Ke Xu Group

Publications

|| - these authors contributed equally to this work

2022


B. Wang, Z. Zhao, M. Xiong, R. Yan, K. Xu, "The endoplasmic reticulum adopts two distinct tubule forms," [Link]
Proc. Natl. Acad. Sci. U.S.A., 119, e2117559119, 2022.

C. Kaplan, S. J. Kenny, X. Chen, J. Schöneberg, E. Sitarska, A. Diz-Muñoz, M. Akamatsu, K. Xu, D. G. Drubin, "Load adaptation by endocytic actin networks," [Link] [Cover]
Mol. Biol. Cell, 33, ar50, 2022.

Y. Li, B. Wang, W. Li, K. Xu, "Dynamic, spontaneous blistering of substrate-supported graphene in acidic solutions," [Link] [Cover]
ACS Nano, 16, 6145-6152, 2022.

A. A. Choi, H. H. Park, K. Chen, R. Yan, W. Li, K. Xu, "Displacement statistics of unhindered single molecules show no enhanced diffusion in enzymatic reactions," [Link]
J. Am. Chem. Soc., 144, 4839-4844, 2022.

R. Yan, K. Chen, B. Wang, K. Xu, "SURF4-induced tubular ERGIC selectively expedites ER-to-Golgi transport," [Link]
Dev. Cell, 57, 512-525, 2022.

B. Wang, M. Xiong, J. Susanto, X. Li, W.-Y. Leung, K. Xu, "Transforming rhodamine dyes for (d)STORM super-resolution microscopy via 1,3-disubstituted imidazolium substitution," [Link]
Angew. Chem. Int. Ed., 61, e202113612, 2022.

Z. L. Newman, D. Bakshinskaya, R. Schultz, S. J. Kenny, S. Moon, K. Aghi, C. Stanley, N. Marnani, R. Li, J. Bleier, K. Xu, E. Y. Isacoff, "Determinants of synapse diversity revealed by super-resolution quantal transmission and active zone imaging," [Link]
Nat. Commun., 13, 229, 2022.



2021


L. Xiang||, K. Chen||, K. Xu, "Single molecules are your quanta: A bottom-up approach toward multidimensional super-resolution microscopy," [Invited Perspective] [Link]
ACS Nano, 15, 12483-12496, 2021.

K. Chen, R. Yan, L. Xiang, K. Xu, "Excitation spectral microscopy for highly multiplexed fluorescence imaging and quantitative biosensing," [Link]
Light Sci. Appl., 10, 97, 2021.

S. Li, R. Yan, J. Xu, S. Zhao, X. Ma, Q. Sun, M. Zhang, Y. Li, J.-J. G. Liu, L. Chen, S. Li, K. Xu, L. Ge, "A new type of ERGIC–ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis," [Link]
Cell Res., 32, 119-138, 2021.

M. Jin, C. Shirazinejad, B. Wang, A. Yan, J. Schöneberg, S. Upadhyayula, K. Xu, D. G. Drubin, "Rescue of stalled clathrin-mediated endocytosis by asymmetric Arp2/3-mediated actin assembly," [Link]
bioRxiv, 2021.07.16.452693.

R. Tian, A. Abarientos, J. Hong, S. H. Hashemi, R. Yan, N. Dräger, K. Leng, M. A. Nalls, A. B. Singleton, K. Xu, F. Faghri, M. Kampmann, "Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis," [Link]
Nature Neurosci., 24, 1020-1034, 2021.

M. E. Truong, S. Bilekova, S. P. Choksi, W. Li, L. J. Bugaj, K. Xu, J. F. Reiter, "Vertebrate cells differentially interpret ciliary and extraciliary cAMP," [Link]
Cell, 184, 1911-2926, 2021.

W. Li, Y. Li, K. Xu, "Facile, electrochemical chlorination of graphene from an aqueous NaCl solution," [Link]
Nano Lett., 21, 1150-1155, 2021.



2020


R. Yan, K. Chen, K. Xu, "Probing nanoscale diffusional heterogeneities in cellular membranes through multidimensional single-molecule and super-resolution microscopy," [Link]
J. Am. Chem. Soc., 142, 18866-18873, 2020.

B. Belardi, T. Hamkins-Indik, A. R. Harris, J. Kim, K. Xu, D. A. Fletcher, "A weak link with actin organizes tight junctions to control epithelial permeability," [Link]
Dev. Cell, 54, 792-804, 2020.

