Biophysical Journal5

bioRxiv (Cold Spring Harbor Laboratory)5

eLife5

Publications per year

Works this academic published in each year, by the year each work appeared; an undated work is in no year, and a work two colleagues wrote counts for each of them. The kind, works and year filters decide which works are here at all.

Citations per year

Citations received in each year, from this academic’s verified Scholar profile, which counts every citation to everything they ever wrote: no publication filter reaches this line - not the kinds, not the works switch, not the year window on publication - and no journal weight either. It is a profile total, so it does not match the works listed below.

Publications 192 works

Every work these filters select, most cited first and the works with no count at the end: a work nobody has a figure for is unknown, never a zero to be ranked among the works that have one, and it prints an em dash. Each figure is that work’s own citations - Scholar’s count where there is one, else OpenAlex’s - and is not weighted.

Year	Title	Venue	Kind	Citations
2006	Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)	Nature Methods	article	10,471
2008	Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy	Science	article	3,660
2015	Spatially resolved, highly multiplexed RNA profiling in single cells	Science	article	3,604
2009	Super-resolution fluorescence microscopy	Annual Review of Biochemistry	article	2,313
2007	Multicolor super-resolution imaging with photo- switchable fluorescent probes	Science	article	1,965
2004	Electrical detection of single viruses	Proceedings of the National Academy of Sciences	article	1,789
2011	Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging	Nature Methods	article	1,721
2013	Actin, spectrin and associated proteins form a periodic cytoskeleton structure in axons	Science	article	1,617
2018	Molecular, Spatial and Functional Single- Cell Profiling of the Hypothalamic Preoptic Region	Science	article	1,543
2010	Breaking the diffraction barrier: Super-resolution imaging of cells	Cell	article	1,499
2023	A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain	Nature	article	1,398
1999	Mapping molecular orientation and conformation at interfaces by surface nonlinear optics	Physical review. B, Condensed matter	article	1,174
2018	Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells	Science	article	1,159
2021	Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	Nature Methods	article	1,078
2016	Super-resolution imaging reveals distinct chromatin folding for different epigenetic states	Nature	article	1,029
2011	Fast three-dimensional super-resolution imaging of live cells	Nature Methods	article	988
2000	A single-molecule study of RNA catalysis and folding	Science	article	977
2003	Visualizing infection of individual influenza viruses	Proceedings of the National Academy of Sciences	article	947
2010	Super-resolution imaging of chemical synapses in the brain	Neuron	article	927
2019	Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression	Proceedings of the National Academy of Sciences	article	894
2008	Whole cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution	Nature Methods	article	830
2018	Visualizing and discovering cellular structures with super- resolution microscopy	Science	article	820
2016	Spatial organization of chromatin domains and compartments in single chromosomes	Science	article	815
2006	Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes	Cell	article	715
2009	Dissecting the cell entry pathway of single Dengue virus particles in living cells	PLoS Pathogens	article	697
2004	Assembly of endocytic machinery around individual influenza viruses during viral entry	Nature Structural & Molecular Biology	article	695
2016	High-throughput single- cell gene expression profiling with multiplexed error-robust fluorescence in situ hybridization (MERFISH)	Proceedings of the National Academy of Sciences	article	672
2020	The human tumor atlas network: charting tumor transitions across space and time at single-cell resolution	Cell	article	670
2002	Correlating structural dynamics and function in single ribozyme molecules	Science	article	664
2021	Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma	Cancer Cell	article	661
2011	Coupled, Circumferential Motions of the Cell Wall Synthesis Machinery and MreB Filaments in B. subtilis	Science	article	660
2014	Isotropic three-dimensional super-resolution imaging with a self-bending point spread function	Nature Photonics	article	651
