Associate Professor, Sloan Research Fellow, Scialog Fellow, and Hellman Fellow

Short Bio: http://jacobsschool.ucsd.edu/faculty/faculty_bios/index.sfe?fmp_recid=487

Lingyan Shi is currently a tenured Associate Professor in the Shu Chien-Gene Lay Department of Bioengineering at UCSD. She arrived at UCSD in October, 2019, following her postdoctoral training in the Department of Chemistry (Min Lab) at Columbia University. Her lab focuses on developing and applying super resolution multimodal nanoscopy for studying metabolic changes in aging and diseases. Notably, she discovered the "Golden Window" (wavelength from 1550nm to 1870nm) for deep tissue imaging and pioneered the "DO-SRS" metabolic imaging platform, which visualizes metabolic dynamics in cells and tissues with heavy water probing. Her group advanced stimulated Raman scattering (SRS) microscopy into a super-resolution multiplex nanoscopy by developing A-PoD and PRM platforms, revealing various lipid metabolic changes in organ tissues under physiological and pathological conditions. Dr. Shi holds 10 awarded patents and 8 pending. She won Blavatnik Regional Award for Young Scientists (2018), Nature Light Science &Applications’ Rising Star Award (2021), Hellman Fellow Award 2022, the Advancing Bioimaging Scialog Fellow Award 2023, the David L. Williams Lecture Scholarship Award (2023), the Sloan Research Fellowship in Chemistry (2023), the Cellular Molecular Bioengineering Rising Star Faculty Award (2024), the Davos Summit iCANx Young Scientist Award (2024), 2024 ICBME Rising Star Award, 2024 IUPS Young Faculty Awad, and Featured in the 2025 Optics Notebook--Woman in Optics. 

​Email: L2shi@ucsd.edu 

Teaching:

1. BENG 112B. Fluid and Cell Biomechanics (4) Prerequisites: BENG 112A or consent of department. (S)

2. BENG 247A Advanced Biophotonics/ Nano 247A Advanced Biophotonics/ ECE 247 A Advanced Biophotonics 

3. BENG 168. Biomolecular Engineering (4) Prerequisites: BILD 1 and BENG 100, or consent of department. (W)

4. BENG 281 Seminar series (2022 SP)

Department Link: Shu Chien-Gene Lay Department of Bioengineering, UC San Diego, 

Social Media links: https://orcid.org/0000-0003-1373-3206 ; https://scholar.google.com/citations?user=xC9dMQ8rRXMC&hl=en ;https://twitter.com/StimulatedRaman ;https://www.linkedin.com/in/lingyanshi2018/ 

Shu Chien-Gene Lay Department of Bioengineering, UCSD

Dr. Yajuan Li received her PhD in Cell Biology and Genetics from Peking University. She is passionate about in situ metabolic imaging with novel optical imaging techniques. 

Shu Chien-Gene Lay Department of Bioengineering, UCSD

Dr. Hongje Jang received his PhD in Physics from Georg-August-Universität Göttingen. He is passionate about the development of a new imaging platform and super-resolution chemical image analysis. He is investigating the nanoscopic distribution of various biomolecules in single cells and tissues. Inside and outside of the lab, he always enjoys learning something new and finding connections between new ones and already learned ones. 

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Dr. Anthony A. Fung received his PhD in Bioengineering from Shi Lab at UC San Diego,  now a postdoc passionate about the advanced imaging technologies. He earned his B.S. in Bioengineering from UC San Diego. Outside of the lab, he enjoys creating new recipes in the kitchen for his family, friends, and pet parrotlets.

PhD Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Zhi is a PhD student at UC San Diego with a focus in developing and applying biophotonics and optical imaging technologies for solving important biological questions. Outside of of the lab, he enjoys playing soccer, basketball and learning programming. 

PhD Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Jorge is a PhD student in the Shu Chien-Gene Lay Department of Bioengineering focusing on utilizing novel imaging and image analysis techniques for the study of biological metabolic/signaling pathways, particularly in the field of neuroscience. He earned his B.S. in Bioengineering from UC San Diego. Outside of lab, he enjoys spending time with friends, gaming, and working out. 

