Publications

Total Citations: 5646, H-index: 25 (as of December, 2023 from Google Scholar)

Papers

2018-Current (Group members are underlined)

• Cheng, C. Stefani, T. Skillman, A. Klimas, A. Lee, E. DiBernardo, K. Brown, T. Milman, Y. Wang, B. Gallagher, K. Lagree, B. Jena, J. Pulido, A. Mitchell, S. Filler, L. Hiller, A. Lacy-Hulbert, Y. Zhao*, “MicroMagnify: a multiplexed expansion microscopy method for pathogens and infected tissues“,Advanced Science, 2023, 2302249. [Editors’ choice]
• 
• [Cover Article] A. Klimas, B. Gallagher, P. Wijesekara, S. Fekir, E. F. DiBernardo, Z. Cheng, D. Stolz, F. Cambi, S. Watkins, S. L. Brody, A. Horani, A. L. Barth, C. Moore, X. Ren, Y. Zhao*, “Magnify is a universal molecular anchoring strategy for expansion microscopy”.Nature Biotechnology 41, pages858–869 (2023). Full text is available here.

• F. Han, S. Gu, A. Klimas, N. Zhao, Y. Zhao* (co-corresponding), S-C, Chen*, “Three-dimensional nanofabrication via ultrafast laser patterning and kinetically regulated material assembly”, Science, 2022, 378, 6626, full text available here.
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• L. Shi, A. Klimas, B. Gallagher, Z. Cheng, F. Fu, P. Wijesekara, Y. Miao, X. Ren, Y Zhao* (co-corresponding author), W Min*, “Super-resolution vibrational imaging using expansion stimulated Raman scattering microscopy”, Advanced Science,2022, 2200315.
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• A. Abdelfattah, S. Ahuja, T. Akkin, S.R. Allu, D.A. Boas, J. Brake, E.M. Buckley, …, Y. Zhao, “Neurophotonic tools for microscopic measurements and manipulation: status report”,Neurophotonics 9 (S1), 013001
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• B. Gallagher, Y. Zhao*, ‘Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists’, Neurobiology of Disease, 2021. DOI: 10.1016/j.nbd.2021.105362
• A. Klimas, Y. Zhao*, ‘Expansion Microscopy: Toward Nanoscale Imaging of a Diverse Range of Biomolecules’, ACS Nano, 2020, 14, 7, 7689–7695, DOI: 10.1021/acsnano.0c04374

• O. Bucur, F. Fu, M. Calderon, G. H. Mylvaganam, N. L. Ly, J. Day, S. Watkin, B. D. Walker, E. S. Boyden*, Y. Zhao*, ‘Expansion Pathology: Conventional and Rapid Protocols for Nanoscale Imaging of Clinical Specimens’, Nature Protocol, 2020, 4, https://doi.org/10.1038/s41596-020-0300-1.

• B. Gallagher, Y. Zhao*, Nanoscale Imaging of Synaptic Connections with Expansion Microscopy, Discoveries, 2019, 7, e101 [Cover paper]
• S. Cheng, Y. Zhao*, Nanoscale imaging of E. coli cells by expansion microscopy, Discoveries, 2019,7, e98 [Cover paper]
• A. Klimas, B. Gallagher, Y Zhao*, Basics of Expansion Microscopy, Current Protocols in Cytometry, 2019, 91 (1), e67
• A. Klimas, O. Bucur, B. Njeri, Y. Zhao*, Nanoscopic Imaging of Human Tissue Sections via Physical and Isotropic Expansion. J. Vis. Exp. 2019, e60195.
• Y. Zhao, W. Zhang, Y. Zhao, R.E. Campbell, D.J. Harrison, ‘A single-phase flow microfluidic cell sorter for multiparameter screening to assist the directed evolution of Ca2+ sensors’, Lab on a Chip, 19 (22), 3880-3887
• Y. Adam, J. J. Kim, S. Lou, Y. Zhao, M. E. Xie, D. Brinks, H. Wu, M. A. Mostajo-Radji, S. Kheifets, V. Parot, S. Chettih, K. J. Williams, B. Gmeiner, S. L. Farhi, L. Madisen, E. K. Buchanan, I. Kinsella, D. Zhou, L. Paninski, C. D. Harvey, H. Zeng, P. Arlotta, R. E. Campbell, A. E. Cohen. ‘Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics’, Nature, 2019, 569, 413–417
• R. Gao, S. M. Asano, S. Upadhyayula, I. Pisarev, D. E. Milkie, T. L. Liu, V. Singh, A. Graves, G. H Huynh, Y. Zhao, J. Bogovic, J. Colonell, C. M Ott, C. Zugates, S. Tappan, A. Rodriguez, K. R Mosaliganti, S.-H. Sheu, H A. Pasolli, S. Pang, C S. Xu, S. G Megason, H. Hess, J. Lippincott-Schwartz, A. Hantman, G. M Rubin, T. Kirchhausen, S. Saalfeld, Y. Aso, E. S. Boyden, E. Betzig, ‘Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution’, Science, 2019, 363 (6424), eaau8302
• A. T. Wassie (co-first), Y. Zhao (co-first), E.S. Boyden*, ‘Expansion microscopy: principles and uses in biological research‘, Nature Methods 2019, 16, p. 33–41

