Haonan Lin, Scott Seitz, Yuying Tan, Jean-Baptiste Lugagne, Le Wang, Guangrui Ding, Hongjian He, Tyler J. Rauwolf, Mary J. Dunlop, John H. Conor, John A. Porco, Jr., Lei Tian, Ji-Xin Cheng. “Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering.” Nature Methods 22.5 (2025): 1040-1050.

Haonan Lin# *, Mark Cherepashensky*, Chinmayee Vallabh Prabhu Dessai, Vikrant Sharma, Ji-Xin Cheng#. Comprehensive MATLAB-Based Analysis Featuring Non-Negative Parallel LASSO for Quantifiable Spectral Signature Unmixing. Nature Protocol. Revision. 

Guangrui Ding, Chang Liu, Jiaze Yin, Xinyan Teng, Yuying Tan, Hongjian He, Haonan Lin#, Lei Tian#, Ji-Xin Cheng#. Self-Supervised Elimination of Non-Independent Noise in Hyperspectral Imaging." Newton 1.6 (2025): 100195.

Le Wang*, Haonan Lin*, Yifan Zhu, Xiaowei Ge, Jianing Liu, Fukai Chen, Meng Zhang, Ji-Xin Cheng. “High-resolution and high-sensitivity vibrational imaging via overtone photothermal microscopy.” Nature Communications 15.1 (2024): 5374.

Hongli Ni*, Chinmayee Prabhu Dessai*, Haonan Lin*, Wei Wang, Shaoxiong Chen, Ji-Xin Cheng. “High content stimulated Raman scattering histology of breast cancer.” Theranostics 14.4 (2024): 1361-1370. 

Yuying Tan*, Haonan Lin*, and Ji-Xin Cheng. “Profiling single cancer cell metabolism via high-content SRS imaging with chemical sparsity.” Science Advances 9.33 (2023): eadg6061.

Haonan Lin, and Ji-Xin Cheng. "Computational coherent Raman scattering imaging: breaking physical barriers by fusion of advanced instrumentation and data science." eLight 3.1 (2023): 1-19.

 Haonan Lin, Hyeon Jeong Lee, Nathan Tague, Jean-Baptiste Lugagne, Cheng Zong, Fengyuan Deng, Wilson Wong, Mary J. Dunlop and Ji-Xin Cheng. “Microsecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learning.” Nature Communications 12.1 (2021): 1-12.

Nathan Tague*, Haonan Lin*, Jean-Baptiste Lugagne, Owen M. O'Connor, Deeya Burman, Wilson W. Wong, Ji-Xin Cheng, Mary J. Dunlop. "Longitudinal Single‐Cell Imaging of Engineered Strains with Stimulated Raman Scattering to Characterize Heterogeneity in Fatty Acid Production." Advanced Science 10.20 (2023): 2206519.

Jing Zhang*, Jian Zhao*, Haonan Lin*, Yuying Tan, and Ji-Xin Cheng. “High-speed chemical imaging by Dense-Net learning of femtosecond stimulated Raman scattering”. The Journal of Physical Chemistry Letters 11.20 (2020): 8573-8578.

Haonan Lin, Chien-Sheng Liao, Pu Wang, Nan Kong and Ji-Xin Cheng. "Spectroscopic stimulated Raman scattering imaging of highly dynamic specimens through matrix completion." Light: Science & Applications 7.5 (2018): 17179. 

Jing Zhang, Haonan Lin, Jiabao Xu, Meng Zhang, Chi Zhang, Wei E. Huang, Ji-Xin Cheng. “High-throughput single-cell sorting by stimulated Raman-activated cell ejection.” Science Advances, 10.50 (2024): eadn6373.

Yifan Zhu, Xiaowei Ge, Hongli Ni, Jiaze Yin, Haonan Lin, Le Wang, Yuying Tan, Chinmayee V. Prabhu Dessai, Yueming Li, Xinyan Teng, and Ji-Xin Cheng. Stimulated Raman photothermal microscopy towards ultrasensitive chemical imaging. Science Advances. 9.43 (2023): eadi2181

Meng Zhang, Pu-Ting Dong, Hassan E. Eldesouky, Yuewei Zhan, Haonan Lin, Zian Wang, Ehab A. Salama, Cheng Zong, Zhicong Chen, Mohamed N. Seleem, and Ji-Xin Cheng "Fingerprint Stimulated Raman Scattering Imaging Unveils Ergosteryl Ester as a Metabolic Signature of Azole-Resistant Candida albicans." Analytical Chemistry 95.26 (2023), 9901-9913.

Jing Zhang, Jonghyeon Shin, Nathan Tague, Haonan Lin, Meng Zhang, Xiaowei Ge, Wilson Wong, Mary J. Dunlop, and Ji-Xin Cheng "Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy." Advanced Science 9.32 (2022): 2203887.

Minghua Zhuge, Kai‐Chih Huang, Hyeon Jeong Lee, Ying Jiang, Yuying Tan, Haonan Lin, Pu‐Ting Dong Guangyuan Zhao, Daniela Matei, Qing Yang, and Ji-Xin Cheng. "Ultrasensitive vibrational imaging of retinoids by visible preresonance stimulated Raman scattering microscopy." Advanced Science 8.9 (2021): 2003136.

Cheng Zong, Chi Zhang, Yeran Bai, Haonan Lin, Bin Ren, and Ji-Xin Cheng. “Imaging surface chemical reactions in real-time by electrochemical photothermal reflectance microscopy”. Chemical Science 12.5 (2021): 1930-1936.

Jean-Baptiste Lugagne, Haonan Lin, and Mary J. Dunlop. "DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning." PLoS Computational Biology 16.4 (2020): e1007673.

Cheng Zong, Ranjith Premasiri, Haonan Lin, Yimin Huang, Chi Zhang, Chen Yang, Bin Ren, Lawrence D. Ziegler, and Ji-Xin Cheng. "Plasmon-enhanced stimulated Raman scattering microscopy with single-molecule detection sensitivity." Nature Communications 10.1 (2019): 5318.

Pu-Ting Dong, Haonan Lin, Kai-Chih Huang, and Ji-Xin Cheng. "Label-free quantitation of glycated hemoglobin in single red blood cells by transient absorption microscopy and phasor analysis." Science Advances 5.5 (2019): eaav0561.

Chi Zhang, Kai-Chih Huang, Bartek Rajwa, Junjie Li, Shiqi Yang, Haonan Lin, Chien-Sheng Liao, Gregory Eakins, Shihuan Kuang, Valery Patsekin, J. Paul Robinson and Ji-Xin Cheng. "Stimulated Raman scattering flow cytometry for label-free single-particle analysis." Optica 4.1 (2017): 103-109.