Preprints (*Equal Contribution; #Corresponding)

4. Guangrui Ding*, Haonan Lin*, Rong Tang, Bethany Weinberg, Jianpeng Ao, Qing Xia, Guorong Hu, Dingcheng Sun, Jiaze Yin, Lei Tian, Ji-Xin Cheng#. "Background2Background: a self-supervised background removal framework for high dimensional microscopy." arXiv:2610.17615 (2026). 

3. Pin-Tian Lyu, Yifan Zhu, Qing Xia, Guangrui Ding, Arvind Pillai, Xinru Wang, Jianpeng Ao, Haonan Lin, Lulu Jiang, David Baker, Ji-Xin Cheng#. "Label-free Imaging of Single-Biomolecule Structure and Interaction by Stimulated Raman Photothermal Encoded Scattering." arXiv: 2603.25534 (2026). 

2. Dingcheng Sun, Guangrui Ding, Haonan Lin, Guo Chen, Chun-Chin Wang, Seema Bachoo, Sarah E Bohndiek, Ji-Xin Cheng#. "SPEND-hSRS imaging of fumarate uncovers mitochondrial metabolic heterogeneity." bioRxiv: 2026.04.03.716311 (2026). 

1. Guangrui Ding, Dingcheng Sun, Yifan Zhu, Rong Tang, Hongli Ni, Yuhao Yuan, Haonan Lin#, Ji-Xin Cheng#. "Micromolar chemical imaging by high-energy low-photodamage Coherent Anti-stokes Raman Scattering (HELP-CARS)." arXiv:2602.09245 (2026).

Peer-reviewed (*Equal Contribution; #Corresponding)

27. Mark Cherepashensky*, Guangrui Ding*, Chinmayee Vallabh Prabhu Dessai, Dingcheng Sun, Le Wang, Mingsheng Li, Qing Xia, Ji-Xin Cheng#, Haonan Lin#. " DECIPHER: A Modular Pipeline for Quantifiable Spectral Unmixing in Vibrational Hyperspectral Imaging." Nature Protocols, In Press. 

26. Leyla Anne Akay, Anna Bright, Daiyun Dong, Ethan D. Smith, Robert C. Hurt, Carles A. Boix, Kate Louderback, Janine Medrano, Dingcheng Sun, Haonan Lin, Oisín King, Gwyneth M. Welch, Hiba Nawaid, Emre Agbas, Alan Jiang, Adele Bubnys, Ji-Xin Cheng, Joel W. Blanchard, Li-Huei Tsai#. "Genome-wide CRISPR screen reveals that Wnt signaling regulates lipid accumulation in APOE4 oligodendrocytes." Cell Stem Cell, 2026. 

25. Jianpeng Ao*, Jiaze Yin*, Haonan Lin, Guangrui Ding, Youchen Guan, Bethany Weinberg, Dashan Dong, Qing Xia, Zhongyue Guo, Marzia Savini, Biwen Gao, Ji-Xin Cheng#, Meng C. Wang#. "In vivo mapping organellar metabolism by optical-boxcar enhanced fluorescence-detected mid-infrared photothermal microscopy." Nature Methods, 23.6 (2026): 1196–1206. 

24. Sanjun Fan*, Ran Cheng*, Haonan Lin*, Zhewen Luo, Abigail E. Smith, Chih-Feng Wang, Jinna He, Brian T. Scarpitti, Deben N. Shoup, Hannah C. Schorr, Erjun Liang, Jian Ye, Ji-Xin Cheng#, Zachary D. Schultz#. "Single-Particle Surface-Enhanced Coherent Anti-Stokes Raman Scattering: Nanoparticle Design and Mechanism." Science Advances 12.5 (2026): eady0545.

23. Chinmayee V Prabhu Dessai, Zhuoying Huang, Haonan Lin, Guangrui Ding, Hongjian He, Menna Siddiqui, Meng Zhang, Wilson Wong, Ji‐Xin Cheng#. "High‐Content SRS Imaging Unveils Altered Cholesterol Metabolism in Ovarian Cancers Under CAR‐T Treatment." Advanced Science 12.23 (2026): e18334. 

22. Hongjian He, Haonan Lin, Le Wang, Xinyan Teng, Samar Aldahan, Meng Zhang, Meihui Yi, Guangrui Ding, Bing Xu#, Ji‐Xin Cheng#. "Enzyme-Instructed Self-Assembly Reprograms Fatty Acid Metabolism for Cancer Therapeutics." Advanced Healthcare Materials 14.14 (2025): 2500469.

21. Meng Zhang, Yuewei Zhan, Haonan Lin, Jiyang Chen, Mohamed N. Seleem, Michael Mansour, Ji-Xin Cheng#. "SIP-SRS Imaging of Cell Wall Synthesis Identifies a Synergy between Micafungin and Amphotericin B." Advanced Science (2025): e07331.

20. 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.

19. 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.

18. 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.

17. 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.

16. 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. 

15. 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.

14. 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.

13. 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.

12. 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

11. 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.

10. 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.

9. 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.

8. 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.

7. 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.

6. 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.

5. 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.

4. 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.

3. 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.

2. 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. 

1. 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.