T. D. Roberts, R. Yuan, L. Xiang, M. Delor, R. Pokhrel, K. Yang, E. Aqad, T. Marangoni, P. Trefonas, K. Xu, N. S. Ginsberg, "Direct correlation of single-particle motion to amorphous microstructural components of semicrystalline poly(ethylene oxide) electrolytic films," [Link]
J. Phys. Chem. Lett., 11, 4849-4858, 2020.

K. J. Wolf, P. Shukla, K. Springer, S. Lee, J. D. Coombes, C. J. Choy, S. J. Kenny, K. Xu, S. Kumar, "A mode of cell adhesion and migration facilitated by CD44-dependent microtentacles," [Link]
Proc. Natl. Acad. Sci. U.S.A., 117, 11432-11443, 2020.

S. Moon||, W. Li||, M. Hauser, K. Xu, "Graphene-enabled, spatially controlled electroporation of adherent cells for live-cell super-resolution microscopy," [Link]
ACS Nano, 14, 5609-5617, 2020.

L. Xiang||, K. Chen||, R. Yan, W. Li, K. Xu, "Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity," [Link]
Nature Methods, 17, 524-530, 2020.

X. Guo, G. Aviles, Y. Liu, R. Tian, B. A. Unger, Y.-H. T. Lin, A. P. Wiita, K. Xu, M. A. Correia, M. Kampmann, "Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway," [Link]
Nature, 579, 427-432, 2020.

S. Köhler||, M. Wojcik||, K. Xu, A. F. Dernburg, "The interaction of crossover formation and the dynamic architecture of the synaptonemal complex during meiosis," [Link]
bioRxiv, 2020.02.16.947804.

W. Li, Y. Li, K. Xu, "Azidated graphene: direct azidation from monolayers, click chemistry, and bulk production from graphite," [Link]
Nano Lett., 20, 534-539, 2020.



2019


S. J. Kenny||, X. S. Chen||, L. Ge, K. Xu, "Super-resolution microscopy unveils FIP200-scaffolded, cup-shaped organization of mammalian autophagic initiation machinery," [Link]
bioRxiv, 712828.

Y. Sun, J. Schöneberg, X. Chen, T. Jiang, C. Kaplan, K. Xu, T. D. Pollard, D. G. Drubin, "Direct comparison of clathrin-mediated endocytosis in budding and fission yeast reveals conserved and evolvable features,"[Link]
eLife, 8, e50749, 2019.

L. Xiang, K. Xu, "Super-resolution writing," [News & Views] [Link]
Nature Chem., 11, 969-971, 2019.

P. D. Sohn, C. T.-L. Huang, R. Yan, L. Fan, T. E. Tracy, C. M. Camargo, K. M. Montgomery, T. Arhar, S.-A. Mok, R. Freilich, J. Baik, M. He, S. Gong, E. D. Roberson, C. M. Karch, J. E. Gestwicki, K. Xu, K. S. Kosik, L. Gan, "Pathogenic tau impairs axon initial segment plasticity and excitability homeostasis," [Link]
Neuron, 104, 458-470, 2019.

J. Kim, M. Wojcik, Y. Wang, S. Moon, E. A. Zin, N. Marnani, Z. L. Newman, J. G. Flannery, K. Xu, X. Zhang, "Oblique-plane single-molecule localization microscopy for tissues and small intact animals," [Link]
Nature Methods, 16, 853-857, 2019.
Accompanying News & Views: R. Fiolka, “Resolution upgrades for light-sheet microscopy” [Link]

D. I. Danylchuk||, S. Moon||, K. Xu, A. S. Klymchenko, "Tailor-made switchable solvatochromic probes for live-cell super-resolution imaging of plasma membrane organization," [Link]
Angew. Chem. Int. Ed., 58, 14920-14924, 2019.
Featured in C&EN: “Probe reveals nanometer-scale chemical environment of cell membranes” [Link]

Y. Li, W. Li, M. Wojcik, B. Wang, L.-C. Lin, M. B. Raschke, K. Xu, "Light-assisted diazonium functionalization of graphene and spatial heterogeneities in reactivity," [Link]
J. Phys. Chem. Lett., 10, 4788-4793, 2019.

R. Yan, B. Wang, K. Xu, "Functional super-resolution microscopy of the cell," [Invited review] [Link]
Curr. Opin. Chem. Biol., 51, 92-97, 2019.

