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

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…

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


Yuanchen Dong, Shuwen Zhang, Zhaolong Wu. Xuemei Li, Wei Li Wang, Yanan Zhu, Svetla Stoilova-McPhie, Ying Lu, Daniel Finley, Youdong Mao.   Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature 2019 Jan;565(7737):49-55

Jason Hon, Ying Lu.  Single-molecule methods for measuring ubiquitination and protein stability.   2019;619:225 247.


Yanan Zhu, Wei Li Wang, Daqi Yu, Qi Ouyang, Ying Lu*, Youdong Mao* (2017). Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.    2018 Apr 10;9(1):1360.  * Co-corresponding author


Ying Lu*, Jiayi Wu*, Yuanchen Dong, Shuobing Chen, 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 Jul 20;67(2):322-333 *equal contribution


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 (* equal contribution). 10/21/2016. “Structural Basis for Dynamic Regulation of The Human 26S Proteasome.” PNAS , 46, 113: 12991-12996. Publisher's Version

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, and Brenda A. Schulman. 6/2/2016. “Dual RING E3 Architectures for Substrate Polyubiquitination Visualized for Anaphase Promoting Complex/Cyclosome.” Cell, 6, 165: 1440–1453. Publisher's Version

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. 4/21/2016. “USP14 Deubiquitinates Proteasome-bound Substrates that are Ubiquitinated at Multiple Sites.” Nature, 532: 398–401. Publisher's Version


Ying Lu, Weiping Wang, and Marc W. Kirschner. 4/10/2015. “Specificity of the Anaphase-Promoting Complex: A Single-Molecule Study.” Science, 6231, 348. Publisher's Version

Ying Lu, Byung-hoon Lee, Randall King, Daniel Finley, and Marc W. Kirschner. 4/10/2015. “Substrate Degradation by the Proteasome: A Single-Molecule Kinetic Analysis.” Science, 6231, 348: 1250834. Publisher's Version


Hidefumi* Fukushima, Lixin* Wan, Hiroyuki* Inuzuka, Ying Lu*, Daming Gao, Victor Li, Pengda Liu, Alan W Lau, Tao Wu, Marc W. Kirschner, and Wenyi (* equal contribution) Wei. 8/29/2013. “SCF-mediated Cdh1 Destruction Defines a Negative Feedback Regulation to Coordinate Cell Cycle Progression.” Cell Reports, 4, 4: 803–816. Publisher's Version


Ying Lu and Frederick Cross. 4/16/2010. “Periodic Cyclin-Cdk Activity Entrains an Autonomous Cdc14 Release Oscillator.” Cell, 2, 141: 224-226. Publisher's Version


Benjamin J. Drapkin, Ying Lu, Andrea L. Procko, Benjamin L. Timney, and Frederick R. Cross. 11/17/2009. “1. Analysis of The Mitotic Exit Control System Using Locked Levels of Stable Mitotic Cyclin.” Molecular System Biology, 5: 328. Publisher's Version

Ying Lu and Frederick Cross. 3/1/2009. “Mitotic Exit in the Absence of Separase Activity.” Mol Biol Cell, 5, 20: 1576-91. Publisher's Version


Xiaonan Wang, Ying Lu, Minxi Jiang, and Xi Ouyang. 5/27/2004. "Attraction of spiral waves by localized inhomogeneities with small-world connections in excitable media." Physical Review E, 5, 69: 056223. Publisher's Version

Fangting Li*, Tao Long*, Ying Lu*, Chao Tang, and Qi Ouyang (*equal contribution). 4/6/2004. “The Yeast Cell-Cycle Network is Robustly Designed.” PNAS, 14, 101: 4781-6. Publisher's Version