2024
Xu, C.; Liu, Y,; Arus, B. A.; Mishra, K.; Luciano, M. P. Bandi, V. G.; Kumar, A.; Manton, J.; Guo, Z.; Bick, M. J.; Xu, M.; Zhang, K.; Kang, A.; De La Cruz, J.; Brackenbrough, E.; Gerben, S. R.; Bera, A. K.; Vaughan, J. C.; Derivery, E.; Schnermann, M. J.; Stiel, A. C.; Bruns, O. T.; Baker, D. “De novo design of near infrared fluorescent proteins,” Nature Chemistry (In Review). [link]
Guo, Z.; Poudel, C.; Sarfatis, M. C.; Yu, J.; Wong, M.; Chui, D. T.*; Vaughan, J. C.* “Highly multiplexed fluorescence microscopy with spectrally tunable semiconducting polymer dots,” Science Advances (In Press). [link] [bioRxiv]
Bishop, K. W.; Erion Barner, L. A.; Baraznenok, E.; Lan, L.; Poudel, C.; Brenes, D.; Serafin, R. B.; True, L. D.; Vaughan, J. C.; Glaser, A. K.; Liu, J. T. C. “Axially swept open-top light-sheet microscopy for densely labeled clinical specimens,” Optics Letters, 13, 2794-2797 (2024). [link]
Bishop, K. W.; Erion Barner, L.A.; Han, Q.; Baraznenok, E.; Lan, L.; Poudel, C.; Gao, G.; Serafin, R.B.; Chow, S. S. L.; Glaser, A. K.; Janowzczyk, A.; Brenes, D. R.; True, L. D.; Kang, S.; Vaughan, J. C.; Liu, J. T. C. “An end-to-end workflow for non-destructive 3D pathology,” Nature Protocols, 19, 1122-1148 (2024). [link]
2023
Jung, S. R.; Kim, J.; Vojtech, L.; Vaughan, J. C.; Chui, D. T. “Error-correction method for high-throughput sizing of nanoscale vesicles with single-molecule localization microscopy,” J. Phys. Chem. B, 127 (12), 2701-2707 (2023). [link]
Liu, J. T. C.; Glaser, A. K.; Poudel, C.; Vaughan, J. C. “Nondestructive 3D pathology with light-sheet fluorescence microscopy for translational research and clinical assays,” Annu. Rev. Anal. Chem., 16, 231-252 (2023). [link]
N. Kaverina, R.A. Schweickart, G.C. Chan, J.C. Maggiore, D.G. Eng, Y. Zeng, S.R. McKinzie, H.S. Perry, A. Ali, C. O’Connor, B.M.V. Pereira, A.B. Theberge, J.C. Vaughan, C.J. Loretz, A. Chang, N.A. Hukriede, M. Bitzer, J.W. Pippin, O. Wessely, S.J. Shankland, “Inhibiting NLRP3 signaling in aging podocytes improves their life- and health-span,” Aging, 15, (2023). [link]
2022
J.W. Pippin, N. Kaverina, Y. Wang, D.G. Eng, Y. Zeng, U. Tran, C.J. Loretz, A. Cheng, S. Akilesh, C. Poudel, H.S. Perry, C. O’Connor, J.C. Vaughan, M. Bitzer, O. Wessely*, S.J. Shankland*, “Upregulated PD-1 signaling antagonizes glomerular health in aged kidneys and disease,” J. Clin. Invest. 132, (16), 155931 (2022). [link] * indicates co-corresponding authors.
L.A. Barner, A.K. Glaser, C. Mao, E.A. Susaki, J.C. Vaughan, S.M. Dintzis, J.T. C. Liu, “Multi-resolution non-destructive 3D pathology of whole lymph nodes for breast cancer staging,” J. Biomed. Opt. 27, (3), 036501 (2022). [link]
M.Y. Lee*, C. Mao*, A.K. Glaser, M.A. Woodworth, A.R. Halpern, A. Ali, J.T.C. Liu, J.C. Vaughan “Fluorescent Labeling of Abundant Reactive Entities (FLARE) for Cleared-Tissue and Super-Resolution Microscopy” Nat. Protoc. 17, 819-846 (2022). [link] [cover] * indicates equal contributions.
A.R. Halpern*, M.Y. Lee, M.D. Howard, M.A. Woodworth, P.R. Nicovich, and J.C. Vaughan*, “Versatile, do-it-yourself, low-cost spinning disk confocal microscope,” Biomed. Opt. Express 13, 1102-1120 (2022). [link] [bioRxiv]. * indicates co-corresponding authors. Article selected as an “Editors’ Pick”.
