Publications
All Publications
29. W. Wang†, X. Ruan†, G. Liu†, D.E. Milkie, W. Li, E. Betzig, S. Upadhyayula*, R. Gao*, “Nanoscale volumetric fluorescence imaging via photochemical sectioning,” bioRxiv 2024.08.01.605857 (2024). [Link]
28. A. Orlowski, J. Karippaparambil, J.-M. Paumier, S. Ghanta, E. Pallares, J. Tandukar, R. Gao, S. Gowrishankar*, “Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer’s disease mouse model,” eNeuro 11, ENEURO.0445-24.2024 (2024). [Link] [bioRxiv]
27. Y.H. Chan, K.C. Pathmasiri, D. Pierre-Jacques, M.C. Hibbard, N. Tao, J.L. Fischer, E. Yang, S.M. Cologna, R. Gao*, “Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics,” Nat. Commun.15, 5036 (2024). [Link] [bioRxiv]
26. J. Sun, S. Song, I. Singaram, A. Sharma, W. Wang, Y. Hu, W.-T. Lo, P.A. Koch, J. J. Zhao, V. Haucke, R. Gao, W. Cho*, “PI(3,5)P2 Controls the Signaling Activity of Class I PI3K,” bioRxiv 2023.01.25.525550 (2023). [Link]
25. J.W. Kim, A.J.H. Yong, E.E. Aisenberg, J.H. Lobel, W. Wang, T.M. Dawson, V.L. Dawson, R. Gao, Y.N. Jan, H.S. Bateup, N.T. Ingolia*, “Molecular recording of calcium signals via calcium-dependent proximity labeling,” Nat. Chem. Biol. 20, 894-905 (2024). [Link] [bioRxiv]
26. M. A. Churgin, D.O. Lavrentovich, M.A. Smith, R. Gao, E.S. Boyden, B. de Bivort*, “A neural correlate of individual odor preference in Drosophila,” eLife 12, RP90511 (2023). [Link] [bioRxiv]
23. X. Pan, Z.H. Coban Akdemir, R. Gao, X. Jiang, G.M. Sheynkman, E. Wu*, J.H. Huang*, N. Sahni*, S. S. Yi*, “AD-Syn-Net: Systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning,” Brief. Bioinform. 24, bbad030 (2023). [Link]
22. J. Lillvis*, H. Otsuna, X. Ding, I. Pisarev, T. Kawase, J. Colonell, K. Rokicki, C. Goina, R. Gao, A. Hu, K. Wang, J. Bogovic., D.E., Milkie, L. Meienberg, E.S. Boyden, S. Saalfeld, P.W. Tillberg, B.J. Dickson*, “Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy,” eLife 11, e81248 (2022). [Link] [bioRxiv]
21. W. Wang†, Y.H. Chan†, S.Y. Kwon, J. Tandukar, R. Gao*, “Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion,” Nano Converg. 9, 30 (2022). [Link]
20. J.-B. Chang, R. Gao, F. Chen, “Chapter 21 - Light-Sheet Fluorescence Microscopy for Multiscale Biological Imaging,” in Molecular Imaging Principles and Practice, 2nd ed. (eds. B. D. Ross & S. S. Gambhir) 373-382 (Academic Press, 2021). [Link]
Before UIC
19. R. Gao†, C.-C. Yu†, L. Gao, K.D. Piatkevich, R.L. Neve, J.B. Munro, S. Upadhyayula, E.S. Boyden*, “A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy,” Nat. Nanotechnol. 16, 698-707 (2021). [Link] [bioRxiv]
18. 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] [bioRxiv]
17. C. Zhang†, J.S. Kang†, S.M. Asano, R. Gao, E.S. Boyden*, “Expansion microscopy for beginners: Visualizing microtubules in expanded cultured HeLa cells,” Curr. Protoc. Neurosci., 92, e96 (2020). [Link]
16. 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] [bioRxiv]
15. 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]
14. 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]
13. 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]
12. 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]
11. R. Gao†, S.M. Asano†, E.S. Boyden*, “Q&A: Expansion microscopy”, BMC Biology 15, 50 (2017). [Link]
10. T. Ozel, B. Zhang, R. Gao, R.W. Day, C.M. Lieber*, D.G. Nocera*, “Electrochemical deposition of conformal and functional layers on high aspect ratio silicon micro/nanowires”, Nano Lett. 17, 4502-4507 (2017). [Link]
