Lingyan Shi


Assistant Professor

Research Focus
Ultrafast laser scanning microscopy, Stimulated Raman Scattering (SRS), multiphoton fluorescence, Brain, metabolism, cancer, bioorthogonal labeling, Raman probe, subcellular resolution, in situ

Research Summary

Dr. Shi is developing and applying new ultrafast laser scanning optical imaging and spectroscopic technologies- this includes stimulated Raman scattering (SRS) spectroscopy, and multiphoton microscopy (MPM).  These imaging techniques are used to investigate cellular metabolism, neurodegenerative diseases, cancer, drug delivery, and development in living organisms. She is combining bioorthogonal labeling SRS and MPM for directly visualizing in situ complex molecular events in brain, tumor, and metabolic diseases at sub-cellular scale. These approaches represent powerful tools for disease detection, diagnosis and treatment, as well as for mechanistic understanding of scientific fundamentals.

Lingyan Shi
Lab Website


Dr. Shi is an Assistant Professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering. She received her Ph.D. in Biomedical Engineering from the City College of New York (CCNY). She was a postdoc at the Institute for Ultrafast Spectroscopy and Lasers at CCNY. She then moved to the Department of Chemistry at Columbia University for her second postdoctoral training in biophotonics, prior to her joining UC San Diego.

Dr. Shi major scientific contributions include the discovery of the “Golden Optical Window” for deep brain imaging, and the development of a breakthrough platform that combines deuterium probing with stimulated Raman scattering microscopy for optical imaging of metabolic dynamics in living organism in situ. Dr. Shi won the Blavatnik Regional Awards for Young Scientists in 2018. Her primary research interests focus on developing and applying novel optical techniques for studying neuroscience, cancer, and metabolism.

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 will teach core undergraduate and graduate courses in the Department of Bioengineering.