Publications

2015-2024 - Neurotoolbox@Duke University:

• Casey M. Baker and Yiyang Gong. A semi-supervised pipeline for accurate neuron segmentation with fewer ground truth labels. eNeuro 0352-23.2024 (2024).

• Casey Baker and Yiyang Gong. Identifying properties of pattern completion neurons in a computational model of the visual cortex. PLOS Computational Biology 19(6): e1011167 (2023).

• Michael B. Ryan, Anne K. Churchland, Yiyang Gong, and Casey Baker. News and Views: Fastest-ever calcium sensors broaden the potential of neuronal imaging. Nature, 615, 804 (2023).

• Xiaoke Bi, Connor Beck, and Yiyang Gong. A kinetic-optimized CoChR variant with enhanced high-frequency spiking fidelity. Biophysical Journal 121, 4166–4178 (2022).

• Connor Beck and Yiyang Gong. Engineering rhodopsins' activation spectra using a FRET-based approach. Biophysical Journal. 121(9):1765-1776 (2022).

• Yiyang Gong, Yuqi Tian, and Casey Baker. A fully water coupled oblique light-sheet microscope. Scientific Reports 12, 5940 (2022).

• Yijun Bao, Emily Redington, Agnim Agarwal, and Yiyang Gong. Decontaminate Traces From Fluorescence Calcium Imaging Videos Using Targeted Non-negative Matrix Factorization. Frontiers in Neuroscience, 15:797421 (2022).

• Diming Zhang, Emily Redington, and Yiyang Gong. Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins. Communications Biology (2021) 4:924.

• Depeng Wang, Suva Roy, Andra M. Rudzite, Greg D. Field, and Yiyang Gong. High-resolution light-field microscopy with patterned illumination. Biomedical Optics Express Vol. 12, Issue 7, pp. 3887-3901 (2021)

• Yijun Bao, Somayyeh Soltanian-Zadeh, Sina Farsiu, and Yiyang Gong. Segmentation of neurons from fluorescence calcium recordings beyond real time. Nature Machine Intelligence volume 3, pages 590–600 (2021).

• Xiaoke Bi, Connor Beck, and Yiyang Gong. Genetically Encoded Fluorescent Indicators for Imaging Brain Chemistry. Biosensors 11(4), 116 (2021).

• Depeng Wang, Stephen Xu, Praruj Pant, Emily Redington, Somayyeh Soltanian-Zadeh, Sina Farsiu, and Yiyang Gong. Hybrid light-sheet and light-field microscope for high resolution and large volume neuroimaging. Biomedical Optics Express 10, 6595-6610 (2019).

• Connor Beck*, Diming Zhang*, and Yiyang Gong. Enhanced genetically encoded voltage indicators advance their applications in neuroscience. Current Opinion in Biomedical Engineering (2019).

• Connor Beck and Yiyang Gong . A high-speed, bright, red fluorescent voltage sensor to detect neural activity. Scientific Reports 9, 15878 (2019).

• Tong Zhang, Oscar Hernandez, Radosław Chrapkiewicz, Adam Shai, Mark J. Wagner, Yanping Zhang, Cheng-Hsun Wu, Jin Zhong Li, Masatoshi Inoue, Yiyang Gong, Biafra Ahanonu, Hongkui Zeng, Haruhiko Bito, and Mark J. Schnitzer. Kilohertz two-photon brain imaging in awake mice. Nature Methods 16, 1119–1122 (2019).

• Somayyeh Soltanian-Zadeh, Kaan Sahingur, Sarah Blau, Yiyang Gong, and Sina Farsiu. Fast and robust active neuron segmentation in two-photon calcium imaging using spatiotemporal deep learning. PNAS 116, 8554-8563 (2019).
    Media: Duke BME

• Cheng Huang, Jessica R. Maxey, Supriyo Sinha, Joan Savall, Yiyang Gong, and Mark J. Schnitzer. Long-term optical brain imaging in live adult fruit flies. Nature Communications 9, 872 (2018).

• Somayyeh Soltanian-Zadeh, Yiyang Gong, and Sina Farsiu. Information-Theoretic Approach and Fundamental Limits of Resolving Two Closely-Timed Neuronal Spikes in Mouse Brain Calcium Imaging. IEEE Transactions on Biomedical Engineering 65, 2428 (2018).
  Media: TBME monthly highlights

• Jesse D. Marshall, Jin Zhong Li, Yanping Zhang, Yiyang Gong, François St-Pierre, Michael Z. Lin, Mark J. Schnitzer. Cell-Type-Specific Optical Recording of Membrane Voltage Dynamics in Freely Moving Mice. Cell, 167, 1650-1662 (2016).

• Yiyang Gong, Cheng Huang, Jin Zhong Li, Benjamin F. Grewe, Yanping Zhang, Stephan Eismann, Mark J. Schnitzer. High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor. Science 350,1361-1366 (2015).
  Media: Science, Duke University, MedicalExpress, Spectrum News, SteamRegister, Academic Lab News

• Yiyang Gong, The evolving capabilities of rhodopsin-based genetically encoded voltage indicators, Current Opinion in Chemical Biology, Vol. 27, 84-89 (2015).

