Curriculum Vitae
Name: |
Ying Lu |
Position |
Assistant Professor, Department of Systems Biology, HMS |
Office Address: |
210 Longwood Avenue, ARM 649, Boston, MA 02115 |
Work Phone: |
(617) 432-5143 |
Email: ying_lu@hms.harvard.edu
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2000 - 2004 B. S. Physics Peking University, China (PRC)
2004 - 2010 Ph. D. Biophysics The Rockefeller University
2010 - 2016 Research Associate Single-molecule Harvard Medical School
Biochemistry &
Structural Biology
2017 - |
Assistant Professor |
Systems Biology |
Harvard Medical School
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2010 - |
American Society for Cell Biology |
Member |
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2000 |
Gold Medal (1st place)
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IPHO Organizing Committee |
31st International Physics Olympiad |
2003 |
Chun-Tsung Scholar |
Peking University |
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2004 |
Outstanding Graduate in Beijing |
Higher Education Committee of Beijing
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2011 |
Damon Runyon Fellowship
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Damon Runyon Cancer Research Foundation |
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2014 |
Cold Spring Harbor Asia Fellowship Award |
Cold Spring Harbor Asia Conference Organizing Committee
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2018 |
Mallinckrodt Scholar Award
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Edward Mallinckrodt, Jr. Foundation |
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Research Interests
- Biochemistry/The ubiquitin-proteasome system
- Cell Biology/Neurodegenerative diseases
- Biophysics/Single-molecule enzymology
- Structural biology/Cryo-electron microscopy
- Fangting Li*, Tao Long*, Ying Lu*, Chao Tang, Qi Ouyang (2004). The Yeast Cell-Cycle Network is Robustly Designed. PNAS 101(14):4781-6. *equal contribution
- Xiaonan Wang, Ying Lu, Minxi Jiang, Qi Ouyang (2004). Attraction of Spiral Waves by Localized Inhomogeneities with Small-World Connections in Excitable Media. Phys. Rev. E 69(5 Pt 2):056223.
- Ying Lu, Frederick Cross (2009). Mitotic Exit in the Absence of Separase Activity. Mol Biol Cell. 20(5):1576-91.
- Ying Lu, Frederick Cross (2010). Periodic Cyclin-Cdk Activity Entrains an Autonomous Cdc14 Release Oscillator. Cell 141(2):268-79.
- Hidefumi Fukushima*, Lixin Wan*, Hiroyuki Inuzuka*, Ying Lu*, Daming Gao, Victor Li, Pengda Liu, Alan W Lau, Tao Wu, Marc W. Kirschner and Wenyi WeI (2013). SCF-mediated Cdh1 Destruction Defines a Negative Feedback Regulation to Coordinate Cell Cycle Progression. Cell Reports 4:1-14. *equal contribution
- Ying Lu, Weiping Wang, and Marc W. Kirschner (2015). Specificity of the Anaphase-Promoting Complex: A Single-Molecule Study. Science 348:1248737.
- Ying Lu, Byung-hoon Lee, Randall King, Daniel Finley and Marc W. Kirschner (2015). Substrate Degradation by the Proteasome: A Single-Molecule Kinetic Analysis. Science, 348:1250834.
- Byung-Hoon Lee, Ying Lu, Miguel A. Prado, Yuan Shi, Shuangwu Sun, Suzanne Elsasser, Marc W. Kirschner, Steven P. Gygi, Randall W. King, and Daniel Finley (2016). USP14 Deubiquitinates Proteasome-bound Substrates that are Ubiquitinated at Multiple Sites. Nature 532:398-401.
- Nicholas G. Brown, Ryan VanderLinden, Edmond R. Watson, Florian Weissmann, Alban Ordureau, Kuen-Phon Wu, Wei Zhang, Shanshan Yu, Joseph S. Harrison, Renping Q. Coudevylle, Iain F. Davidson, Ying Lu, Prakash Dube, Michael R. Brunner, Christy R. R. Grace, Darcie J. Miller, Marc A. Jarvis, Masaya Yamaguchi, Peter Y. Mercredi, Sachdev S. Sidhu, Brian Kuhlman, Marc W. Kirschner, J. Wade Harper, Jan-Michael Peters, Holger Stark, Brenda A. Schulman (2016). Dual RING E3 Architectures for Substrate Polyubiquitination Visualized for Anaphase Promoting Complex/Cyclosome. Cell 165(6);1440-53.
