Yang Zhang

BPS2026 - Integrating spectroscopic single-molecule localization microscopy with DNA-PAINT for simultaneous multiplexing super-resolution microscopy

Shahid, M. A., Patel, K., & Zhang, Y. (2026, February 1). Biophysical Journal, Vol. 2.

Framework for Accurate Single-Molecule Spectroscopic Imaging Analyses Using Monte Carlo Simulation and Deep Learning

Mao, H., Liu, Y., KanchanadeviVenkataraman, O., Shahid, M. A., Laplante, C., Xu, D., … Zhang, Y. (2025, July 4). Analytical Chemistry, Vol. 7.

Functional super-resolution microscopy of fibers and polymers: convergence of artificial and biological systems at the nanoscale

Rao, S.-J., Gong, X., Shahid, M. A., Liu, Y., Mao, H., & Zhang, Y. (2025, December 17). Nanoscale Horizons.

Mineral Deposition from Liquid Precursors Triggered by Complementary Polyelectrolytes

Patoary, M. K., Pierce, E. H., Siu, E., Gallagher, B., Shahid, M. A., Zhang, Y., & Schroeder, T. B. H. (2025, December 10).

Photoactivation of BODIPY Fluorescence with Green Light

Tomassini, A., Liu, Y., Zheng, Y., Shahid, M. A., Singh, A., Singh, A. K., … Raymo, F. M. (2025, June 6). The Journal of Organic Chemistry, Vol. 6.

Photoswitchable Fluorescent Hydrazone for Super-Resolution Cell Membrane Imaging

Qi, Q., Liu, Y., Puranik, V., Patra, S., Svindrych, Z., Gong, X., … Aprahamian, I. (2025, May 2). Journal of the American Chemical Society, Vol. 5.

Solvatochromic BODIPYs with Polarity-Independent Absorption for Functional Super-resolution Imaging of Live Cell Membranes

Liu, Y., Gong, X., Yoder, B., Gluck, J. M., Vinueza, N. R., Liu, X., & Zhang, Y. (2025, November 18). Chemical & Biomedical Imaging.

Multiscale imaging of corneal endothelium damage and Rho-kinase inhibitor application in mouse models of acute ocular hypertension

Cai, Z., Zhang, Y., Fang, R. S., Brenner, B., Kweon, J., Sun, C., … Zhang, H. F. (2024, January 17). Biomedical Optics Express, Vol. 15.

Quantifying nanoscopic alterations associated with mitochondrial dysfunction using three-dimensional single-molecule localization microscopy

Brenner, B., Xu, F., Zhang, Y., Kweon, J., Fang, R., Sheibani, N., … Zhang, H. F. (2024, February 6). Biomedical Optics Express, Vol. 15, pp. 1571–1584.

Integrating Machine Learning and Color Chemistry: Developing a High-School Curriculum toward Real-World Problem-Solving

Jiang, S., McClure, J., Mao, H., Chen, J., Liu, Y., & Zhang, Y. (2023, December 7). Journal of Chemical Education, Vol. 12.

Investigating Uncertainties in Single-Molecule Localization Microscopy Using Experimentally Informed Monte Carlo Simulation

Yeo, W.-H., Zhang, Y., Neely, A. E., Bao, X., Sun, C., & Zhang, H. F. (2023, July 18). Nano Letters, Vol. 7.

Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers

Neely, A. E., Zhang, Y., Blumensaadt, L. A., Mao, H., Brenner, B., Sun, C., … Bao, X. (2023, October 18). Communications Biology, Vol. 6.

Photoactivatable BODIPYs for Live-Cell PALM

Zhang, Y., Zheng, Y., Tomassini, A., Singh, A. K., & Raymo, F. M. (2023, March 7). Molecules, Vol. 28.

Photoactivatable Fluorophores for Bioimaging Applications

Zhang, Y., Zheng, Y., Tomassini, A., Singh, A. K., & Raymo, F. M. (2023, February 27). ACS Applied Optical Materials, Vol. 1, pp. 640–651.