L. Pan, P. Zhang, F. Hu, R. Yan, M. He, W. Li, J. Xu, K. Xu, "Hypotonic stress induces fast, reversible degradation of the vimentin cytoskeleton via intracellular calcium release," [Link]
Adv. Sci., 6, 1900865, 2019.

T. Kim||, S. Moon||, K. Xu, "Information-rich localization microscopy through machine learning," [Link]
Nature Commun., 10, 1996, 2019.

A. A. Polyzos, D. Y. Lee, R. Datta, M. Hauser, H. Budworth, A. Holt, S. Mihalik, P. Goldschmidt, K. Frankel, K. Trego, M. J. Bennett, J. Vockley, K. Xu, E. Gratton, C. T. McMurray, "Metabolic reprogramming in astrocytes distinguishes region-specific neuronal susceptibility in Huntington mice," [Link]
Cell Metab., 29, 1258-1273, 2019.

W. Li, M. Wojcik, K. Xu, "Optical microscopy unveils rapid, reversible electrochemical oxidation and reduction of graphene," [Link]
Nano Lett., 19, 983-989, 2019.



2018


L. Yuan, S. J. Kenny, J. Hemmati, K. Xu, R. Schekman, "TANGO1 and SEC12 are copackaged with procollagen I to facilitate the generation of large COPII carriers," [Link]
Proc. Natl. Acad. Sci. U.S.A., 115, E12255-E12264, 2018.

M. R. Miller||, S. J. Kenny||, N. Mannowetz||, S. A. Mansell, M. Wojcik, S. Mendoza, R. S. Zucker, K. Xu, P. V. Lishko, "Asymmetrically positioned flagellar control units regulate human sperm rotation," [Link]
Cell Rep., 24, 2606-2613, 2018.

M. Hauser, R. Yan, W. Li, N. A. Repina, D. V. Schaffer, K. Xu, "The spectrin-actin-based periodic cytoskeleton as a conserved nanoscale scaffold and ruler of the neural stem cell lineage," [Link]
Cell Rep., 24, 1512-1522, 2018.

D. Joshi||, M. Hauser||, G. Veber, A. Berl, K. Xu, F. R. Fischer, "Super-resolution imaging of clickable graphene nanoribbons decorated with fluorescent dyes," [Link]
J. Am. Chem. Soc.,140, 9574-9580, 2018.

L. Xiang, M. Wojcik, S. J. Kenny, R. Yan, S. Moon, W. Li, K. Xu, "Optical characterization of surface adlayers and their compositional demixing at the nanoscale," [Link]
Nature Commun., 9, 1435, 2018.
Featured in Physics Today: "Surface nanodroplets show their spots," Physics Today 71(6), 72, 2018, [Link]

V. Serpooshan||, S. Sheibani||, P. Pushparaj||, M. Wojcik||, A. Y. Jang||, M. R. Santoso, J. H. Jang, H. Huang, R. Safavi-Sohi, N. Haghjoo, H. Nejadnik, H. Aghaverdi, H. Vali, J. M. Kinsella, J. Presley, K. Xu, P. C.-M. Yang, M. Mahmoudi, "Effect of cell sex on uptake of nanoparticles: the overlooked factor at the nanobio interface," [Link]
ACS Nano, 12, 2253-2266, 2018.

R. Yan||, S. Moon||, S. J. Kenny||, K. Xu, "Spectrally resolved and functional super-resolution microscopy via ultrahigh-throughput single-molecule spectroscopy," [Invited review] [Link]
Acc. Chem. Res., 51, 697-705, 2018.

L. Pan, R. Yan, W. Li, K. Xu, "Super-resolution microscopy reveals the native ultrastructure of the erythrocyte cytoskeleton," [Link]
Cell Rep., 22, 1151-1158, 2018.
Featured on UC-Berkeley homepage (1/30/2018) [Link]

M. Jacko, S. M. Weyn-Vanhentenryck, J. W. Smerdon, R. Yan, H. Feng, D. J. Williams, J. Pai, K. Xu, H. Wichterle, C. Zhang, "Rbfox splicing factors promote neuronal maturation and axon initial segment assembly,"[Link]
Neuron, 97, 853-868, 2018.



2017


C. L. Hueschen, S. J. Kenny, K. Xu, S. Dumont, "NuMA recruits dynein activity to microtubule minus-ends at mitosis," [Link]
eLife, 6, e29328, 2017.

