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Welcome to Xiaogen Zhou's Homepage!

  Xiaogen Zhou Ph.D
  Correspondence Department of Computational Medicine and Bioinformatics, University of Michigan, Medical School
100 Washtenaw Avenue, Ann Arbor, MI 48109-2218
  Email zxg@zjut.edu.cn or xiaogenz@umich.edu
  OCRID https://orcid.org/0000-0001-6839-1923
  ResearchGate https://www.researchgate.net/profile/Xiaogen_Zhou
Brief Biography 

Dr. Xiaogen Zhou received his Ph.D. from Guijun Zhang's Lab at the College of Information Engineering, Zhejiang University of Technology, in 2018. From July 2018 to December 2022, he served as a Post-Doctoral Fellow in Yang Zhang's Lab at the Department of Computational Medicine and Bioinformatics, University of Michigan (Ann Arbor). He is currently a professor at the College of Information Engineering, Zhejiang University of Technology. His research interests include structural bioinformatics, computational intelligence, and deep learning.

Publications (>> Google Scholar Citation Profile)
Journal Papers
  • Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang. Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature Computational Science, 2: 265-275, 2022. [Web Server]

  • Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang, Yang Zhang. I-TASSER-MTD: A deep-learning based platform for multi-domain protein structure and function prediction. Nature Protocols, 17: 2326-2353, 2022. [Web Server]

  • Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research, 50(W1): W235-W245, 2022. [Web Server]

  • Ziying Zhang, Yaxian Cai, Biao Zhang, Wei Zheng, Lydia Freddolino, Guijun Zhang, Xiaogen Zhou. DEMO-EM2: Assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Briefings in Bioinformatics, 25(2): bbae113, 2024. [Web Server]

  • Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang. Assembling multidomain protein structures through analogous global structural alignments . Proceedings of the National Academy of Sciences, 2019, 116(32): 15930-15938. [Web Server]

  • Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, and Guijun Zhang. Underestimation-assisted global-local cooperative differential evolution and the application to protein structure prediction . IEEE Transactions on Evolutionary Computation, 2020, 24(3): 536-550.

  • Xiaogen Zhou and Guijun Zhang. Differential Evolution With Underestimation-Based Multimutation Strategy . IEEE Transactions on Cybernetics, 2019, 49(4): 1353-1364.

  • Xiaogen Zhou and Guijun Zhang. Abstract convex underestimation assisted multistage differential evolution . IEEE Transactions on Cybernetics, 2017, 47(9): 2730-2741.

  • Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, and Li Yu. A novel differential evolution algorithm using local abstract convex underestimate strategy for global optimization . Computers & Operations Reasearch, 2016, 75(11): 132-129.

  • Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, Li Yu, and Dongwei Xu. Enhanced differential evolution using local Lipschitz underestimate strategy for computationally expensive optimization problems . Applied Soft Computing, 2016, 48(11): 169-181.

  • Xiaogen Zhou, Guijun Zhang, and Xiaohu Hao. Differential evolution algorithm with local abstract convex region rartition . Acta Automatica Sinica , 2015, 41(07): 1315-1327.

  • Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, and Li Yu. Differential evolution algorithm based on local Lipschitz underestimate supporting hyperplanes . Chinese Journal of Computers, 2016, 39(12): 2631-2651.

  • Xiaogen Zhou, Guijun Zhang, Shan Mei, and Jie Ming. Differential evolution algorithm based on abstract convex underestimate selection strategy . Control Theory & Applications, 2015, 32(03): 388-397.

  • Guijun Zhang, Xiaogen Zhou, Xufeng Yu, and Xiaohu Hao. Enhancing protein conformational space sampling using distance profile-guided differential evolution . IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(6): 1288-1301.

  • Zhangwei Li, Ke Sun, Xiaohu Hao, Jun Hu, Laifa Ma, Xiaogen Zhou, and Guijun Zhang. Loop enhanced conformational resampling method for protein structure prediction. IEEE Transactions on NanoBioscience. DOI:10.1109/TNB.2019.2922101, 2019.

  • Guijun Zhang, Tengyu Xie, Xiaogen Zhou, Liujing Wang, and Jun Hu. Protein structure prediction using population-based algorithm guided by information entropy. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2019.2921958, 2019.

