Ying Lu CV

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

 

Education

 

 

 

 

 

 

2000 - 2004     B. S.                                        Physics                        Peking University, China (PRC)

 

2004 - 2010     Ph. D.                                      Biophysics                  The Rockefeller University   

 

Postdoctoral Training

 

2010 - 2016     Research Associate                 Single-molecule            Harvard Medical School

Biochemistry &

Structural Biology     

 

Faculty Academic Appointments

 

2017 -

Assistant Professor

Systems Biology

Harvard Medical School

 

Professional Societies

 

2010 -

American Society for Cell Biology

Member

 

 

 

 

 

Honors and Prizes

 

2000

Gold Medal (1st place)

 

IPHO Organizing Committee

31st International Physics Olympiad

2003

Chun-Tsung Scholar

Peking University

 

 

2004

 

Outstanding Graduate in Beijing

 

Higher Education Committee of Beijing

 

 

2011

Damon Runyon Fellowship

 

Damon Runyon Cancer Research Foundation

 

2014

Cold Spring Harbor Asia Fellowship Award

Cold Spring Harbor Asia Conference Organizing Committee

 

 

 

2018

Mallinckrodt Scholar Award

 

Edward Mallinckrodt, Jr. Foundation

 

Research Interests

 

  • Biochemistry/The ubiquitin-proteasome system
  • Cell Biology/Neurodegenerative diseases
  • Biophysics/Single-molecule enzymology
  • Structural biology/Cryo-electron microscopy

 

Publications

 

  1. 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

 

  1. 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.

 

  1. Ying Lu, Frederick Cross (2009). Mitotic Exit in the Absence of Separase Activity.  Mol Biol Cell. 20(5):1576-91.

 

  1. Ying Lu, Frederick Cross (2010). Periodic Cyclin-Cdk Activity Entrains an Autonomous Cdc14 Release Oscillator. Cell 141(2):268-79.

 

  1. 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

 

  1. Ying Lu, Weiping Wang, and Marc W. Kirschner (2015). Specificity of the Anaphase-Promoting Complex: A Single-Molecule Study. Science 348:1248737.

 

  1. 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.

 

  1. 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.

 

  1. 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.

 

  1. 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

 

  1. 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

 

  1. 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

 

  1. 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

 

  1. 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.

 

  1. 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

 

  1. 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

 

  1. 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

 

 

2009

Periodic cyclin-cdk activity entrains an autonomous Cdc14 release oscillator

The Cell Cycle Meeting, Salk Institute, La Jolla, CA

 

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

 

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

 

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