Xi Zhang

Education

Ph.D. - School of Physics and Technology, Wuhan University, Wuhan, China, 2017

Dissertation: Interaction between ions and polyelectrolytes: From macroions to nucleic acids. Advisor: Prof. Zhi-Jie Tan

B.S. in Physics - School of Physics and Technology, Wuhan University, Wuhan, China, 2012

Thesis: Poisson-Boltzmann theory for nucleic acid-ion interactions. Advisor: Prof. Zhi-Jie Tan

Research Interests

Protein structure prediction from cryo-EM density map and related field, computational biology, bioinformatics, de novo protein structure prediction, biophysics, molecular modeling, deep learning, algorithm design.

I focus on developing new algorithms to predict biomolecule structure from cryo-EM density maps by integrating deep learning and traditional force field. Our first pipeline, CR-I-TASSER (cryo-EM I-TASSER), was released in 2022, and we are currently extending it towards complex modeling, as well as structure prediction from lower-resolution density maps.

Professional History

2021 to present: Postdoctoral Fellow

Freddolino Lab, Department of Biological Chemistry, University of Michigan

2019 to 2021: Postdoctoral Fellow

Zhang Lab, Department of Computational Medicine and Bioinformatics, University of Michigan

2017 to 2018: Research Assistant

Prof. Zhi-Jie Tan's research group, School of Physics and Technology, Wuhan University

2015 to 2017: Lab Manager

Prof. Zhi-Jie Tan's research group, School of Physics and Technology, Wuhan University

Co-supervisor for one Ph.D. and one master student

Co-supervisor for one Ph.D. and one master student with Prof. Zhi-Jie Tan

Selected Publications

Xi Zhang, Biao Zhang, Peter Freddolino*, and Yang Zhang*, "CR-I-TASSER: Assemble Protein Structures from Cryo-EM Density Maps using Deep Convolutional Neural Networks" Nature Methods 19:195-204, 2022.

Biao Zhang, Xi Zhang, Robin Pearce, Hongbin Shen, and Yang Zhang*, "A new protocol for atomic-level protein structure modeling and refinement using low-to-medium resolution cryo-EM density maps" Journal of Molecular Biology 432:5365-5377, 2020.

Cheng Lin, Xi Zhang, Xiaowei Qiang, Jin-Si Zhang, and Zhi-Jie Tan*. "Apparent repulsion between equally and oppositely charged spherical polyelectrolytes in symmetrical salt solutions" The Journal of Chemical Physics 151(11):114902, 2019. (co-first author)

Xi Zhang, Lei Bao, Yuan-Yan Wu, Xiao-Long Zhu, and Zhi-Jie Tan*, "Radial distribution function of semiflexible oligomers with stretching flexibility" The Journal of Chemical Physics 147(5):054901, 2017. (featured article; editor recommended as newsworthy)

Lei Bao, Xi Zhang, Ya-Zhou Shi, Yuan-Yan Wu, Zhi-Jie Tan*, "Understanding the relative flexibility of RNA and DNA duplexes: stretching and twist-stretch coupling" Biophysical Journal, 112:1094-1104, 2017. (co-first author)

Xi Zhang, Jin-Si Zhang, Ya-Zhou Shi, Xiao-Long Zhu, Zhi-Jie Tan*, "Potential of mean force between like-charged nanoparticles: Many-body effect" Scientific Reports 6, 23434, 2016.

Fellowships and Awards

2016 Jia-Wei Special Scholarship

2016 Graduate School Scholarship

2016 Excellent Graduate Student

2016 Champion (both single & men’s doubles) of badminton match in School of Physics and Technology

2014 Champion (single) of badminton match in School of Physics and Technology

2013 National Scholarship for graduates

2012 Enrolled with Full Scholarship for graduates

2011 Third Prize in the 2^nd China Undergraduate Physics Tournament