Youdong MAO

2019-08-16 21:32:41 0

Youdong MAO


Phone: 010-62750295
E-mail: ymao_at_pku.edu.cn
Website: http://www.phy.pku.edu.cn/~ymao/


Principal Investigator

Institute of Condensed Matter and Material Physics, School of Physics

Center of Quantitative Biology

Peking University

Beijing, China

 


Education:

B.Sc, Physics, Wuhan University, China, 1999; 

Ph.D. Condensed Matter Physics, Peking University, China, 2005.

 

Research interests:

The main goal of my research group is to develop cryo-EM methodology, in combination with various biochemical, biophysical and computational approaches, to address fundamental mechanistic problems in biological complexity, with emphasis on the complex dynamics and energetics of significant biomolecular machineries at the atomic level. We are interested in the following topics in the interdisciplinary areas across cryo-electron microscopy (cryo-EM), molecular medicine, machine learning, and bioinformatics:

(1)   Developing novel cryo-EM imaging approaches and machine-learning algorithms in expanding the technical capability of biomolecular imaging to enable 4D visualization of highly dynamic and heterogeneous biomolecular complex systems at atomic resolution. We are currently focusing on 4D cryo-EM, 4D electron tomography and phase-plate imaging. We are particularly interested in innovating algorithms in manifold learning, deep learning and artificial intelligence for analyzing cryo-EM data in broadly-defined biomedical applications.

(2)   Applications of these novel imaging methods to enhance our understanding of the molecular basis for human diseases and to expedite the development of therapies and vaccines. Our current research emphasizes a mechanistic understanding of the molecular basis of neurodegenerative diseases, immune responses, and immunodeficiency. We are interested in applying this mechanistic understanding to make translational innovations in cancer immunotherapy and immunogen engineering.


Academic experiences:

2005-2007: Visiting Scholar, National Center for Nanoscience and Nanotechnology, China;

2007-2012: Postdoc, Harvard Medical School, USA;

2012-2014: Instructor, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, USA;

2014-2015: Principal Investigator, Director, Intel® Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, USA;

2015-present: Principal Investigator, Assistant Professor of Biophysics (Tenure-Track), Institute of Condensed Matter and Material Physics, School of Physics, Peking University, China.

2016-present: Principal Investigator, Center for Quantitative Biology, Peking University, China.


Selected publications:

1.     Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW, Mao Y. Conformational landscape of the p28-bound human proteasome regulatory particle. Mol. Cell 2017; 67: 322-333.e6.

2.     Wu J, Ma Y, Congdon C, Brett B, Chen S, Ouyang Q, Mao Y. Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning. PLoS One 2017; 12: e0182130.

3.     Zhu Y, Ouyang Q, Mao Y. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. BMC Bioinformatics 2017; 18: 348.

4.     Chen S, Wu J, Lu Y, Ma YB, Lee BH, Yu Z, Ouyang Q, Finley D, Kirschner MW, Mao Y. Structural basis for dynamic regulation of the human 26S proteasome. Proc. Natl. Acad. Sci. USA 2016; 113: 12991-12996.

5.     Xu Y, Wu J, Yin CC, Mao Y. Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm. PLoS One 2016; 11: e0167765.

6.     Zhang L, Chen S, Ruan J, Wu J, Tong AB, Yin Q, Li Y, David L, Lu A, Wang WL, Marks C, Ouyang Q, Zhang X, Mao Y*, Wu H*. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Science 2015; 350: 404-409.

7.     Mao Y, Wang L, Gu C, Herschhorn A, Désormeaux A, Finzi A, Xiang SH, Sodroski JG. Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. Proc. Natl. Acad. Sci. USA 2013; 110:12438-12443.

8.     Mao Y, Castillo-Menendez LR, Sodroski J. Validity of the cryo-electron microscopy structures of the HIV-1 envelope glycoprotein complex. Proc. Natl. Acad. Sci. USA 2013; 110: E4178-E4182.

9.     Mao Y, Wang L, Gu C, Herschhorn A, Xiang SH, Haim H, Yang X, Sodroski J. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nat. Struct. Mol. Biol. 2012; 19:893-899.

10.  Mao Y, Zhang J. Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions. J. Am. Chem. Soc. 2012; 134:631-639.

11.  Mao Y, Wang WL, Wei D, Kaxiras E, Sodroski JG. Graphene structures at an extreme degree of buckling. ACS Nano 2011; 5:1395-400. 

12.  Mao Y, Sun Q, Wang X, Ouyang Q, Han L, Jiang L, Han D. In vivo nanomechanical imaging of blood-vessel tissues directly in mammals using atomic force microscopy. Appl. Phys. Lett. 2009; 95:013704.

13.  Mao Y, Chang S, Yang S, Ouyang Q, Jiang L. Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux. Nat. Nanotechnol. 2007; 2:366-371.

14.  Mao Y, Liu D, Wang S, Luo S, Wang W, Yang Y, Ouyang Q, Jiang L. Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH. Nucleic Acids Res. 2007; 35:e33.

15.  Mao Y, Luo C, Deng W, Jin G, Yu X, Zhang Z, Ouyang Q, Chen R, Yu D. Reversibly switchable DNA nanocompartment on surfaces. Nucleic Acids Res. 2004; 32:e144.

16.  Mao Y, Luo C, Ouyang Q. Studies of temperature-dependent electronic transduction on DNA hairpin loop sensor. Nucleic Acids Res. 2003; 31:e108.