• O. Bucur*, Y. Zhao*, ‘Nanoscale Imaging of Kidney Glomeruli Using Expansion Pathology.‘ Frontiers in Medicine, 2018, https://doi.org/10.3389/fmed.2018.00322

Prior to 2018

• Y. Zhao (equal contribution), O. Bucur (equal contribution), H. Irshad, F. Chen, A. Weins, A. L. Stancu, E-Y. Oh, M. DiStasio, V. Torous, B. Glass, I. E. Stillman, S. J. Schnitt, A. H. Beck*, E. S. Boyden*, ‘Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.’ Nature Biotechnology, 2017, 35 (8), 757–764. [See also MIT News and BIDMC News]

 

• P. W. Tillberg, F. Chen, K.D. Piatkevich, Y. Zhao, C.-C. Yu, B. P. English, L. Gao, A. Martorell, H.-J. Suk, F. Yoshida, E. M. DeGennaro, D. H.Roossien, G.. Gong, U. Seneviratne, S. R. Tannenbaum, R. Desimone, D. Cai, E. S. Boyden*, ‘Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies’, Nature Biotechnology, 2016, 34 (9), 987–992. [Cover article in September 2016 issue of Nature Biotechnology (volume 34, No. 9).]

• L. Tang, Y. Wang, W. Liu, Y. Zhao, R. E. Campbell, and C. Fang, ‘Illuminating Photochemistry of an Excitation Ratiometric Fluorescent Protein Calcium Biosensor’, The Journal of Physical Chemistry B, 2017, 121 (14), 3016–3023
• A. S. Abdelfattah, S. L. Farhi (equal contribution), Y. Zhao (equal contribution), D. Brinks, P. Zou, A. Ruangkittisaku, J. Platisa,V. A. Pieribone, K. Ballanyi, A. E. Cohen, and R. E. Campbell* , ‘A bright and fast red fluorescent protein voltage indicator that reports neuronal activity in organotypic brain slices’, The Journal of Neuroscience, 2016 , 36 (8): 2458-2472
• F. Hatahet, J. L Blazyk, E. Martineau, E. Mandela, Y. Zhao, R. E Campbell, J. Beckwith, D. Boyd*, ‘Altered Escherichia coli membrane protein assembly machinery allows proper membrane assembly of eukaryotic protein vitamin K epoxide reductase’, Proceedings of the National Academy of Sciences, 2015, 112 (49): 15184-15189
• L. Tang, W. Liu, Y. Wang, Y. Zhao, B. G. Oscar, R. E. Campbell, C. Fang*, ‘Unraveling ultrafast photoinduced proton transfer dynamics in a fluorescent protein biosensor for Ca²⁺ imaging’, Chemistry-A European Journal, 2015, 21 (17), 6481-6490
• T. Albrecht (equal contribution), Y. Zhao (equal contribution), T. Nguyen, R. E. Campbell* and J. D. Johnson*, ‘Fluorescent biosensors illuminate calcium levels within defined beta-cell endosome subpopulations’, Cell Calcium, 2015, 57 (4), 263-274
• Y. Wang , L. Tang , W. Liu , Y. Zhao , B. G. Oscar , R. E. Campbell, and C. Fang*, ‘Excited State Structural Events of a Dual-Emission Fluorescent Protein Biosensor for Ca²⁺ Imaging Studied by Femtosecond Stimulated Raman Spectroscopy’, The Journal of Physical Chemistry B, 2015, 119 (6), 2204–2218.
• D. R. Hochbaum (equal contribution), Y. Zhao (equal contribution), S. L. Farhi, N. Klapoetke, C. A. Werley, V. Kapoor, P. Zou, J. M. Krajl, D. Maclaurin, N. Smedemark-Margulies, J. Saulnier, G. L. Bouting, Y. Cho, M. Melkonian, G. K. Wong, D. J. Harrison, V. Murthy, B. Sabatini, E. S. Boyden (equal contribution), R. E. Campbell (equal contribution; *correspondence related to directed evolution), A. E. Cohen*, ‘All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins’, Nature Methods, 2014, 11, 825–833.

