# denotes equal contribution, * denotes corresponding author

1. W.H. Yeo, Y. Zhang*, A. E. Neely, X. Bao, C. Sun, and H. F. Zhang. Investigating Uncertainties in Single-Molecule Localization Microscopy Using Experimentally Informed Monte Carlo Simulation. Nano Letters, 2023, in press.

2. J. Chen, X. Tang, Z. Wang, A. Perez, B. Yao, K. Huang, Y. Zhang, and M. W. King. Techniques for Navigating Post-Surgical Adhesions: Insights into Mechanisms and Future Directions. Bioengineering & Translational Medicine, 2023, e10565.

3. Y. Liu, M. A. Shahid, H. Mao, J. Chen, M. Waddington, K. Song, and Y. Zhang*. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. ACS Chemical & Biomedical Imaging, 2023, in press.

4. Y. Zhang*,Yeting Zheng, Andrea Tomassini, Ambarish Kumar Singh, and Françisco M. Raymo*. Photoactivatable BODIPYs for Live-Cell PALM. Molecules, 2023, 28, 2447.

5. Y. Zhang*,Yeting Zheng, Andrea Tomassini, Ambarish Kumar Singh, and Françisco M. Raymo*. Photoactivatable Fluorophores for Bioimaging Applications. ACS Applied Optical Materials, 2023, 3, 640-651.

Prior to NCSU

1. Y. Zhang*, G. Wang, P. Huang, E. Sun, J. Kweon, Q. Li, J. Zhe, L. L. Ying, Hao F. Zhang. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Analytical Chemistry, 2022, 94, 40, 13834–13841.

2. K. Song, B. Brenner, W. H. Yeo, J Kweon, Z. Cai, Y. Zhang, Y. Lee, X. Yang, C. Sun, H. F. Zhang, Monolithic dual-wedge prism-based spectroscopic single-molecule localization microscopy, Nanophotonics, 2022, 11(8): 1527–1535. 

3. Y. Zhang*,#, Yu Zhang#, K. Song, W. Lin, C. Sun, G. C. Schatz, H. F. Zhang, Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy. J. Phys. Chem. Lett., 2021, 3914-3921.

4. Y. Zhang*, Y. Zheng, Y. Meana, F. M. Raymo. BODIPYs with Photoactivatable Fluorescence. Chem. Eur. J., 2021, 27, 11257-11267.

5. Z. Cai, Y. Zhang#, Z. Zhang, K. Song, L. Beckmann, A. Djalilian, C. Sun, H. F. Zhang, Super-resolution imaging of flat-mounted whole mouse cornea. Exp. Eye Res., 2021, 108499.

6. K. Song#, Y. Zhang#, B. Brenner, C. Sun, H. F. Zhang. Symmetrically-dispersed spectroscopic single-molecule localization microscopy. Light Sci. Appl., 2020, 9, 92: 1-10.

7. S. K. Gaire, Y. Zhang, H. Li, R. Yu, H. F. Zhang, L. Ying. Accelerating multicolor spectroscopic single-molecule localization microscopy using deep learning. Biomed. Opt. Exp., 2020, 11, 2705-2721.

8. W. Wang, E. A. van Niekek, Y. Zhang, L. Du, X. Jin, S. Wang, J. D. Baker, K. Groengier, F. M. Raymo, H. Mattousi. Compact, "Clickable" Quantum Dots Photoligated with Multifunctional Zwitterionic Polymers for Immunofluorescence and In-Vivo Imaging. Bioconjugate Chem., 2020, 31,1497-1509.

9. Y. Zhang*, F. M. Raymo. Photoactivatable fluorophores for single-molecule localization microscopy of live cells. Methods Appl. Fluoresc., 2020, 8 032002.

10. Y. Zhang*, F. M. Raymo. Live-Cell Imaging at the Nanoscale with Bioconjugatable and Photoactivatable Fluorophores. Bioconjugate Chem., 2020, 31, 1052-1062.

11. J. Davis, Y. Zhang, S. Yi, F. Du, K. Song, E. A. Scott, C. Sun, H. F. Zhang. Super-resolution imaging of self-assembled nanocarriers using quantitative spectroscopic analysis for cluster extraction. Langmuir, 2020, 36, 2291-2299

12. Y. Zhang, S. Tang, L. Ravelo, J. Cusido, F. M. Raymo, Far-red photoactivatable BODIPYs for the super-resolution imaging of live cells. Methods Enzymol., 2020, 640, 131-147.