W. Xie, N.P. Reder, C. Koyuncu, P. Leo, S. Hawley, H. Huang, C. Mao, N. Postupna, S. Kang, R. Serafin, G. Gao, Q. Han, K. Bishop, L. Barner, C.D. Keene, J.C. Vaughan, A. Janowczyk, A.K. Glaser, A. Madabhushi, L.D. True, J.T.C. Liu “Prostate cancer risk stratification via non-destructive 3D pathology with deep learning-assisted gland analysis” Cancer Res. 82, 334-345 (2022). [link]
W.R. Hardin, G.C. Alas, N. Taparia, E.B. Thomas, M. Steele-Ogus, K.L. Hvorecny, A.R. Halpern, P. Tůmová, J.M. Kollman, J.C. Vaughan, N.J. Sniadecki, A.R. Paredez “The Giardia lamellipodium-like ventrolateral flange supports attachment and rapid cytokinesis,” PLoS Pathog. 18, e1010496 (2022). [link] [bioRxiv]
2021
M. Rahmati, S. Stötzel, T. El Khassawna, C. Mao, A. Ali, J.C. Vaughan, K. Iskhahova, D.C. Wieland, A. Gonzalez Cantalapiedra, G. Perale, F. Betge, E.P. Dillon, S. Lyngstadaas, H. Haugen “Intrinsically disordered peptides enhance regenerative capacities of bone composite xenografts” Materials Today (2021, online). [link]
S. Shankland, Y. Wang, A. Shaw, J.C. Vaughan, J. Pippin, and O. Wessely, “Podocyte Aging: Why and How Getting Old Matters,” J. Am. Soc. Nephrol. 32, 2697-2713 (2021). [link]
M.A. Woodworth, K.K.H. Ng, A.R. Halpern, N.A. Pease, P.H.B. Nguyen, H.Y. Kueh,* and J.C. Vaughan* “Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy.” Nucleic Acids Res. 49, e82 (2021). [link] [bioRxiv] [protocols.io] * indicates co-corresponding authors.
N.A. Pease, P.H.B. Nguyen, M.A. Woodworth, K.K.H. Ng, B. Irwin, J.C. Vaughan, H.Y. Kueh “Tunable, division-independent control of gene activation timing by a polycomb switch.” Cell Reports 34, 108888 (2021). [link] [supp]
J.C. Klima, L.D. Doyle, J.H. Lee., M. Rappleye, L.A. Gagnon, M.Y. Lee, E.P. Barros, A.A. Vorobieva, J. Dou, S. Bremner, J.S. Quon, C.M. Chow, L. Carter, D.L. Mack, R.E. Amaro, J.C. Vaughan, A. Berndt, B.L. Stoddard, D. Baker, D. “mFAPs: A Versatile Platform for New Fluorescent Protein Sensor Engineering.” Nat. Comm. 12, 856-875 (2021). [link] [supp]
2020
C. Mao, M.Y. Lee, J.-R. Jhan, A.R. Halpern, M.A. Woodworth, A.K. Glaser, T.J. Chozinski, L. Shin, J.W. Pippin, S.J. Shankland, J.T.C. Liu, J.C. Vaughan “Feature-rich covalent stains for super-resolution and cleared tissue fluorescence microscopy.” Sci. Adv. 6, eaba4542 (2020). [link] [supp] [movie]
2019
A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, P. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C. Stoltzfus, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, J.T.C. Liu “Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues.” Nat. Commun. 10, 2781 (2019). [link] [supp]
N.V. Kaverina, D.G. Eng, B.S. Freedman, N.J. Kutz, T.J. Chozinski, J.C. Vaughan, J.H. Miner, J.W. Pippin, S.J. Shankland “Dual Lineage Tracing Shows That Glomerular Parietal Epithelial Cells Can Transdifferentiate Towards The Adult Podocyte Fate” Kidney Int. 96, 597–611 (2019).[link] [supp. meth.]
