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Molecular Medicine


Li Ye, Ph.D.

Assistant Professor
Department of Neuroscience
California Campus
Laboratory Website
(858) 784-8081

Scripps Research Joint Appointments

Dorris Neuroscience Center
Assistant Professor, Department of Molecular Medicine

Research Focus

The brain plays a pivotal role in integrating homeostatic signals and regulating whole-body metabolism. But the high energy demand of neurons also makes the CNS highly sensitive to systemic metabolic stress. We are interested in how the brain adapts to both acute and chronic metabolic changes and how such adaptation, in turn, affects the control of organismal physiology by the CNS, at the biochemical, cellular, and circuit levels.  Our long-term goal is to harness the molecular and circuit mechanisms underlying these adaptations to target metabolic disorders including obesity and type 2 diabetes as well as certain neurodegenerative diseases.

We employ and design novel systems tools optimized for brain-wide structural mapping (whole-brain labeling, tissue clearing (“CLARITY”) and large-volume light-sheet imaging), in vivo multi-region Ca2+ imaging, and activity/connectivity-defined optogenetics. Based in TSRI, we also develop and apply high throughput screens (small molecules, genomic, proteomic, etc.) in conjunction with circuit-based tools to unleash the power of large scale unbiased screens in intact mammalian brains.


Ph.D., Harvard University, 2012
B.S., Tsinghua University, 2006

Professional Experience

2013-2017   Postdoctoral Fellow, Stanford University/HHMI, Stanford, CA 
2007-2008   Chemical Biology Visiting Student, MIT/Broad Institute, Cambridge, MA

Awards & Professional Activities

2017-NIDDK Mentored Career Development Award (K01)                         
2017-Keystone Symposia Future of Science Fund Scholarship
2016-Sammy Kuo Awards in Neuroscience, 3rd Place, Stanford University
2012-Keystone Symposia Scholarship

Selected References

Kim CK,* Ye L*, Jennings JH, Pichamoorthy N, Tang DD, Wang AC, Ramakrishnan C, Deisseroth K. Molecular and Circuit-dynamical Identification of Top-down Neural Mechanisms for Restraint of Reward-seeking. Cell. 2017 Aug 24;170(5):1013-1027.e14.

Ye L*, Allen WE*, Thompson KR*, Tian Q, Hsueh B, Ramakrishnan C, Wang AC, Jennings JH, Adhikari A, Halpern CH, Witten IB, Barth AL, Luo L, McNab JA, Deisseroth K. Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences. Cell. 2016 Jun 16;165(7):1776-88. (Cover and Highlighted) 

Lerner TN, Ye L, Deisseroth K. Communication in Neural Circuits: Tools, Opportunities and Challenges. Cell. 2016 Mar 10;164(6):1136-50

Tomer R, Ye L, Hsueh B, Deisseroth K. Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat Protoc. 2014 Jul;9(7):1682-97

Cadavieco M*, Gorbati M*, Ye L, Kosse C, Börgers C, Veldt S, Lee SY, Ramakrishnan C, Denisova N, Ramm F, Hu Y, Bender F, Burdakov D, Deisseroth K, Ponomarenko A & Korotkova T. Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking.  Nature. 2017 Feb 9;542(7640):232-236.

Ye L, Wu J, Cohen P, Kazak L, Khandekar MJ, Jedrychowski MP, Zeng X, Gygi SP and Spiegelman BM. Fat cells directly sense temperature to activate thermogenesis. Proc Natl Acad Sci U S A. July 1, 2013, 10.1073 

Ye L, Kleiner S, Wu J, Sah R, Gupta RK, Banks AS, Cohen P,  Khandekar MJ, Boström P, Mepani R, Laznik D, Kamenecka TM, Song X, Liedtke W, Mootha VK, Puigserver P, Griffin PR, Clapham DE and Spiegelman BM. TRPV4 is a regulator of adipose oxidative metabolism, inflammation and energy homeostasis. Cell. 2012 Sep 28;151(1):96-110. 

Wu J, Boström P, Sparks LM, Ye L, Choi JH, Giang A, Khandekar M, Nuutila P, Schaart G, Huang K, Tu H, van Marken Lichtenbelt WD, Hoeks J, Enerbäck S, Schrauwen P and Spiegelman BM. Beige Adipocytes are a Distinct Type of Thermogenic Fat Cell in Mouse and Human. Cell. 2012 Jul 20;150(2):366-76.

(*co-first authors)

Molecular Medicine Seminar Series
Center for Physiological Proteomics
Department Contacts

CA Faculty

Asahara, Hiroshi
Balch, William E.
Boddy, Michael
Buxbaum, Joel
Catz, Sergio
Conti, Bruno
Cravatt, Benjamin
D'Lima, Darryl
DerMardirossian, Celine
Deryugina, Elena
Elias, Darlene
Encalada, Sandra
Felding, Brunhilde
Fowler, Velia
Friedlander, Martin
Gerace, Larry
Gottesfeld, Joel
Griffin, John
Hanneken, Anne
Heeb, Mary Jo
Henderson, Scott
Hoch, James
Johnson, Eric
Kanaji, Taisuke
Koziol, James
Lamia, Katja
Lipton, Stuart
Loring, Jeanne F.
Loskutoff, David
Lotz, Martin
Makarenkova, Helen P.
Mc Millan, Robert
Miles, Lindsey
Milner, Richard
Modena, Brian
Mosnier, Laurent
Nicholson, Laura
Paulson, James C.
Perego, Marta
Petrascheck, Michael
Pollard, Kenneth Michael
Quigley, James P.
Reed, Steven
Roberts, Edward
Rosen, Hugh
Ruggeri, Zaverio
Russell, Paul
Saez, Enrique
Smider, Vaughn
Srinivasan, Supriya
Steinhubl, Steven
Sutcliffe, J.
Tan, Eng
Topol, Eric
Vanderklish, Peter
Vogt, Peter K.
Wiseman, Luke
Wittenberg, Curt
Wolan, Dennis W.
Wu, Peng
Wu, Xiaohua
Yang, Xiang-Lei
Yates III, John

FL Faculty

Bannister, Thomas
Bohn, Laura M.
Cameron, Michael
Duckett, Derek
Gill, Matt
Griffin, Patrick
Hansen, Scott
Joazeiro, Claudio
Kamenecka, Theodore
Kissil, Joseph
Luo, Junli
McDonald, Patricia
Miller, Courtney
Niedernhofer, Laura
Phinney, Donald G.
Robbins, Paul
Scampavia, Louis
Schimmel, Paul
Smith, Roy
Spicer, Timothy

Affiliated Faculty

Cline, Hollis
Kojetin, Douglas
Lairson, Luke
Paegel, Brian
Rumbaugh, Gavin
Shen, Ben
Solt, Laura A
Su, Andrew
Wu, Chunlei
Ye, Li

Adjunct Faculty