Photoactivatable fluorophores for bioimaging applications

Zhang, Y., Zheng, Y., Tomassini, A., Hayter, C. E., & Raymo, F. M. (2023, March 18). COLLOIDAL NANOPARTICLES FOR BIOMEDICAL APPLICATIONS XVIII, Vol. 12395.

Spectral precision improvement with demagnifying spectral images in spectroscopic nanoscopy

Song, K.-H., & Zhang, Y. (2023, November 17). Journal of the Optical Society of America A, Vol. 41, pp. 39–44.

Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy

Liu, Y., Shahid, M. A., Mao, H., Chen, J., Waddington, M., Song, K.-H., & Zhang, Y. (2023, June 28). Chemical & Biomedical Imaging.

Techniques for navigating postsurgical adhesions: Insights into mechanisms and future directions

Chen, J., Tang, X., Wang, Z., Perez, A., Yao, B., Huang, K., … King, M. W. (2023, June 26). Bioengineering & Translational Medicine, Vol. 6.

Experimental Parameters-Based Monte-Carlo Simulation of Single-Molecule Localization Microscopy of Nuclear Pore Complex to Evaluate Clustering Algorithms

Yeo, W.-H., Zhang, Y., Neely, A. E., Bao, X., Sun, C., & Zhang, H. F. (2022, September 22).

Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy

Zhang, Y., Wang, G., Huang, P., Sun, E., Kweon, J., Li, Q., … Zhang, H. F. (2022, September 27). Analytical Chemistry.

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy

Zhang, Y., Zhang, Y., Song, K.-H., Lin, W., Sun, C., Schatz, G. C., & Zhang, H. F. (2021, April 16). The Journal of Physical Chemistry Letters, Vol. 12, pp. 3914–3921.

Accelerating multicolor spectroscopic single-molecule localization microscopy using deep learning

Gaire, S. K., Zhang, Y., Li, H., Yu, R., Zhang, H. F., & Ying, L. (2020, April 14). Biomedical Optics Express.

Compact, “Clickable” Quantum Dots Photoligated with Multifunctional Zwitterionic Polymers for Immunofluorescence and In Vivo Imaging

Wang, W., Niekerk, E. A., Zhang, Y., Du, L., Ji, X., Wang, S., … Mattoussi, H. (2020, April 25). Bioconjugate Chemistry, Vol. 31, pp. 1497–1509.

Live-Cell Imaging at the Nanoscale with Bioconjugatable and Photoactivatable Fluorophores

Zhang, Y., & Raymo, F. M. (2020, March 9). Bioconjugate Chemistry, Vol. 31, pp. 1052–1062.

Photoactivatable fluorophores for single-molecule localization microscopy of live cells

Zhang, Y., & Raymo, F. M. (2020, April 23). Methods and Applications in Fluorescence.

Super-Resolution Imaging of Self-Assembled Nanocarriers Using Quantitative Spectroscopic Analysis for Cluster Extraction

Davis, J. L., Zhang, Y., Yi, S., Du, F., Song, K.-H., Scott, E. A., … Zhang, H. F. (2020, February 18). Langmuir, Vol. 36, pp. 2291–2299.

High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores

Sansalone, L., Zhang, Y., Mazza, M. M. A., Davis, J. L., Song, K.-H., Captain, B., … Raymo, F. M. (2019, October 17). The Journal of Physical Chemistry Letters, Vol. 10, pp. 6807–6812.

Machine-learning based spectral classification for spectroscopic single-molecule localization microscopy

Zhang, Z., Zhang, Y., Ying, L., Sun, C., & Zhang, H. F. (2019, November 27). Optics Letters.

Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion

Zhang, Y., Song, K.-H., Dong, B., Davis, J. L., Shao, G., Sun, C., & Zhang, H. F. (2019, March 14). Applied Optics.