2013	Super-resolution fluorescence imaging of telomeres reveals TRF2-dependent t-loop formation	Cell	article	629
2012	Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton	Nature Methods	article	622
2020	Genome-scale imaging of the 3D organization and transcriptional activity of chromatin	Cell	article	621
2012	Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes	Proceedings of the National Academy of Sciences	article	614
2021	Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH	Nature	article	588
2023	Molecularly defined and spatially resolved cell atlas of the whole mouse brain	Nature	article	561
2014	Effects of immediate blood pressure reduction on death and major disability in patients with acute ischemic stroke: the CATIS randomized clinical trial	JAMA	article	544
2004	Endocytosis of influenza viruses	Microbes and Infection	article	544
2007	Virus trafficking – learning from single-virus tracking	Nature Reviews Microbiology	article	534
2009	Photoswitching mechanism of cyanine dyes	Journal of the American Chemical Society	article	525
2005	Short-range spectroscopic ruler based on a single-molecule optical switch	Physical Review Letters	article	507
2012	Molecular architecture and assembly principles of Vibrio Cholerae biofilms	Science	article	506
2015	The 2015 super-resolution microscopy roadmap	MPG.PuRe (Max Planck Society)	article	496
2011	Chromosome organization by a nucleoid associated protein	Science	article	476
2015	Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes	Nature Communications	article	474
2013	Nanotools for neuroscience and brain activity mapping	ACS Nano	article	465
2023	Molecular and spatial signatures of mouse brain aging at single cell resolution	Cell	article	457
2014	Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging	Proceedings of the National Academy of Sciences	article	450
2007	Imaging poliovirus entry in live cells	PLoS Biology	article	442
2016	Real-time imaging of translation on single mRNA transcripts in live cells	Cell	article	434
2020	m6A-binding YTHDF proteins promote stress granule formation	Nature Chemical Biology	article	392
2016	High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing	Proceedings of the National Academy of Sciences	article	374
2007	Internalization and trafficking of cell surface proteoglycans and proteoglycan binding ligands	Traffic	article	371
2018	Multiplexed imaging of high density libraries of RNAs with MERFISH and expansion microscopy	Scientific Reports	article	367
1999	Ligand-induced conformational changes of single RNA molecules	Proceedings of the National Academy of Sciences	article	367
2007	Characterization of the early events in Dengue virus cell entry by biochemical assays and single-virus tracking	Journal of Virology	article	353
2000	Nonlinear optical studies of liquid crystal alignment on a rubber polyvinyl alcohol surface	Physical review. E, Statistical physics, plasmas, fluids, a…	article	340
2015	High-performance probes for light and electron microscopy	Nature Methods	article	332
2014	Structurally Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and Motility	Cell	article	323
2022	Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH	Science	article	317
2002	Exploring the folding landscape of a structured RNA	Proceedings of the National Academy of Sciences	article	314
2003	Single-molecule folding	Current Opinion in Structural Biology	article	303
2016	RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)	Methods in enzymology on CD-ROM/Methods in enzymology	article	301
2008	Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes	Current Opinion in Chemical Biology	article	295
2012	Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging	Nature Methods	article	290
2014	Developmental mechanism of the periodic membrane skeleton in axons	eLife	article	288
2006	Stochastic optical reconstruction microscopy (STORM) provides sub-diffraction-limit image resolution	Nature Methods	article	284
2003	Single-molecule transition-state analysis of RNA folding	Proceedings of the National Academy of Sciences	article	274
2000	Fluorescence quenching: a tool for single-molecule protein-folding study	Proceedings of the National Academy of Sciences	article	272
2016	Spatial colocalization and functional link of purinosomes with mitochondria	Science	article	269
2021	Spatially resolved single-cell genomics and transcriptomics by imaging	Nature Methods	article	262