9. R. Gao†, I. Gupta†, E.S. Boyden*, “Sonofragmentation of ultrathin 1D nanomaterials”, Part. Part. Syst. Charact. 34, 1600339 (2017). [Link]
8. S.G. Rodriques†, A. Marblestone†, J. Scholvin, J. Dapello, D. Sarkar, M. Mankin, R. Gao, L. Wood, E.S. Boyden*, “Multiplexed neural recording along a single optical fiber via optical reflectometry”, J. Biomed. Opt. 21, 057003 (2016). [Link]
7. Y-S. No†, R. Gao†, M. Mankin, R. Day, H-G. Park, C.M. Lieber*, “Encoding active device elements at nanowire tips,” Nano Lett. 16, 4713–4719 (2016). [Link]
6. M. Mankin, R. Day, R. Gao, Y-S. No, S-K. Kim, A. Maclleland, D. Bell, H-G. Park, C.M. Lieber*, “Facet-selective epitaxy of compound semiconductors on faceted silicon nanowires,” Nano Lett. 15, 4776-4782 (2015). [Link]
5. R. Day†, M. Mankin†, R. Gao, Y-S. No, S-K. Kim, D. Bell, H-G. Park, C.M. Lieber*, “Plateau-Rayleigh crystal growth of periodic shells on one-dimensional substrates,” Nat. Nanotechnol. 10, 345-352 (2015). [Link]
4. Q. Qing†, Z. Jiang†, L. Xu, R. Gao, L. Mai, C.M. Lieber*, “Free-standing kinked nanowire transistor probes for targeted intracellular recording in three dimensions,” Nat. Nanotechnol. 9, 142-147 (2014). [Link]
3. 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]
2. Z. Jiang†, Q. Qing†, P. Xie, R. Gao, C.M. Lieber*, “Kinked p-n junction nanowire probes for high spatial resolution sensing and intracellular recording,” Nano Lett. 12, 1711-1716 (2012). [Link]
1. X. Duan, R. Gao, P. Xie, T. Cohen-Karni, Q. Qing, H-S. Choe, B. Tian, X. Jiang, C.M. Lieber*, “Intracellular recordings of action potentials by an extracellular nanoscale field-effect transistor,” Nat. Nanotechnol. 7, 174-179 (2012). [Link]
(†: equal contribution; *: corresponding)
29. W. Wang†, X. Ruan†, G. Liu†, D.E. Milkie, W. Li, E. Betzig, S. Upadhyayula*, R. Gao*, “Nanoscale volumetric fluorescence imaging via photochemical sectioning,” bioRxiv 2024.08.01.605857 (2024). [Link]
28. A. Orlowski, J. Karippaparambil, J.-M. Paumier, S. Ghanta, E. Pallares, J. Tandukar, R. Gao, S. Gowrishankar*, “Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer’s disease mouse model,” eNeuro 11, ENEURO.0445-24.2024 (2024). [Link] [bioRxiv]
27. Y.H. Chan, K.C. Pathmasiri, D. Pierre-Jacques, M.C. Hibbard, N. Tao, J.L. Fischer, E. Yang, S.M. Cologna, R. Gao*, “Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics,” Nat. Commun.15, 5036 (2024). [Link] [bioRxiv]
26. J. Sun, S. Song, I. Singaram, A. Sharma, W. Wang, Y. Hu, W.-T. Lo, P.A. Koch, J. J. Zhao, V. Haucke, R. Gao, W. Cho*, “PI(3,5)P2 Controls the Signaling Activity of Class I PI3K,” bioRxiv 2023.01.25.525550 (2023). [Link]
25. J.W. Kim, A.J.H. Yong, E.E. Aisenberg, J.H. Lobel, W. Wang, T.M. Dawson, V.L. Dawson, R. Gao, Y.N. Jan, H.S. Bateup, N.T. Ingolia*, “Molecular recording of calcium signals via calcium-dependent proximity labeling,” Nat. Chem. Biol. 20, 894-905 (2024). [Link] [bioRxiv]
26. M. A. Churgin, D.O. Lavrentovich, M.A. Smith, R. Gao, E.S. Boyden, B. de Bivort*, “A neural correlate of individual odor preference in Drosophila,” eLife 12, RP90511 (2023). [Link] [bioRxiv]
23. X. Pan, Z.H. Coban Akdemir, R. Gao, X. Jiang, G.M. Sheynkman, E. Wu*, J.H. Huang*, N. Sahni*, S. S. Yi*, “AD-Syn-Net: Systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning,” Brief. Bioinform. 24, bbad030 (2023). [Link]