Three-dimensional biplane spectroscopic single-molecule localization microscopy

Song, K.-H., Zhang, Y., Wang, G., Sun, C., & Zhang, H. F. (2019, May 21). Optica.

Three-dimensional biplane spectroscopic single-molecule localization microscopy: erratum

Song, K.-H., Zhang, Y., Wang, G., Sun, C., & Zhang, H. F. (2019, October 14). Optica.

A Photoactivatable Far-Red/Near-Infrared BODIPY To Monitor Cellular Dynamics in Vivo

Sansalone, L., Tang, S., Garcia-Amorós, J., Zhang, Y., Nonell, S., Baker, J. D., … Raymo, F. M. (2018, June 4). ACS Sensors, Vol. 3, pp. 1347–1353.

Far-Red Photoactivatable BODIPYs for the Super-Resolution Imaging of Live Cells

Zhang, Y., Song, K.-H., Tang, S., Ravelo, L., Cusido, J., Sun, C., … Raymo, F. M. (2018, September 24). Journal of the American Chemical Society, Vol. 140, pp. 12741–12745.

Fluorescence activation with switchable oxazines

Zhang, Y., Tang, S., Thapaliya, E. R., Sansalone, L., & Raymo, F. M. (2018, January 1). Chemical Communications.

Photochemical Barcodes

Tang, S., Zhang, Y., Dhakal, P., Ravelo, L., Anderson, C. L., Collins, K. M., & Raymo, F. M. (2018, March 21). Journal of the American Chemical Society, Vol. 140, pp. 4485–4488.

A photoactivatable light tracer

Liu, X., Zhang, Y., Baker, J. D., & Raymo, F. M. (2017, January 1). Journal of Materials Chemistry C.

Bioimaging with Macromolecular Probes Incorporating Multiple BODIPY Fluorophores

Thapaliya, E. R., Zhang, Y., Dhakal, P., Brown, A. S., Wilson, J. N., Collins, K. M., & Raymo, F. M. (2017, April 21). Bioconjugate Chemistry, Vol. 28, pp. 1519–1528.

Detection of nitroaromatic explosives by a 3D hyperbranched σ–π conjugated polymer based on a POSS scaffold

Ma, X., Tao, F., Zhang, Y., Li, T., Raymo, F. M., & Cui, Y. (2017, January 1). Journal of Materials Chemistry A.

Facile fabrication of AIE/AIEE-active fluorescent nanoparticles based on barbituric for cell imaging applications

Li, K., Zhang, Y., Qiao, B., Tao, F., Li, T., Ding, Y., … Cui, Y. (2017, January 1). RSC Advances, Vol. 7, pp. 30229–30241.

Fluorescence patterning with mild illumination in polymer films of photocleavable oxazines

Thapaliya, E. R., Zhang, Y., & Raymo, F. M. (2017, January 1). Journal of Materials Chemistry C, Vol. 5, pp. 1179–1183.

Highlighting cancer cells with macromolecular probes

Tang, S., Zhang, Y., Thapaliya, E. R., Brown, A. S., Wilson, J. N., & Raymo, F. M. (2017, February 22). (M. Osiński, W. J. Parak, & X.-J. Liang, Eds.). Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE.

Probing the intracellular fate of supramolecular nanocarriers and their cargo with FRET schemes

Thapaliya, E. R., Fowley, C., Callan, B., Tang, S., Zhang, Y., Callan, J. F., & Raymo, F. M. (2017, February 22). (M. Osiński, W. J. Parak, & X.-J. Liang, Eds.). Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE.

Supramolecular delivery of photoactivatable fluorophores in developing embryos

Zhang, Y., Tang, S., Sansalone, L., Thapaliya, E. R., Baker, J. D., & Raymo, F. M. (2017, February 22). (M. Osiński, W. J. Parak, & X.-J. Liang, Eds.). Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE.