- Shuobing Chen*, Jiayi Wu*, Ying Lu*, Yong-Bei Ma, Byung-hoon Lee, Zhou Yu, Qi Ouyang, Daniel J. Finley, Marc W. Kirschner, and Youdong Mao (2016). Structural Basis for Dynamic Regulation of The Human 26S Proteasome. PNAS Nov. 15; 113(46): 12991-12996. *equal contribution
- Ying Lu*, Jiayi Wu*, Shuangwu Sun, Yong-Bei Ma, Qi Ouyang, Daniel Finley, Marc W. Kirschner, Youdong Mao (2017). Conformational Landscape of the p28-bound Human Proteasome Regulatory Particle. Molecular Cell Jun 26; S1097-2765(17). *equal contribution
- Yanan Zhu, Wei Li Wang, Daqi Yu, Qi Ouyang, Ying Lu*, Youdong Mao* (2018). Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nature Communication Apr 10;9(1):1360. * Co-corresponding author
- Jason Hon, and Ying Lu* (2018). Single-molecule methods for measuring ubiquitination and protein stability. Methods in Enzymology 619: 225-247. *corresponding author *review article
- Yuanchen Dong, Shuwen Zhang, Zhaolong Wu, Xuemei Li, Weili Wang, Yanan Zhu, Svetla Stoilova-McPhie, Ying Lu*, Daniel Finley, Youdong Mao (2019). Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature. 565(7737):49-55.
- Rui Fang, Jason Hon, Mengying Zhou and Ying Lu* (2022). An empirical energy landscape reveals the mechanism of proteasome in polypeptide translocation. eLife. 10.7554/eLife.71911
- Alba Jiménez, Ying Lu, Ashwini Jambhekar, Galit Lahav (2022). Principles, mechanisms and functions of entrainment in biological oscillators. Interface Focus. 12(3): 20210088 *review article
- Ka Ying Sharon Hung, Sven Klumpe, Markus R. Eisele, Suzanne Elsasser, Geng Tian, Shuangwu Sun, Jamie A. Moroco, Tat Cheung Cheng, Tapan Joshi, Timo Seibel, Duco Van Dalen, Xin-Hua Feng, Ying Lu, Huib Ovaa, John R. Engen, Byung-Hoon Lee, Till Rudack, Eri Sakata and Daniel Finley (2022). Allosteric control of Ubp6 and the proteasome via a bidirectional switch. Nature Communication Feb 11. doi: 10.1038/s41467-022-28186-y
Invited seminars
2008 |
Factorial control and the role of separase in budding yeast mitotic exit Department of Biology, VirginiaTech University, Blacksburg, VA |
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2009 |
Periodic cyclin-cdk activity entrains an autonomous Cdc14 release oscillator The Cell Cycle Meeting, Salk Institute, La Jolla, CA
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2012 Kinetics of APC-mediated ubiquitylation reaction by single-molecule methods
The Rockefeller University, New York, NY
2013 Kinetics analysis of substrate degradation by the proteasome
American Society of Cell Biology Conference, New Orleans, LA
2014
2014 |
Single-molecule analysis of protein degradation by the proteasome Cold Spring Harbor Asia Conference, SuZhou, China
Kinetic analysis of protein degradation using single-molecule approaches International Young Scholars Systems and Synthetic Biology Symposium, Beijing, China
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2015 Kinetics analysis of substrate degradation by the proteasome
The ubiquitin family, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
2016 Specificity, efficiency and specificity in the eukaryotic protein degradation system
Quantitative biology lecture series, UCSD, La Jolla, CA
2016 |
Kinetic amplification of substrate specificity by the anaphase promoting complex Cold Spring Harbor Asia Conference, SuZhou, China
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2017 Specificity, efficiency and specificity in the eukaryotic protein degradation system
Department of Mechanical Engineering, John Hopkins University
2017 Kinetic and structural analysis of the eukaryotic protein degradation system
Department of Cell Biology, Penn State University
2017 Kinetic and structural analysis of protein degradation by the proteasome
Quantitative Biology: Computational and Single-Molecule Biophysics, Beijing China
2018 Decoding the ubiquitin signaling in protein degradation
2018 Harvard-Shanghai Conference on Brain Health - a special meeting for understanding and intervention of Alzheimer’s disease, Shanghai, China
2020 An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
Keystone Symposia: AAA+ Proteins, Tahoe, CA
2020 An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
Baylor College of Medicine, TX
2021 An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
9th Proteasome and Autophagy Congress, Clermont-Ferrand, France
2022 Identify the Ubiquitin Configurations on Endogenous Substrates using Digital Ubiquitin Proteomics
FASEB The Ubiquitin and Ub-like Proteins Conference, Southbridge, MA, USA
Ad hoc Reviewer
National Institute of Health Grant Review
PLOS Computational Biology
EMBO J.
Physical Review E
Physical Review Letters
Molecular Systems Biology
Physical Biology
J. Theoretical Biology
Nature Cell Biology
Genome
ACS Synthetic Biology
International Symposium on Bio- and Medical Informatics and Cybernetics
Elife
Nature Communication