13. J. Davis, B. Soetikno, K. Song,  Y. Zhang, C. Sun, H. F. Zhang, RainbowSTORM: An open-source ImageJ plugin for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction. Bioinformatics, 2020,.36,4972-4974.

14. Z. Zhang#, Y. Zhang#, L. Ying, C. Sun, H. F. Zhang, Machine-learning based spectral classification for spectroscopic single-molecule localization microscopy. Optics Letters, 2019, 44, 5864-5867. (Editor’s Pick)

15. L. Sansolone, Y. Zhang*, M. A. Mazza, J.L. Davis, B. Captain, H. F. Zhang, F. M. Raymo*, High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores. J. Phys. Chem. Lett., 2019, 10, 6807-6812.

16. K. Song, Y. Zhang, G. Wang, C. Sun and H. F. Zhang, Three-dimensional biplane spectroscopic single-molecule localization microscopy. Optica, 2019, 6, 709-715.

17. Y. Zhang#, K. Song#, B. Dong, J. Davis, G. Shao, C. Sun, H. F. Zhang, Multi-color Super-Resolution Imaging using spectroscopic single-molecule localization microscopy. Applied Optics, 2019, 58, 2248-2255.

18. Y. Zhang, K. Song, S. Tang, L. Ravelo, J. Cusido, C. Sun, H. F. Zhang, and F.M. Raymo, Far-Red Photoactivatable BODIPYs for the Super-Resolution Imaging of Live Cells. J. Am. Chem. Soc., 2018, 140, 12741-12745.

19. L. Sansalone, S. Tang, J. Garcia-Amoros, Y. Zhang, N. Santi, J. D. Baker, B. Captain, F. M. Raymo, A Photoactivatable Far-Red/Near-Infrared BODIPY to Monitor Cellular Dynamics in Vivo. ACS Sens., 2018, 3, 1347-1353.

20. Y. Zhang, S. Tang, E. Thapaliya, L. Sansalone, F.M. Raymo, Fluorescence Activation With Switchable Oxazines. Chem. Comm., 2018, 54, 8799-8809. (Front Cover)

21. Tang#, Y. Zhang#, P. Dhakal#, L. Ravelo, C. L. Anderson, K. M. Collins, F. M. Raymo, Photochemical Barcodes. J. Am. Chem. Soc., 2018, 140,4485-4488.

22. E. Thapaliya, Y. Zhang, P. Dhakal, A. S. Brown, J. N. Wilson, K. M. Collins, F. M. Raymo, Bright and compact macromolecular probes for bioimaging applications. Proc. Of SPIE, 2018,105070P.

23. X. Liu, Y. Zhang, J.D. Baker, F.M. Raymo, A Photoactivatable Light Tracer. J. Mater. Chem. C, 2017, 5, 12714-12719

24. X. Ma, F. Tao, Y. Zhang, T. Li, F.M. Raymo, Y. Cui, Detection of nitroaromatic explosives by 3D hyperbranched σ-π conjugate polymer on the basis of the POSS scaffold. J. Mater. Chem. A, 2017, 5, 14343-14354

25. K. Li, Y. Zhang, B. Qiao, F. Tao, T. Li, Y. Ding, F. M. Raymo, Y. Cui, Facile fabrication of AIE/AIEE-active fluorescent nanoparticles based on barbituric for cell imaging applications. RSC Advances, 2017, 7, 30229-30241

26. E. Thapaliya, Y. Zhang, P. Dhakal, A. S. Brown, J. N. Wilson, K. M. Collins, F. M. Raymo, Bioimaging with Macromolecular Probes Incorporating Multiple BODIPY Fluorophores. Bioconjugate Chem., 2017, 28, 1519-1528.

27. E. Thapaliya, Y. Zhang, F. M. Raymo, Fluorescence patterning with mild illumination in polymer films of photocleavable oxazines. J. Mater. Chem. C, 2017, 5, 1179-1183.