N. Jiang, J.P. Rasmussen, J.A. Clanton, M.F. Rosenberg, K. Luedke, M.R. Cronan, E. Parker, H.-J. Kim, J.C. Vaughan, A. Sagasti, J.Z. Parrish “A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites.” eLife 8, e42455 (2019). [link]
Y. Chen, W. Xie, A.K. Glaser, N.P. Reder, C. Mao, S.M. Dintzis, J.C. Vaughan, J.T.C. Liu “Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy.” Biomed. Opt. Exp. 10, 1257-1271 (2019). [link]
W. Xie, Y. Chen, Y. Wang, M.E. Fauver, E.J. Seibel, J.C. Vaughan, N.P. Reder, J.T.C. Liu “Microscopy with ultraviolet surface excitation (MUSE) for comprehensive pathology of breast surgical margins.” J. Biomed. Opt. 24, 026501 (2019). [link]
2018
C. Yan, F. Wang, Y. Peng, C.R. Williams, B. Jenkins, J. Wildonger, H.-J. Kim, J.B. Perr, J.C. Vaughan, M.E. Kern, M.R. Falvo, E.T. O’Brien III, R. Superfine, J.C. Tuthill, Y. Xiang, S.L. Rogers, J.Z. Parrish, “Microtubule Acetylation is Required for Mechanosensation in Drosophila.” Cell Reports, 25, 1051-1065 (2018). [link] [supp]
H. Li, J.C. Vaughan, “Switchable Fluorophores for Single-Molecule Localization Microscopy.” Chem. Rev., 118, 9412-9454 (2018). [link] [supp]
J. Dou, A.A. Vorobieva, W. Sheffler, L.A. Doyle, H. Park, M.J. Bick, B. Mao, G.W. Foight, M.Y. Lee, L.A. Gagnon, L. Carter, B. Sankaran, S. Ovchinnikov, E. Marcos, P. Huang, J.C. Vaughan, B.L. Stoddard, D. Baker, “De novo design of a fluorescence-activating beta barrel.” Nature (2018, online).
T.J. Chozinski, C. Mao, A.R. Halpern, J.W. Pippin, S.J. Shankland, C.E. Alpers, B. Najafian, J.C. Vaughan, “Volumetric, Nanoscale Optical Imaging of Mouse and Human Kidney via Expansion Microscopy.” Sci. Rep. 8 (1), No. 10396 (2018). [link] [supp] [movie1] [movie2]
N. Jiang, H.-J. Kim, T.J. Chozinski,J.E. Azpurua, B.E. Eaton, J.C. Vaughan*, J.Z. Parrish*, “Super-resolution imaging of Drosophila tissues using expansion microscopy,” Mol. Biol. Cell 29, 1413-1421 (2018). [link] [supp] [cover] * indicates co-corresponding authors.
R. Hao*, Y. Fan*, M.D. Howard, J.C. Vaughan, B. Zhang “Single-Molecule Fluorescence Labeling Allows Real-Time Imaging of Nanobubble Nucleation and Hydrogen Spillover,” Proc. Natl. Acad. Sci. USA, 115, 5878-5883, (2018). * indicates equal contributions. [link] [supp]
D. Lin*, L.A. Gagnon*, M.D. Howard, A.R. Halpern, J.C. Vaughan, “Extended depth 3D super-resolution imaging using probe refresh STORM (prSTORM),” Biophys. J., 114, 1980-1987 (2018). * indicates equal contributions. [link]
2017
A.R. Halpern, G.C.M. Alas, T.J. Chozinski, A.R. Paredez*, J.C. Vaughan*, “Hybrid Structured Illumination Expansion Microscopy Reveals Microbial Cytoskeleton Organization,” ACS Nano, 11, 12677-12686 (2017). [link] [supp] [protocol] * indicates co-corresponding authors.
J. Decarreau, M. Wagenbach, E. Lynch, A.R. Halpern, J.C. Vaughan, J. Kollman, L. Wordeman, “A tetrameric kinesin, Ki25, suppresses pre-mitotic centrosome separation to establish proper spindle orientation,” Nat. Cell Biol., 19, 394-390 (2017). [link]
J. Lu, Y. Fan, M.D. Howard, J.C. Vaughan, and B. Zhang, “Single Molecule Electrochemistry on a Porous Silica-Coated Electrode,” J. Am. Chem. Soc., 139, 2964-2971 (2017). [link]
2015
A.R. Halpern, M.D. Howard, J.C. Vaughan, “’Point by Point’: An Introductory Guide to Sample Preparation for Single-Molecule Super-Resolution Fluorescence Microscopy,” Curr. Protoc. Chem. Biol. 7, 103-120 (2015). [link]
2014
T.J. Chozinksi*, L.A. Gagnon*, J.C. Vaughan, “Twinkle, Twinkle Little Star: Photoswitchable Fluorophores for Super-Resolution Imaging,” FEBS Lett, 588, 3603-3612 (2014). [link] * indicates equal contributions.