2007	Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein	Nature	article	259
2009	Nano-imaging with STORM	Nature Photonics	article	255
2008	Epsin1 is a cargo specific adaptor for the clathrin-mediated endocytosis of influenza virus	Proceedings of the National Academy of Sciences	article	252
2009	Dynamics of nucleosome remodeling by individual ACF complexes	Nature	article	248
2022	Spatially resolved epigenomic profiling of single cells in complex tissues	Cell	article	242
2016	Prevalent presence of periodic actin-spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species	Proceedings of the National Academy of Sciences	article	233
2008	Dynamic binding orientations direct activity of HIV reverse transcriptase	Nature	article	233
2021	Decoding molecular and cellular heterogeneity of mouse nucleus accumbens	Nature Neuroscience	article	227
2013	ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single- base- pair exit steps	Cell	article	227
2012	Statistical deconvolution for super-resolution fluorescence Microscopy	Biophysical Journal	article	224
2016	Chromatin topology is coupled to Polycomb group protein subnuclear organization	Nature Communications	article	223
2019	Multiplexed detection of RNA using MERFISH and branched DNA amplification	Scientific Reports	article	221
2005	Single-molecule RNA Science	Annual Review of Biophysics and Biomolecular Structure	article	220
2012	A high-density 3D localization algorithm for stochastic optical reconstruction microscopy	Optical Nanoscopy	article	213
2021	CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains	Nature Genetics	article	211
2012	Multicolor super-resolution fluorescence imaging through via multi-parameter fluorophore detection	ChemPhysChem	article	211
2016	System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes	Molecular Cell	article	207
2008	Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrate	Science	article	205
2021	Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities	Genome Research	article	203
2004	Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance	Proceedings of the National Academy of Sciences	article	194
2017	CatSperζ Regulates the Structural Continuity of Sperm Ca2+ Signaling Domains and is Required for Normal Fertility	eLife	article	193
2022	A Preoptic neuronal population controls fever and appetite during sickness	Nature	article	192
2004	Using single-particle tracking to study nuclear trafficking of viral genes	Biophysical Journal	article	192
2017	Structural Organization of the Actin-spectrin-based Membrane Skeleton in Dendrites and Soma of Neurons	Proceedings of the National Academy of Sciences	article	190
1999	Sum-Frequency vibrational spectroscopic study of a rubbed polymer surface	Physical Review Letters	article	190
2013	Phospine Quenching of Cyanine Dyes as a Versatile Tool for Fluorescence Microscopy	Journal of the American Chemical Society	article	187
2016	Spatial organization shapes the turnover of a bacterial transcriptome	eLife	article	184
2010	Coupling between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free system	Nature Cell Biology	article	183
2001	Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains	Journal of the American Chemical Society	article	177
2016	Chromium speciation in tannery effluent after alkaline precipitation: Isolation and characterization	Journal of Hazardous Materials	article	166
2019	Structural maturation of cortical perineuronal nets and their perforating synapses revealed by super-resolution imaging	Proceedings of the National Academy of Sciences	article	161
2014	A model for the generation and interconversion of ER morphologies	Proceedings of the National Academy of Sciences	article	161
2015	Mapping synaptic input fields of neurons with super-resolution imaging	Cell	article	158
2008	Luminescent and Raman active silver nanoparticles with polycrystalline structure	Journal of the American Chemical Society	article	153
2019	Membrane-associated periodic skeleton is a signaling platform for RTK transactivation in neurons	Science	article	152
2019	Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization	Proceedings of the National Academy of Sciences	article	150
2019	Rotation tracking of genome-processing enzymes using DNA origami rotors	Nature	article	147
2016	An RNA-aptamer-based two-color CRISPR labeling system	Scientific Reports	article	137
2019	Synaptic Neurexin-1 Assembles into Dynamically Regulated Active Zone Nanoclusters	The Journal of Cell Biology	article	136