Graduate Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Pegah is a graduate student studying Bioengineering at UC San Diego who is interested in using imaging techniques for biological applications. She earned her B.S. from UC San Diego, where she studied Mechanical Engineering. She has previously worked with Dr. McKittrick in the Mechanical Engineering department and with Dr. Mali in the Bioengineering department. Outside of lab, she enjoys running, biking, and going to the beach. 

Graduate Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Sahran is a graduate student in the Bioengineering Department at UC San Diego focusing on biophotonics and imaging. He earned his B.S. from University of Illinois at Urbana-Champaign. Prior to attending graduate school at UCSD he worked for Luminex Corporation in the Imaging Flow Cytometry division working with the Biology and Manufacturing teams. Outside of work and school, he enjoys playing soccer and hanging out with his cats.

ENLACE Program Student Researcher 

Bioengineering Department, UC San Diego

Veronica is a fifth year undergraduate student studying Medicine. She has previously worked under Susana Brugues in the Swartz Center for Computational Neuroscience Laboratory. In her free time she enjoys crafting and swimming.

ENLACE Program Student Researcher 

Bioengineering Department, UC San Diego

Etna is a third-year undergraduate studying Medicine, who is interested in the development of tumor recognition techniques; she previously worked with Doctor Celia González Castillo in the department of biosciences at El Tecnologico de Monterrey and with the traumatologist surgeon Doctor Victor Manuel Hernández Robles at El IMSS public health institution in México; in her free time, she enjoys literature and photography.

Graduate student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Yu is a graduate student in the Bioengineering Department at UC San Diego. He is interested in doing research on metabolic activities and dynamics in different organ tissues. He earned his B.S. with a major in Biology and a minor in Chemistry from University of Utah. He had experience working with Dr. Lixin Song at University of North Carolina at Chapel Hill focusing on improving survivorship care for cancer patients and their family caregivers. Outside of the lab, he enjoys exploring new restaurants, hiking and snowboarding.

NIH HuBMAP Summer Scholarship Winner

School of Biomedical Engineering and Department of Computer Science, Cornell University

Rosie is going into her third year as an undergraduate at Bates College, double majoring in Biochemistry and Psychology. She is interested in the development of imaging techniques for cancer and other metabolic diseases. She is also a student researcher in the Bates College Office of Institutional Research, Analysis and Planning. Outside of research, she enjoys playing her flute in the orchestra and pole vaulting for the track and field team.

Undergraduate Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Khang is a third year undergraduate student studying Bioengineering: Biotechnology. He previously worked in the Chemistry/Biochemistry department stockroom under Dr. Mary Sever. In his free time, he enjoys cooking, gaming, and trying new boba drinks.

Undergraduate Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Mos is a first year undergraduate student studying Bioengineering: Bioengineering. In his free time, he enjoys baking high quality cookies.

Undergrad Researcher

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Matthew is a motivated undergrad researcher in Shi Lab at UC San Diego. He has been studying Bioengineering: Biotechnology. He is most interested in exploring applications for biotechnology in improving efficacy of medicine. Outside of the laboratory, Matthew enjoys nature, spending time with friends, and working on personal projects.​

Undergraduate Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

​Darragh is entering his fourth year as an undergraduate studying Bioengineering with an emphasis on biotechnology. He is interested in novel imaging techniques for understanding biology and metabolism. In his free time, Darragh enjoys playing soccer, basketball, and going to the beach. 

Senior Design Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Derek is a fourth year undergraduate studying Bioengineering at UC San Diego. He has worked with Dr. Christian Metallo in the Bioengineering department at UC San Diego and Dr. Albert Leung at the Center of Pain and Headache Research for the Department of Veterans Affairs. Outside of the lab, he enjoys fitness training, cooking, and chess. 

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Senior Design Student

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Chloe is a fourth year undergraduate studying Bioengineering: Biotechnology. In addition to being a senior design student in the Shi Lab, she is also a research assistant in the UCSD Biodynamics Lab, where she utilizes synthetic biology techniques to enable the engineering of bacterial communities. In her free time, Chloe enjoys creating balloon decorations and traveling. 

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