Carnegie Mellon University

Yongxin (Leon) Zhao

Associate Professor

202A Mellon Institute
Department of Biological Sciences

Carnegie Mellon University
4400 Fifth Avenue
Pittsburgh, PA 15213

Office: 412-268-8236
Lab: 412-268-1809


Lab website

Yongxin Zhao


Ph.D., University of Alberta
Postdoctoral Appointment, Massachusetts Institute of Technology


Our lab is an interdisciplinary research group that combines diverse bioengineering and chemical approaches to develop novel techniques for interrogation of biological and pathological processes in cells and tissues. Our long-term objective is to foster and develop new diagnostic and therapeutic approaches for complex diseases.

Tools for mapping structural and molecular properties of complex biological systems

Complex biological systems are delicate machines consist of building blocks (such as proteins, nucleic acids, lipids, and carbohydrates) that are precisely organized in the nanoscale. This presents a fundamental challenge for humanity to understand the biology and/or pathology underlying these complex systems. To gain the insight into physiological/pathological functions, one might need to map a large diversity of nanoscale building blocks, over a wide spatial scale. To tackle this challenge, we are developing a set of novel technologies that enable large scale visualization of biological samples with nanoscale precision, by physically expanding the sample rather than magnifying the light from the sample via lenses. This principle is called expansion microscopy (ExM). By combining various material engineering and chemical approaches, we are advancing ExM-based tools that may elucidate biological insights into the brain and other complex systems, such as cancer and infectious diseases.

Tools for probing dynamics of biological processes.

Biological systems are essentially 3D, highly-linked networks that sense, compute and respond to internal or external stimuli via widely distributed and diversified cells interacting over various timescales. To understand such complex biological systems, ideally, it would require observation of the activity of numerous populations of cells with a high degree of precision and resolution down to molecular building block. In this way, we can understand the functions and dynamics that are produced by the interactions between different cells as well as subcellular signaling events within individual cells.

In the Zhao Biophotonics lab, we are developing a spectrum of innovations to enable such analyses of dynamics of biological processes. Our tools will enable insight into how biological components work together to implement physiological functions, and how these interactions go awry in disease states. We also seek to harness our tools to assay disease biomarkers and indicators of drug effects. We will build upon our previous development of genetically encoded calcium ion indicators and voltage indicators to create probes for diverse signaling molecules, (e.g., neurotransmitters) and molecular events (e.g., protein-protein interactions).

Recent Publications

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 published 02 Jan. 2023.

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

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, 2022, 9 (S1), 013001 [Review]

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.

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

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,



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; DOI: 10.1038/nbt.3892 [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 Calcium2015, 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.

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

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