1994	Surface-monolayer-induced bulk alignment of liquid crystals	Physical Review Letters	article	135
2015	Purinosome formation as a function of the cell cycle	Proceedings of the National Academy of Sciences	article	134
2024	A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features	Nature Medicine	article	133
2003	Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA	Journal of Molecular Biology	article	129
2017	Analyzing single molecule localization microscopy data using cubic splines	Scientific Reports	article	126
2013	Dual function of CD81 in influenza uncoating and budding	PLoS Pathogens	article	124
2004	Unraveling DNA condensation by optical tweezers	Science	article	124
1997	Dye-Induced Enhancement of Optical Nonlinearity in Liquids and Liquid Crystals	Physical Review Letters	article	123
2005	Single-molecule RNA folding	Accounts of Chemical Research	article	120
2015	Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy	PLoS ONE	article	119
2014	Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA	Nature	article	117
2014	A PIK3C3–Ankyrin-B–Dynactin pathway promotes axonal growth and multiorganelle transport	The Journal of Cell Biology	article	114
2012	3D Multicolor Super- Resolution Imaging Offers Improved Accuracy in NeuronTracing	PLoS ONE	article	110
2007	Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic fingerprinting	Proceedings of the National Academy of Sciences	article	110
2019	Direct observation of coordinated DNA movements on the nucleosome during chromatin remodeling	Nature Communications	article	106
2013	Fast compressed sensing analysis for super- resolution imaging using L1-homotopy	Optics Express	article	104
2018	Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria	Proceedings of the National Academy of Sciences	article	97
2016	Stepwise nucleosome translocation by RSC remodeling complexes	eLife	article	95
2017	High-throughput, image-based screening of pooled genetic variant libraries	Nature Methods	article	93
2013	Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains	Nature Structural & Molecular Biology	article	88
2013	Clathrin and AP2 are required for PtdIns(4,5)P2-mediated formation of LRP6 signalosomes	The Journal of Cell Biology	article	87
2010	Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription	Nature Structural & Molecular Biology	article	87
2014	Risk score to predict hospital-acquired pneumonia after spontaneous intracerebral hemorrhage	—	article	86
2017	The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction	Genes & Development	article	83
2020	Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos	Molecular Cell	article	80
2025	Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue	Cell	article	77
2013	Dissecting the role of COPI complexes on influenza virus infection	Journal of Virology	article	76
2013	Live cell imaging of viral entry	Current Opinion in Virology	article	76
2019	βII-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport	Proceedings of the National Academy of Sciences	article	74
2014	Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells	The Journal of Experimental Medicine	article	74
1995	Orientation of amphiphilic molecules on polar substrates	Physical Review Letters	article	74
2023	Three-dimensional single-cell transcriptome imaging of thick tissues	bioRxiv (Cold Spring Harbor Laboratory)	article	73
2019	Structural plasticity of actin-spectrin membrane skeleton and functional role of actin and spectrin in axon degeneration	eLife	article	73
2006	Two distinct binding mode of a protein cofactor with its target RNA	Journal of Molecular Biology	article	72
2022	Proteomic and functional analyses of the periodic membrane skeleton in neurons	Nature Communications	article	69
2010	Structure-Activity Analysis of Vinylogous Urea Inhibitors of Human Immunodeficiency Virus-Encoded Ribonuclease H	Antimicrobial Agents and Chemotherapy	article	63
2019	Multiplexed imaging using merfish, expansion microscopy, and related technologies	—	article	62
2007	Kinetic analysis of sequential multi-step reactions	The Journal of Physical Chemistry B	article	62
2019	Matrix imprinting and clearing	—	article	60
2011	Portfolio adjusting optimization with added assets and transaction costs based on credibility measures	—	article	55
2011	Functional importance of telomerase pseudoknot revealed by single-molecule analysis	Proceedings of the National Academy of Sciences	article	53