S. Moon||, R. Yan||, S. J. Kenny, Y. Shyu, L. Xiang, W. Li, K. Xu, "Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes," [Link]
J. Am. Chem. Soc., 139, 10944-10947, 2017.

D. Kim, Z. Zhang, K. Xu, "Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules, "[Link]
J. Am. Chem. Soc., 139, 9447-9450, 2017.

P. G. Cao||, P. Bai||, A. A. Omrani||, Y. Xiao, K. L. Meaker, H.-Z. Tsai, A. Yan, H. S. Jung, R. Khajeh, G. F. Rodgers, Y. Kim, A. S. Aikawa, M. A. Kolaczkowski, Y. Liu, A. Zettl, K. Xu, M. F. Crommie, T. Xu, "Preventing thin film dewetting via graphene capping, "[Link]
Adv. Mater., 29, 1701536, 2017. (Frontispiece)

L. Ge, M. Zhang, S. J. Kenny, D. Liu, M. Maeda, K. Saito, A. Mathur, K. Xu, R. Schekman, "Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis, "[Link]
EMBO Rep., 18, 1586-1603, 2017.

T. Heydari, M. Heidari, O. Mashinchian, M. Wojcik, K. Xu, M. J. Dalby, M. Mahmoudi, M. R. Ejtehadi, "Development of a virtual cell model to predict cell response to substrate topography, "[Link]
ACS Nano, 11, 9084-9092, 2017.

S. Köhler||, M. Wojcik||, K. Xu, A. F. Dernburg, "Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue, "[Link]
Proc. Natl. Acad. Sci. U.S.A., 114, E4734-E4743, 2017.

A. Gorur, L. Yuan, S. J. Kenny, S. Baba, K. Xu, R. Schekman, "COPII-coated membranes function as transport carriers of intracellular procollagen-I," [Link]
J. Cell Biol., 216, 1745-1759, 2017.

M. Wojcik||, Y. Li||, W. Li, K. Xu, "Spatially resolved in situ reaction dynamics of graphene via optical microscopy,"[Link]
J. Am. Chem. Soc., 139, 5836-5841, 2017.

A. N. Killilea, R. Csencsits, E. Le, A. M. Patel, S. J. Kenny, K. Xu, K. H. Downing, "Cytoskeletal organization in microtentacles," [Link]
Exp. Cell Res., 357, 291-298, 2017.

M. Hauser||, M. Wojcik||, D. Kim||, M. Mahmoudi, W. Li, K. Xu, "Correlative super-resolution microscopy: new dimensions and new opportunities," [Invited review] [Link]
Chem. Rev., 117, 7428-7456, 2017.



2016


D. M. Jorgens||, J. L. Inman||, M. Wojcik||, C.Robertson||, H. Palsdottir, W. T. Tsai, H. Huang, A. Bruni-Cardoso, C. S. Lopez, M. J. Bissell, K. Xu, M. Auer, "Deep nuclear invaginations linked to cytoskeletal filaments: Integrated bioimaging of epithelial cells in 3D culture,"[Link]
J Cell Sci., 130, 177-189 (Cover Article), doi: 10.1242/jcs.190967, 2016

W. Li||, S. Moon||, M. Wojcik||, K. Xu, "Direct optical visualization of graphene and its nanoscale defects on transparent substrates,"[Link]
Nano Letters, 16, 5027-5031, 2016.
Featured in Physics Today: "Graphene visualized," Physics Today 70(4), 72, 2017, [Link]



2015


M. Zhang, S. J. Kenny, L. Ge, K. Xu, R. Schekman, "Translocation of interleukin-1β into a vesicle intermediate in autophagy-mediated secretion,"[Link]
eLife, 4, e11205, 2015.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, K. Xu, "Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy," [Link]
Nature Methods, 12, 935-938, 2015
Featured in Nature Methods: "Methods to Watch," Nature Methods, 13, 35, 2016. [Link]

M. Wojcik||, M. Hauser||, W. Li, S. Moon, K. Xu, "Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cells," [Link]
Nature Commun., 6, 7384, 2015
Highlighted in Nature: "Microscopy: Graphene protects cells for imaging," Nature, 522, 394-395, 2015. [Link]

K. Xu, J. R. Heath, "Contact with what?" [News & Views] [Link]
Nature Mater., 12, 872-873, 2013



Previous work


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," [Link]
Mol. Cell Neurosci., 61, 241-254, 2014