A Photoswitchable Fluorophore for the Real‐Time Monitoring of Dynamic Events in Living Organisms

Zhang, Y., Tang, S., Sansalone, L., Baker, J. D., & Raymo, F. M. (2016, August 30). Chemistry - A European Journal, Vol. 22, pp. 15027–15034.

A pH‐Gated Photocage

Zhang, Y., Captain, B., & Raymo, F. M. (2016, May 31). Advanced Optical Materials, Vol. 5.

Highlighting Cancer Cells with Halochromic Switches

Tang, S., Zhang, Y., Thapaliya, E. R., Brown, A. S., Wilson, J. N., & Raymo, F. M. (2016, December 21). ACS Sensors, Vol. 2, pp. 92–101.

Semiconductor Quantum Dots with Photoresponsive Ligands

Sansalone, L., Tang, S., Zhang, Y., Thapaliya, E. R., Raymo, F. M., & Garcia-Amorós, J. (2016, October 28). Topics in Current Chemistry Collections, pp. 31–60.

Supramolecular delivery of fluorescent probes in developing embryos

Zhang, Y., Thapaliya, E. R., Tang, S., Baker, J. D., & Raymo, F. M. (2016, January 1). RSC Advances, Vol. 6, pp. 72756–72760.

Supramolecular nanocarriers with photoresponsive cargo

Zhang, Y., Tang, S., Thapaliya, E. R., & Raymo, F. M. (2016, March 8). (W. J. Parak, M. Osinski, & X.-J. Liang, Eds.). Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE.

Synthesis in living cells with the assistance of supramolecular nanocarriers

Ragab, S. S., Thapaliya, E. R., Zhang, Y., Tang, S., McMahan, J. B., Syed, S., … Raymo, F. M. (2016, January 1). RSC Advances, Vol. 6, pp. 32441–32445.

A fluorescent and halochromic indolizine switch

Zhang, Y., Garcia-Amorós, J., Captain, B., & Raymo, F. M. (2015, November 9). Journal of Materials Chemistry C, Vol. 4, pp. 2744–2747.

Energy-Transfer Schemes To Probe Fluorescent Nanocarriers and Their Emissive Cargo

Thapaliya, E. R., Fowley, C., Callan, B., Tang, S., Zhang, Y., Callan, J. F., & Raymo, F. M. (2015, August 14). Langmuir, Vol. 31, pp. 9557–9565.

Optical writing and reading with a photoactivatable carbazole

Garcia-Amorós, J., Swaminathan, S., Zhang, Y., Nonell, S., & Raymo, F. M. (2015, January 1). Physical Chemistry Chemical Physics, Vol. 17, pp. 11140–11143.

Photoactivatable BODIPYs Designed To Monitor the Dynamics of Supramolecular Nanocarriers

Zhang, Y., Swaminathan, S., Tang, S., Garcia-Amorós, J., Boulina, M., Captain, B., … Raymo, F. M. (2015, March 20). Journal of the American Chemical Society, Vol. 137, pp. 4709–4719.

Self-Assembling Nanoparticles of Amphiphilic Polymers for In Vitro and In Vivo FRET Imaging

Garcia-Amorós, J., Tang, S., Zhang, Y., Thapaliya, E. R., & Raymo, F. M. (2015, November 20). Topics in Current Chemistry, pp. 29–59.

Two-Photon Absorption Properties of <i>s</i>-Triazine Derivatives With Near Octupolar Symmetry

Cui, Y. Z., Zhang, Y., Zhou, L. L., & Yu, F. (2013, January 25). Advanced Materials Research, Vol. 652-654, pp. 542–545.

Optical Properties of Chromophores with Different Six-Membered N-Heterocyclic Aromatic Ring

Peng, H. T., Cui, Y. Z., Zhang, T., Zhang, Y., & Guan, H. X. (2011, May 1). Advanced Materials Research, Vol. 236-238, pp. 1598–1602.