22. J. Lillvis*, H. Otsuna, X. Ding, I. Pisarev, T. Kawase, J. Colonell, K. Rokicki, C. Goina, R. Gao, A. Hu, K. Wang, J. Bogovic., D.E., Milkie, L. Meienberg, E.S. Boyden, S. Saalfeld, P.W. Tillberg, B.J. Dickson*, “Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy,” eLife 11, e81248 (2022). [Link] [bioRxiv]
21. W. Wang†, Y.H. Chan†, S.Y. Kwon, J. Tandukar, R. Gao*, “Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion,” Nano Converg. 9, 30 (2022). [Link]
20. J.-B. Chang, R. Gao, F. Chen, “Chapter 21 - Light-Sheet Fluorescence Microscopy for Multiscale Biological Imaging,” in Molecular Imaging Principles and Practice, 2nd ed. (eds. B. D. Ross & S. S. Gambhir) 373-382 (Academic Press, 2021). [Link]
Before UIC
19. R. Gao†, C.-C. Yu†, L. Gao, K.D. Piatkevich, R.L. Neve, J.B. Munro, S. Upadhyayula, E.S. Boyden*, “A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy,” Nat. Nanotechnol. 16, 698-707 (2021). [Link] [bioRxiv]
18. 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] [bioRxiv]
17. C. Zhang†, J.S. Kang†, S.M. Asano, R. Gao, E.S. Boyden*, “Expansion microscopy for beginners: Visualizing microtubules in expanded cultured HeLa cells,” Curr. Protoc. Neurosci., 92, e96 (2020). [Link]
16. 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] [bioRxiv]
15. 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]
14. 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]
13. 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]
12. 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]
11. R. Gao†, S.M. Asano†, E.S. Boyden*, “Q&A: Expansion microscopy”, BMC Biology 15, 50 (2017). [Link]
10. T. Ozel, B. Zhang, R. Gao, R.W. Day, C.M. Lieber*, D.G. Nocera*, “Electrochemical deposition of conformal and functional layers on high aspect ratio silicon micro/nanowires”, Nano Lett. 17, 4502-4507 (2017). [Link]
9. R. Gao†, I. Gupta†, E.S. Boyden*, “Sonofragmentation of ultrathin 1D nanomaterials”, Part. Part. Syst. Charact. 34, 1600339 (2017). [Link]
8. S.G. Rodriques†, A. Marblestone†, J. Scholvin, J. Dapello, D. Sarkar, M. Mankin, R. Gao, L. Wood, E.S. Boyden*, “Multiplexed neural recording along a single optical fiber via optical reflectometry”, J. Biomed. Opt. 21, 057003 (2016). [Link]
7. Y-S. No†, R. Gao†, M. Mankin, R. Day, H-G. Park, C.M. Lieber*, “Encoding active device elements at nanowire tips,” Nano Lett. 16, 4713–4719 (2016). [Link]
6. M. Mankin, R. Day, R. Gao, Y-S. No, S-K. Kim, A. Maclleland, D. Bell, H-G. Park, C.M. Lieber*, “Facet-selective epitaxy of compound semiconductors on faceted silicon nanowires,” Nano Lett. 15, 4776-4782 (2015). [Link]
5. R. Day†, M. Mankin†, R. Gao, Y-S. No, S-K. Kim, D. Bell, H-G. Park, C.M. Lieber*, “Plateau-Rayleigh crystal growth of periodic shells on one-dimensional substrates,” Nat. Nanotechnol. 10, 345-352 (2015). [Link]
4. Q. Qing†, Z. Jiang†, L. Xu, R. Gao, L. Mai, C.M. Lieber*, “Free-standing kinked nanowire transistor probes for targeted intracellular recording in three dimensions,” Nat. Nanotechnol. 9, 142-147 (2014). [Link]
3. 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]
2. Z. Jiang†, Q. Qing†, P. Xie, R. Gao, C.M. Lieber*, “Kinked p-n junction nanowire probes for high spatial resolution sensing and intracellular recording,” Nano Lett. 12, 1711-1716 (2012). [Link]
1. X. Duan, R. Gao, P. Xie, T. Cohen-Karni, Q. Qing, H-S. Choe, B. Tian, X. Jiang, C.M. Lieber*, “Intracellular recordings of action potentials by an extracellular nanoscale field-effect transistor,” Nat. Nanotechnol. 7, 174-179 (2012). [Link]
(†: equal contribution; *: corresponding)