Welcome to Wei Zheng's Homepage!

Dr. Wei Zheng is a fourth-year postdoc fellow in the Yang Zhang lab. His primary research interests involve the protein structure prediction, protein function annotation.

Educations

• 2017/08-now Postdoctoral fellow, University of Michigan (USA), Department of Computational Medicine and Bioinformatics

• 2015/10-2017/02 Joint Ph.D. Student, University of Michigan (USA), Department of Computational Medicine and Bioinformatics

• 2014/09-2017/06 Ph.D., Nankai University (China), School of Mathematical Science, Bioinformatics

• 2011/09-2012/04 Exchange Student, Keio University (Japan), JLP exchange program (6C)

• 2011/09-2014/06 Master, Nankai University (China), School of Mathematical Science, Bioinformatics

• 2010/09-2011/04 Exchange Student, Keio University (Japan), JLP exchange program (3C)

• 2007/09-2011/06 Bachelor, Nankai University (China), School of Mathematical Science, Information science

• Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang. FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, (2020). [Web Server]

• Chengxin Zhang, Wei Zheng, S.M. Mortuza, Yang Li, Yang Zhang. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics, (2020), co-first author. [Web Server]

• Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics, (2020). [Web Server]

• Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W Bell, Xiaogen Zhou, Yang Zhang. Protein structure and sequence re-analysis of 2019-nCoV genome refutes snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1. Journal of proteome research, 19: 1351-1360 (2020).

• Zhui Tu, Xiaoqiang Huang, Jinheng Fu, Na Hu, Wei Zheng, Yanping Li, Yang Zhang. Landscape of Variable Domain of Heavy-chain-only Antibody Repertoire from Alpaca. Immunology, 161: 53-65 (2020).

• Siqi Wu, Chang Tian, Panpan Liu, Dongjie Guo, Wei Zheng, Xiaoqiang Huang, Yang Zhang, Lijun Liu. Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions. Journal of Medical Virology, (2020).

• Stephanie S. Tseng-Rogenski, Koji Munakata, Daniel Y. Choi, Paul K. Martin, Supal Mehta, Minoru Koi, Wei Zheng, Yang Zhang, John M. Carethers. The human DNA mismatch repair protein MSH3 contains nuclear localization and export signals that enable nuclear-cytosolic shuttling in response to inflammation. Molecular and Cellular Biology, 40: 00029-20 (2020).

• Sang Ho Park, Alex Ayoub, Young-Tae Lee, Jing Xu, Hanseong Kim, Wei Zheng, Biao Zhang, Liang Sha, Sojin An, Yang Zhang, Michael A. Cianfrocco, Min Su, Yali Dou, Uhn-Soo Cho. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nature Communications, (2019).

• Wei Zheng, Qiqige Wuyun, S.M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang. CEthreader: fold-recognition for distant-homology proteins using contact map guided threading. PloS Computational Biology,(2019). [Web Server]

• Wei Zheng, Yang Li Y, Chengxin Zhang, Robin Pearce, S.M. Mortuza, Yang Zhang. Deep-learning contact-map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics,(2019). [Web Server]

• Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang. LOMETS2: Improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research,(2019). [Web Server]

• Wei Zheng,Chengxin Zhang, Eric W Bell, Yang Zhang. I-TASSER Gateway: A Protein Structure and Function Prediction Server Powered by XSEDE. Future Generation Computer Systems,99: 73-85 (2019). [Web Server]

• Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang. MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology, 30: 2256-2265 (2018). [Web Server]

• Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang. BindProfX: Assessing mutation-induced binding affinity change by protein interface profiles with pseudo counts. Journal of Molecular Biology, 429: 426-434 (2017). [Web Server]

• Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. , submitted. [Web Server]

• Chengxin Zhang, Wei Zheng, Micah Cheng, Gilbert S. Omenn, Peter L. Freddolino and Yang Zhang. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. ,co-first author, submitted.

• S. M. Mortuza, Wei Zheng, Chengxin Zhang, Yang Li, Yang Zhang. C-QUARK: Template-free protein structure modeling using low-accuracy contact-map prediction. , submitted. [Web Server]

• Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang. Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps. , submitted. [Web Server]

• Yang Li, Chengxin Zhang, Eric W Bell, Wei Zheng, Dongjun Yu, Yang Zhang. Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. , submitted. [Web Server]

• Young-Tae Lee, Alex Ayoub, Sang-Ho Park, Liang Sha, Jing Xu, Fengbiao Mao, Wei Zheng, Yang Zhang, Uhn-Soo Cho, Yali Dou. Mechanism for Disordered Regions in ASH2L and DPY30 to Modulate MLL/SET1 Activity on Chromatin. , submitted.