2009	Rapid actin-dependent viral motility in live cells	Biophysical Journal	article	50
2025	High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer	Science	article	49
2017	Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across cellular and model membranes	PLoS Pathogens	article	49
1998	Surface studies of polyimide thin films via surface enhanced Raman scattering and second harmonic generation	Macromolecular Rapid Communications	article	48
2020	Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics	bioRxiv (Cold Spring Harbor Laboratory)	article	44
2014	Postsynaptic actin regulates active zone spacing and glutamate receptor apposition at the Drosophila neuromuscular junction	Molecular and Cellular Neuroscience	article	44
2000	Platinum–aluminum nitride–silicon carbide diodes as combustible gas sensors	Journal of Applied Physics	article	42
2020	Spatial organization of the transcriptome in individual neurons	bioRxiv (Cold Spring Harbor Laboratory)	article	41
2016	Novel stability control strategy for distributed drive electric vehicle based on driver operation intention	—	article	41
2011	New fluorescent probes for super-resolution imaging	Nature Biotechnology	article	39
2009	A Single-molecule assay for telomerase structural-function analysis	Nucleic Acids Research	article	37
2022	Three-dimensional interrogation of cell types and instinctive behavior in the periaqueductal gray	bioRxiv (Cold Spring Harbor Laboratory)	article	36
2021	Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy	Scientific Reports	article	36
2014	Isotropic 3D super-resolution imaging with a self-bending point-spread function	Biophysical Journal	article	35
2012	Monitoring conformational dynamics with single-molecule fluorescence resonance energy transfer: Application in Nucleosome Remodeling	Methods in enzymology on CD-ROM/Methods in enzymology	article	34
2001	Orientation of side chains and adsorbed liquid crystal molecules on a rubbed polyimide surface studied by optical harmonic generation	Physical review. E, Statistical physics, plasmas, fluids, a…	article	34
2025	Cell-type-specific 3D-genome organization and transcription regulation in the brain	Science Advances	article	33
2006	Robust reconstruction of the rate constant distribution using the phase function method	Biophysical Journal	article	33
2017	Three-dimensional super-resolution fluorescence imaging using airy beams and other techniques	—	article	31
2014	Effect of secondary extrusion on the microstructure and mechanical properties of a Mg–RE alloy	—	article	31
2024	The commitment of the human cell atlas to humanity	Nature Communications	article	22
2021	A multimodal cell census and atlas of the mammalian primary motor cortex	Nature	article	22
2013	Preparation of C5 petroleum resins using Et3NHCl-AlCl3 as catalyst	—	article	22
2022	Amplification methods and systems for merfish and other applications	—	article	21
2025	The membrane skeleton is constitutively remodeled in neurons by calcium signaling	Science	article	19
1995	Photo-isomerization of polymer monolayers and multi-layers on water	Chemical Physics Letters	article	19
2017	Blind sparse inpainting reveals cytoskeletal filaments with sub-Nyquist localization	Optica	article	17
1996	Ultrafast orientation dynamics of liquid crystals in smectic phase	Chemical Physics Letters	article	17
2025	A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function	bioRxiv (Cold Spring Harbor Laboratory)	article	13
1999	Surface-monolayer-induced bulk alignment of liquid crystals: from nematic to smectic-a phase	Physical review. E, Statistical physics, plasmas, fluids, a…	article	8
2009	Concealed enzyme coordination	Nature	article	6
1995	Dependence of liquid crystal bulk alignment on its surface monolayer	Molecular crystals and liquid crystals science technology.…	article	3
1998	Dye-induced enhancement of optical nonlinearity in liquid crystals and ordinary liquids	Molecular crystals and liquid crystals science technology.…	article	2
2010	New technologies, Editorial overview	Current Opinion in Neurobiology	article	0
2001	Vibrational spectroscopy of rubbed polymer surfaces	Molecular crystals and liquid crystals science technology.…	article	0
1997	Enhanced optical Kerr effect of dye-doped isotropic liquid	APS	article	0
2011	Circumferential motions of the cell wall synthesis machinery drive cytoskeletal dynamics in B. subtilis	Science	article	—
1996	The application of nonlinear optics to the study of polymers at interfaces	—	article	—
—	untitled	—	article	—