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Lingyan Shi

Associate Professor, Bioengineering
Faculty-Affiliate, Electrical and Computer Engineering
Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering

Multimodal super resolution microscopy, stimulated Raman scattering (SRS), multiphoton fluorescence (MPF), & second harmonic generation (SHG),  bioorthogonal metabolic imaging, metabolic dynamics in aging, diseases, & immunology.

The Shi group is developing and applying laser scanning multimodal microscopy and spectroscopic technologies -- this includes stimulated Raman scattering (SRS) spectroscopy, multiphoton fluorescence microscopy (MPF), and second harmonic generation (SHG) for studying metabolic dynamics during aging and diseases. The imaging platform is used to map in situ cellular metabolic activities, and visualize the spatial distribution of newly synthesized molecules such as protein, lipid, DNA/RNA, and carbohydrates, which is important for studying aging processes, immunosenescence, as well as diseases including neuronal degeneration, diabetes, and cancer. The Shi group is integrating bioorthogonal labeled SRS microscopy the multimodal microscopy, which can automatically image co-registered SRS/MPF/SHG/DO-SRS for directly imaging complex molecular events in various tissues at sub-cellular scale. These approaches represent powerful tools for disease detection, diagnosis and treatment, as well as for mechanistic understanding of scientific fundamentals.

Capsule Bio:

Dr. Lingyan Shi is currently an Associate Professor in the Shu Chien-Gene Lay Department of Bioengineering at UC San Diego. Her research focuses on developing high resolution optical spectroscopy and imaging platforms, and its applications for studying metabolic dynamics in aging and diseases. She discovered the “Golden Window” for deep tissue imaging and developed bioorthogonal metabolic imaging platforms that combine deuterium probing and stimulated Raman scattering (DO-SRS using heavy water and STRIDE with D-glucose) for visualizing metabolic activities in situ. The Shi group transformed SRS into a super resolution microscopy with chemical selectivity by developing Adam optimization-based Pointillism Deconvolution (A-PoD) methods. Dr. Shi holds six awarded patents. She won the Blavatnik Regional Award for Young Scientist in 2018; the Hellman Fellowship Award 2021; the “Rising Star Award” by LaserFocusWorld, and the “Rising Star Award” by Nature Light Science & Applications in 2021; the “Advancing Bioimaging Scialog Fellow” by RCSA and the Chan Zuckerberg Initiative in 2021, 2022, and 2023; and the Sloan Research Fellow Award in Chemistry 2023.

Dr. Shi has been mentoring graduate and undergraduate students to help them achieve excellence in academic work and become successful engineers and scientists. She plans to continue making additional contributions by enhancing more participation of underrepresented groups from the UC San Diego communities. She has been teaching core undergraduate and graduate courses in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering.


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