K. Xu, G. Zhong, and X. Zhuang, "Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons" [Link]
Science, 339, 452-456, 2013

K. Xu, S.-H. Shim, and X. Zhuang, "Super-resolution imaging through stochastic switching and localization of single molecules: an overview" [Link]
Far-Field Optical Nanoscopy (Springer Series on Fluorescence), P. Tinnefeld et al., Eds. Berlin: Springer, pp. 27-64, 2013

K. Xu, H.P. Babcock, and X. Zhuang, "Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton" [Link]
Nature Methods, 9, 185-188, 2012

P. G. Cao, J. O. Varghese, K. Xu, and J. R. Heath, "Visualizing local doping effects of individual water clusters on gold(111)-supported graphene,"
Nano Letters, 12, 1459-1463, 2012

P. G. Cao, K. Xu, J. O. Varghese, and J. R. Heath, "The microscopic structure of adsorbed water on hydrophobic surfaces under ambient conditions"
Nano Letters, 11, 5581-5586, 2011

P. G. Cao, K. Xu, J. O. Varghese, and J. R. Heath, "Atomic force microscopy characterization of room-temperature adlayers of small organic molecules through graphene templating,"
J. Am. Chem. Soc., 133, 2334-2337, 2011

K. Xu, P. G. Cao, and J.R. Heath, "Graphene visualizes the first water adlayers on mica at ambient conditions"
Science, 329, 1188-1191, 2010

K. Xu, P. G. Cao, and J. R. Heath, "Achieving the theoretical depairing current limit in superconducting nanomesh films"
Nano Letters, 10, 4206-4210, 2010

K. Xu, P. G. Cao, and J. R. Heath, "The crossover from two dimensions to one dimension in granular electronic materials"
Nature Nanotechnology, 4, 368-372, 2009

K. Xu, P. G. Cao, and J. R. Heath, "Scanning tunneling microscopy characterization of the electrical properties of wrinkles in exfoliated graphene monolayers"
Nano Letters, 9, 4446-4451, 2009

K. Xu, J.R. Heath, "Long, highly-ordered high-temperature superconductor nanowire arrays"
Nano Letters, 8, 3845-3849, 2008

K. Xu, P. G. Cao, and J. R. Heath, "Controlled fabrication and electrical properties of long quasi-one-dimensional superconducting nanowire arrays"
Nano Letters, 8, 136-141, 2008

P. G. Cao, K. Xu, and J. R. Heath, "Azidation of silicon(111) surfaces,"
J. Am. Chem. Soc., 130, 14910-14911, 2008

K. Xu, J. E. Green, J. R. Heath, F. Remacle, and R. D. Levine, "The emergence of a coupled quantum dot array in a doped silicon nanowire gated by ultrahigh density top gate electrodes"
J. Phys. Chem. C, 111, 17852-17860, 2007

J. E. Green, J. W. Choi, A. Boukai, Y. Bunimovich, E. Johnston-Halperin, E. Delonno, Y. Luo, B. A. Sheriff, K. Xu, Y. S. Shin, H. R. Tseng, J. F. Stoddart, and J. R. Heath, "A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre,"
Nature, 445, 414-417, 2007

A. Boukai, K. Xu, and J. R. Heath, "Size-dependent transport and thermoelectric properties of individual polycrystalline bismuth nanowires,"
Advanced Materials, 18, 864-869, 2006

J. W. Choi, A. H. Flood, D. W. Steuerman, S. Nygaard, A. B. Braunschweig, N. N. P. Moonen, B. W. Laursen, Y. Luo, E. DeIonno, A. J. Peters, J. O. Jeppesen, K. Xu, J. F. Stoddart, and J. R. Heath, "Ground-state equilibrium thermodynamics and switching kinetics of bistable [2]rotaxanes switched in solution, polymer gels, and molecular electronic devices,"
Chemistry - A European Journal, 12, 261-279, 2006

Z. Y. Zhang, K. Xu, W. R. G. Baeyens, and X. R. Zhang, "An energy-transfer cataluminescence reaction on nanosized catalysts and its application to chemical sensors,"
Analytica Chimica Acta, 535, 145-152, 2005

Z. Y. Zhang, K. Xu, Z. Xing, and X. R. Zhang, "A nanosized Y2O3-based catalytic chemiluminescent sensor for trimethylamine,"
Talanta, 65, 913-917, 2005