Photo of Gao, Ruixuan

Ruixuan Gao

Assistant Professor, starting 2021



Living organisms are composed of structures spanning orders of magnitude in size, and are assembled from tens of thousands of, if not more, distinct molecular entities. Our group’s research centers on the molecular nature of biological structures and processes. We explore how basic molecular building blocks—such as proteins, lipids, and RNAs—assemble and interact with one another to achieve specific biological functions, or instead cause dysfunctions.

We develop chemical, physical, and biomolecular tools that map and track these molecular building blocks at their natural length scale and temporal resolution. Basing our approach on chemical synthesis and molecular biology, we apply state-of-the-art methods in light/electron microscopy, bioengineering, and computational sciences to a range of biological questions at the molecular scale.

Molecular Constituents and Chemical Compositions of Living Organisms

Biological structures in living organisms span multiple orders of magnitude in size—ranging from nanometers to centimeters. We use chemical and material tools to study the molecular components and chemical compositions of these structures. Specifically, we leverage rational design and synthesis of macromolecular matrices, supramolecular assemblies, and chemical linkers/probes to selectively target, preserve, and visualize molecular entities in cells and tissues. Additionally, we develop (bio)chemical probes to map and track chemical compositions and dynamics of such systems.

Microscopy and Bioimaging

Observing dynamic biological processes at the molecular scale requires an imaging modality that track thousands of molecular targets or more at nanoscopic spatial resolution and sub-millisecond temporal resolution. Currently, no microscopy methods fulfill these criteria simultaneously. We develop fluorescence microscopy methods that overcome such limitations, including super-resolution microscopy, light-sheet microscopy, and adaptive optics.

Structure, Function, and Pathology

We aim to elucidate structures and processes central to biology and human health. Our group is interested in, for example, functions and dysfunctions of nervous systems. In particular, we study ultrastructure of the synapse and synaptic transmission, long-range neuronal connection, and distribution and pathology of misfolded proteins in neurodegenerative brains. We also apply proteomics and transcriptomics approach to map endogenous and exogenous molecular markers in, for example, cancerous and clinical specimens.

Selected Publications

10. R. Gao*, C.-C. Yu*, L. Gao*, K.D. Piatkevich, Y.-Y. Chou, S. Upadhyayula, E.S. Boyden, “A highly homogeneous expansion microscopy polymer composed of tetrahedron-like monomers,” bioRxiv 814111 (2019). [Link]

9. O.A. Shemesh*, C.-Y. Linghu*, K.D. Piatkevich*, D. Goodwin, O.T. Celiker, H.J. Gritton, M.F. Romano, R. Gao, C.-C. Yu, H.-A. Tseng, S. Bensussen, S. Narayan, C.-T. Yang, L. Freifeld, C. Siciliano, I. Gupta, J. Wang, N. Pak, Y.-G. Yoon, J.F.P. Ullmann, B. Guner-Ataman, H. Noamany, Z.R. Sheinkopf, W.-M. Park, S. Asano, A.E. Keating, J.S. Trimmer, J. Reimer, A. Tolias, M.F. Bear, K.M. Tye, X. Han, M.B. Ahrens, E.S. Boyden, “Precision calcium imaging of dense neural populations via a cell-body-targeted calcium indicator,” Neuron, 107, 1-17 (2020). [Link]

8. 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.G. Megason, 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 363, eaau8302 (2019). [Link] [Cover]

7. D. Oran*, S.G. Rodriques*, R. Gao, S.M. Asano, M.A. Skylar-Scott, F. Chen, P.W. Tillberg, A.H., Marblestone†, E.S. Boyden†, “3-D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds,” Science 362, 1281-1285 (2018). [Link]

6. S.M. Asano*, R. Gao*, A.T. Wassie*, P.W. Tillberg, F. Chen, E.S. Boyden, “Expansion microscopy: Protocols for imaging proteins and RNA in cells and tissues,” Curr. Protoc. Cell Biol., 80, e56 (2018). [Link]

5. B. Migliori*, M.S. Datta*, C. Dupre, M.C. Apak, S. Asano, R. Gao, E.S. Boyden, O. Hermanson, R. Yuste, R. Tomer, “Light sheet theta microscopy for rapid high-resolution imaging of large biological samples,” BMC Biology 16, 57 (2018). [Link]

4. L. Freifeld, I. Odstrcil, D. Forster, A. Ramires, J.A. Gagnon, O. Randlett, E. Costa, S.M. Asano, O. Celiker, R. Gao, D.A. Martin-Alarcon, P. Reginato, C. Dick, L. Chen, D.E. Schoppik, F. Engert, H. Baier, E.S. Boyden, “Expansion microscopy of zebrafish for neuroscience and developmental biology studies,” PNAS, E10799–E10808 (2017). [Link]

3. R. Gao*, S.M. Asano*, E.S. Boyden, “Q&A: Expansion microscopy”, BMC Biology 15, 50 (2017). [Link]

2. R. Gao*, I. Gupta*, E.S. Boyden, “Sonofragmentation of ultrathin 1D nanomaterials”, Part. Part. Syst. Charact. 34, 1600339 (2017). [Link]

1. R. Gao, S. Strehle, B. Tian, T. Cohen-Karni, P. Xie, X. Duan, Q. Qing, C.M. Lieber, “Outside looking in: Nanotube transistor intracellular sensors,” Nano Lett. 12, 3329-3333 (2012). [Link]


Postdoctoral Associate, MIT / HHMI Janelia Research Campus, 2015-2020
Ph.D., Harvard University, 2015
B.S., UC Berkeley, 2009