  • Guijun Zhang, Xiaoqi Wang, Laifa Ma, Liujing Wang, Jun Hu, and Xiaogen Zhou. Two-stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2019.2917452, 2019.

  • Xiaohu Hao, Guijun Zhang, and Xiaogen Zhou. Conformational space sampling method using multi-subpopulation differential evolution for De novo protein structure prediction . IEEE Transactions on NanoBioscience, 2017, 16(7): 618-633.

  • Xiaohu Hao, Guijun Zhang, Xiaogen Zhou, and Xufeng Yu. A Novel Method Using Abstract Convex Underestimation in Ab-initio Protein Structure Prediction for Guiding Search in Conformational Feature Space . IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016, 13(5): 887-900.

  • Xiaohu Hao, Guijun Zhang, and Xiaogen Zhou. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction . Computational biology and chemistry, 2018, 73(4):105-119.

  • Guijun Zhang and Xiaogen Zhou. Population-based global optimization algorithm using abstract convex underestimate . Control and Decision, 2015, 30(06): 1116-1120.

  • Liujing Wang, Guijun Zhang, and Xiaogen zhou. Adaptive multi-strategy differential evolution algorithm based on state estimation feedback, Acta Automatica Sinica, in press.

  • Guijun Zhang, Ming Chen, and Xiaogen Zhou. Two-stage differential evolution algorithm using dynamic niche radius for multimodal optimization, Control and Decision, 2016, 31(07): 1185-1191.

  • Guijun Zhang, Liujing Wang, Xiaogen Zhou, and Qing Ding. Differential evolution algorithm with conjugate enhancement strategy, Control and Decision, 2017, 32(07): 1313-1318.

  • Guijun Zhang, Xiaohu Hao, Xiaogen Zhou, and Chuanqing Qin. Ab-initio dynamic-step-size searching of protein conformational space, Journal of Jilin University, 2016, 46(2): 585-594.

  • Xiaohu Hao, Guijun Zhang, Xiaogen Zhou, and Chuanqing Qian. Protein conformational space optimization algorithm based on fragment-assembly, Computer Science, 2015, 42(03): 237-240.

  • Guijun Zhang, Hudong Xia, Xiaogen Zhou, and Beijin Zhang. Hybrid differential evolution based on tabu search algorithm for distribution network line planning, Computer Science, 2016, 43(10): 248-255.

Conference Papers
  • Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, Li Yu, and Dongwei Xu. Differential Evolution with multi-stage strategies for global optimization . IEEE Congress on Evolutionary Computation, 2016, 2550-2557, Canada.

  • Guijun Zhang, Dongwei Li, Xiaogen Zhou, and Dongwei Xu. Differential evolution with dynamic niche radius strategy for multimodal optimization . The 27th Chinese Control and Decision Conference, 2015, 3059-3064, Qingdao.

  • Guijun Zhang, Xufeng Yu, Xiaogen Zhou, and Xiaohu Hao. A population-based conformational optimal algorithm using replica-exchange in ab-initio protein structure prediction . The 28th Chinese Control and Decision Conference, 2016, 701-706, Yinchuan.

Patents

  • Guijun Zhang, Xiaogen Zhou, Xufeng Xu, Xiaohu Hao, and Liujing Wang. A conformational space sampling method based on the population-based multi-stage strategy, CN, ZL201610121504.8.

  • Guijun Zhang, Xiaogen Zhou, Liujing Wang, and Xiaohu Hao. A population-based Lipschitz underestimation method for the protein structure prediction, CN, ZL201610219089.X.

  • Guijun Zhang, Xiaogen Zhou, Xufeng Yu, and Xiaohu Hao. A centroid mutation differential evolution algorithm for protein structure prediction, CN, ZL201610390675.0.

  • Guijun Zhang, Xiaogen Zhou, Liujing Wang, and Xiaohu Hao. A multi-strategy population-based algorithm using local abstract convex supporting hyperplanes for protein structure prediction, CN, ZL201610884824.9.

  • Guijun Zhang, Xiaogen Zhou, Xufeng Yu, and Xiaohu Hao. A double-layer differential evolution with local Lipschitz hyperplanes for the protein structure prediction, CN, ZL201610265960.X.

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