• P. Zou (equal contribution), Y. Zhao (equal contribution), A. Douglass, D. R. Hochbaum, R. E. Campbell (*correspondence related to directed evolution), A. E. Cohen*, ‘Bright and fast voltage reporters across the visible spectrum via electrochromic FRET (eFRET)’, Nature Communication, 5, Article number: 4625. [Highlighted by Nature Methods 2014, 11, 992]

• B. G. Oscar, W. Liu, Y. Zhao, L. Tang, Y. Wang, R. E. Campbell, and C. Fang, ‘Excited state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging’, Proceedings of the National Academy of Sciences, 2014, 111(28) 10191–10196.
• Y. Zhao, A. S. Abdelfattah, A. Ruangkittisakul, K. Ballanyi, R. E. Campbell* and D. J. Harrison*, ‘Microfluidic cell sorter-aided directed evolution of a protein-based calcium ion indicator with an inverted fluorescent response’, Integrative Biology, 2014, 6, 714-725

• A.S. Abdelfattah, J. Platisa, Y. Zhao, V.A. Pieribone, R.E. Campbell, ‘Development of a Red Genetically-Encoded Voltage Indicator and its use with Channelrhodopsin for All-Optical Electrophysiology’, Biophysical Journal, 2014, 106 (2), 629a-630a
• Y. Zhao, D. Hochbaum, D.J. Harrison, A.E. Cohen, R.E. Campbell, ‘A Comprehensive Live Cell Screening Approach for Developing Improved Microbial Rhodopsin-Based Voltage Biosensors’, Biophysical Journal, 2014, 106 (2), 415a
• Y. Zhao, H. Hoi, R. E. Campbell and D. J. Harrison*, ‘Microfluidic cell sorter aided directed evolution of an improved fluorescent protein-based calcium ion indicator’, Proceeding of the 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2013, 1006-1008.
• Zhao, H. Hoi, R. E. Campbell and D. J. Harrison, ‘Microfluidic cell sorter aided live cell screening for improved fluorescent protein’, Proceeding of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2012, 1120-1122.
• J. Wu, L. Liu, T. Matsuda, Y. Zhao, A. Rebane, M. Drobizhev, Y. Chang, S. Araki, Y. Arai, K. March, T. Hughes, K. Sagou, T. Miyata, T. Nagai, W. Li, and R. E. Campbell, ‘Improved Orange and Red Ca²⁺ Indicators and Photophysical Considerations for Optogenetic Applications’, ACS Chemical Neuroscience, 2013, 4 (6), 963-972
• C. Alford, J. Wu, Y. Zhao, R. E. Campbell, and T. Knöpfel, “Optogenetic Reporters”. Biology of the Cell, 2012, 105, 14–29
• P. Tewson, M. Westenberg, Y. Zhao, R. E. Campbell, A. M. Quinn, T. E. Hughes, “Simultaneous detection of Ca²⁺ and diacylglycerol signaling in living cells”. PLoS ONE, 2012, 7(8): e42791
• Y. Zhao, S. Araki, J. Wu, T. Teramoto, Y-F. Chang, M. Nakano, A. S. Abdelfattah, M. Fujiwara, T. Ishihara, T. Nagai, and R. E. Campbell, “An Expanded Palette of Genetically Encoded Ca²⁺ Indicators”. Science, 2011, 333, 1888-1891. [Highlighted by Science Express, also highlighted in the Science & Technology Concentrates section of Chemical & Engineering News. This paper has been selected in “2011: Signaling Breakthroughs of the Year”, Science Signaling, 3 January 2012: eg1.]

• L. Zhuang, W. Zhang, Y. Zhao, H. Shen, H. Lin and J. Liang, “Preparation and Characterization of Fe₃O₄ Particles with Novel Nanosheets Morphology and Magnetochromatic Property by a Modified Solvothermal Method”, Scientific Reports, 2015, 5, Article number: 9320
• L. Zhuang, W. Zhang, Y. Zhao, L. Da, W. Wu and H. Shen, ‘Temperature sensitive ferrofluid composed of Mn_1-xZn_xFe₂O₄ nanoparticles prepared by a modified hydrothermal process’, Powder technology 2012, 217, 46-49
• L. Zhuang, J. Liang, H. Shen and Y. Zhao, ‘Research progress in Colloidal Magnetic Photonic Crystal’, Material Review, 2011, 25, 70-74
• Y. Zhao, L. Zhuang, H. Shen, W. Zhang and Z. Shao, ‘Study of Polydiethyl Siloxane Based Ferrofluid with Excellent Frost Resistance Property’, Journal of Magnetism and Magnetic Materials, 2009, 321, 377-381

Book chapters

• Y. Zhao, R. E. Campbell, “Fluorescent Proteins for Neuronal Imaging”, New Techniques in Systems Neuroscience, 57-96