T. Shemesh, R.W. Klemm, F.B. Romano, S. Wang, J.C. Vaughan, X. Zhuang, H. Tukachinsky, M.M. Kozlov, T.A. Rapoport, “A model for the generation and interconversion of ER morphologies,” Proc Natl Acad Sci USA, 111, E5243-5251 (2014). * indicates equal contributions. [link] [supp]
S. Jia, J.C. Vaughan, X. Zhuang, “Super-Resolution Imaging With a Self-Bending Point Spread Function,” Nat Photonics, 8, 302-306 (2014). [link] [supp]
Before 2014
J.C. Vaughan, G.T. Dempsey, E. Sun, X. Zhuang, “Phosphine quenching of cyanine dyes as a versatile tool for fluorescence microscopy,” J Am Chem Soc, 135, 1197-2000 (2013). * indicates equal contributions. [link] [supp]
S.-H. Shim, C. Xia, G. Zhong, H. Babcock, J.C. Vaughan, B. Huang, X. Wang, C. Xu, G.-Q. Bi, X. Zhuang, “Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes,” Proc Natl Acad Sci USA, 109, 13978-13983 (2012). [link] [supp]
J.C. Vaughan, X. Zhuang, “New fluorescent probes for super-resolution imaging,” Nat Biotechnol, 29, 880-881 (2011). [link]
G.T. Dempsey*, J.C. Vaughan*, K.H. Chen*, W.M. Bates, X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat Methods, 8, 1027-1036 (2011). * indicates equal contributions. [link] [supp]
J.C. Vaughan*, B. Brandenburg*, J.M. Hogle, X. Zhuang, “Rapid actin-dependent viral motility in live cells,” Biophys J 97, 1647-1656, (2009). * indicates equal contributions. [link] [supp]
J.C. Vaughan, “Ultrafast pulse shaping” Ultrafast Optics, ed. Rick Trebino, (2008). [link] [book]
J.C. Vaughan, T. Hornung, K.A.W. Stone, K.A. Nelson, “Coherently controlled ultrafast four-wave mixing spectroscopy,” feature article, J Phys Chem A 23, 4873-4883 (2007). [link]
T. Feurer, N.S. Stoyanov, D.W. Ward, J.C. Vaughan, E. Statz, K.A. Nelson, “Terahertz Polaritonics,” Annu Rev Mat Res 37, 317-350 (2007). [link]
J.C. Vaughan, T. Feurer, K.W. Stone, K.A. Nelson, “Analysis of replica pulses in femtosecond pulse shaping,” Opt Express 14, 1314-1328 (2006). [link]
J.C. Vaughan, T. Hornung, T. Feurer, K.A. Nelson, “Diffraction-based femtosecond pulse shaping with a 2D SLM,” Opt Lett 30, 323-325 (2005). [link]
G. Popescu, L.P. Deflores, J.C. Vaughan, K. Badizadegan, H. Iwai, R.R. Dasari, M.S. Feld, “Fourier quantitative-phase microscopy for investigation of biological structure and dynamics,” Opt Lett 29, 2503-2505 (2004). [link]
T. Hornung, J.C. Vaughan, T. Feurer, K.A. Nelson “Degenerate four-wave mixing spectroscopy based on two-dimensional femtosecond pulse shaping,” Opt Lett 29, 2052-2054 (2004). [link]
T. Feurer, J.C. Vaughan, T. Hornung, K.A. Nelson, “Typesetting of terahertz waveforms,” Opt Lett 29, 1802-1804 (2004). [link]
J.C. Vaughan, T. Feurer, K.A. Nelson, “Automated spatiotemporal diffraction of ultrashort laser pulses,” Opt Lett 28, 2408-2410 (2003). [link]
T. Feurer, J.C. Vaughan, K.A. Nelson, “Spatiotemporal coherent control of lattice vibrational waves,” Science 299, 374-377 (2003). [link]
J.C. Vaughan, T. Feurer, K.A. Nelson, “Automated two-dimensional femtosecond pulse shaping,” J Opt Soc Am B 19, 2489-2495 (2002). [link]
T. Feurer, J.C. Vaughan, R.M. Koehl, K.A. Nelson, “Multidimensional control of femtosecond pulses using a programmable liquid crystal matrix,” Opt Lett 27, 652-654 (2002). [link]