28. E. Thapaliya, C. Fowley, B. McCaughan, S. Tang, Y. Zhang, J. F. Callan, F. M. Raymo, Probing the intracellular fate of supramolecular nanocarriers and their cargo with FRET schemes. Proc. Of SPIE, 2017,10078, 100781B.

29. S. Tang, Y. Zhang, E. R. Thapaliya, Adrienne S. Brown, James N. Wilson, F. M. Raymo,Highlighting cancer cells with macromolecular probes. Proc. Of SPIE, 2017, 10078, 1007814-1.

30. Y. Zhang, S. Tang, E. R. Thapaliya, J.D. Baker, F. M. Raymo, Supramolecular delivery of photoactivatable fluorophores in developing embryos. Proc. Of SPIE, 2017, 10078, 100781A-1.

31. S. Tang, Y. Zhang, E. Thapaliya, A. Brown, J.N. Wilson and F. M. Raymo, Highlighting Cancer Cells with Halochromic Switches. ACS Sensors, 2017, 2, 91-101.

32. Sansalone, S. Tang, Y. Zhang, E. Thapaliya F. M. Raymo, and J. Garcia-Amorós, Semiconductor Quantum Dots with Photoresponsive Ligands. L Top. Curr. Chem., 2016, 374, 73-1–30

33. Y. Zhang, S. Tang, L. Sansalone, J. D. Baker, F. M. Raymo, A Photoswitchable Fluorophore for the Real-Time Monitoring of Dynamic Events in Living Organisms. Chem. Eur. J.,2016. 22, 15027-15034.

34. Y. Zhang, E. R. Thapaliya, S. Tang, J. D. Baker, F. M. Raymo, Supramolecular Delivery of Fluorescent Probes in Developing Embryos. RSC Advances, 2016, 6, 72756–72760.

35. Y. Zhang, B. Captain and F. M. Raymo. A pH-Gated Photocage. Adv. Optical. Mater., 2016, 4, 1363-1366.

36. S. Ragab, E. Thapaliya, Y. Zhang, S. Tang, J. McMahan, S. Syed, B. Captain and F. M. Raymo, Synthesis in Living Cells with the Assistance of Supramolecular Nanocarriers. RSC Adv., 2016, 6, 32441-32445. 

37. Y. Zhang, S. Tang, E. Thapaliya and F. M. Raymo, Supramolecular nanocarriers with photoresponsive cargo. Proc. Of SPIE, 2016, 9722, 97220C-6

38. J. Garcia-Amorós, S. Tang, Y. Zhang, E. Thapaliya and F. M. Raymo, Self-Assembling Nanoparticles of Amphiphilic Polymers for in Vitro and in Vivo FRET Imaging. Top. Curr. Chem., 2016, 370, 29-60

39. Y. Zhang, J. Garcia-Amoro´s, B. Captain and F. M. Raymo, A fluorescent and halochromic indolizine switch. J. Mater. Chem. C, 2016, 4, 2744-2747

40. E. Thapaliya, C. Fowley, B. McCaughan, S. Tang, Y. Zhang, J. F. Callan and F. M. Raymo. Intracellular Guest Exchange between Dynamic Supramolecular Hosts. Langmuir, 2015, 31, 9557-9565

41. J. Garcia-Amorós, S. Swaminathan, Y. Zhang, S. Nonellb and F. M. Raymo, Optical writing and reading with a photoactivatable carbazole. Phys. Chem. Chem. Phys., 2015, 17, 11140-11143

42. Y. Zhang, S. Swaminathan, S.  Tang, J. Garcia-Amorós, M. Boulina, B. Captain, J.D. Baker, and F. M. Raymo, Photoactivatable BODIPYs Designed to Monitor the Dynamics of Supramolecular Nanocarrier. J. Am. Chem. Soc., 2015, 137, 4709–4719

43. Y. Cui, Y. Zhang, L. Zhou, and F. Yu, Two-Photon Absorption Properties of s-Triazine Derivatives With Near Octupolar Symmetry, Adv. Mat. Res. 2013, 652, 542-545

44. H. Peng, Y. Cui, T. Zhang, Y. Zhang, and H. Guan, Optical Properties of Chromophores with Different Six-membered N-heterocyclic Aromatic Ring. Adv. Mat. Res., 2011, 236, 1598-1602