2011-2014 - Mark Schnitzer Lab:

• Yiyang Gong, Mark J. Wagner, Jin Zhong Li, and Mark J. Schnitzer, Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors, Nature Communications, Vol. 5, 4764 (2014).
      Supplementary Information
      Media: Stanford Report, Stanford Daily, Nature Methods

• Francois St-Pierre, Jesse D. Marshall, Ying Yang, Yiyang Gong, Mark J. Schnitzer, and Michael Z. Lin High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor, Nature Neuroscience, Vol. 17, 884-889 (2014).
      Supplementary Information

• Yiyang Gong, Jin Zhong Li, and Mark J. Schnitzer, Enhanced Archaerhodopsin Fluorescent Protein Voltage Indicators, PLOS One, e66959 (2013).

• Amy J. Lam, Francois St-Pierre, Yiyang Gong, Jesse D. Marshall, Paula J. Cranfill, Michelle A. Baird, Michael R. McKeown, Jörg Wiedenmann, Michael W. Davidson, Mark J. Schnitzer, Roger Y. Tsien, and Michael Z. Lin, Improving FRET dynamic range with bright green and red fluorescent proteins, Nature Methods Vol. 9, 1005–1012 (2012).

2006-2011 - Jelena Vuckovic Lab:

• Yiyang Gong, Armand Rundquist, Arka Majumdar, and Jelena Vuckovic, Low Power Resonant Optical Excitation of an Optomechanical Cavity, Optics Express Vol. 19, 1429-1440 (2011).

• Yiyang Gong, Satoshi Ishikawa, Szu-Lin Cheng, Marika Gunji, Yoshio Nishi, and Jelena Vuckovic, Photoluminescence from silicon dioxide photonic crystal cavities with embedded silicon nanocrystals, Physical Review B , Vol. 81, 235317 (2010).
  Highlights: Featured as an editor's choice article
  Also spotlighted by the APS

• Yiyang Gong, Maria Makarova, Selcuk Yerci, Rui Li, Martin J. Stevens, Burm Baek, Sae Woo Nam, Luca Del Negro, and Jelena Vuckovic, Observation of transparency of erbium-doped silicon nitride in photonic crystal nanobeam cavities, Optics Express, Vol 18, pp. 13863-13873 (2010).

• Yiyang Gong, Bryan Ellis, Gary Shambat, Tomas Sarmiento, James S. Harris, and Jelena Vuckovic, Nanobeam photonic crystal cavity quantum dot laser, Optics Express, Vol 18, pp. 8781-8789 (2010).

• Gary Shambat, Yiyang Gong, Jesse Lu, Selcuk Yerci, Rui Li, Luca Dal Negro, and Jelena Vuckovic, Coupled fiber taper extraction of 1.53 um photoluminescence from erbium doped silicon nitride photonic crystal cavities, Optics Express, Vol 18, pp. 5964-5973 (2010).

• Maria Makarova*, Yiyang Gong*, Szu-Lin Cheng, Yoshio Nishi, Selcuk Yerci, Rui Li, Luca dal Negro, Jelena Vuckovic, Photonic Crystal and Plasmonic Silicon-Based Light Sources, IEEE Journal of Selected Topics in Quantum Electronics, Vol 16, pp. 132-140 (2010).

• Yiyang Gong, Jelena Vuckovic, Photonic crystal cavities in silicon dioxide, Applied Physics Letters, Vol 96, pp. 031107 (2010).
  Highlights: Top 20 most downloaded articles in Applied Physics Letters in January 2010.

• Yiyang Gong*, Maria Makarova*, Selcuk Yerci, Rui Li, Martin J. Stevens, Burm Baek, Sae Woo Nam, Robert H. Hadfield, Sander N. Dorenbos, Val Zwiller, Jelena Vuckovic, Luca dal Negro, Linewidth narrowing and Purcell enhancement in photonic crystal cavities on an Er-doped silicon nitride platform, Optics Express, Vol 18, pp. 2601-2612 (2010).

• Yiyang Gong, Selcuk Yerci, Rui Li, Luca Dal Negro, Jelena Vuckovic, Enhanced Light Emission from Erbium Doped Silicon Nitride in Plasmonic Metal-Insulator-Metal Structures, Optics Express, Vol 17, pp. 20642-20650 (2009).

• Yiyang Gong, Jesse Lu, Szu-Lin Cheng, Yoshio Nishi, Jelena Vuckovic, Plasmonic Enhancement of Emission from Si-nanocrystals, Applied Physics Letters, Vol 94, pp. 013106 (2009).

• Yiyang Gong and Jelena Vuckovic, Design of plasmon cavities for solid-state cavity quantum electrodynamics applications, Applied Physics Letters, vol. 90, pp. 033113 (2007).

*Authors contributed equally.