Xiaogen Zhou's Homepage

周晓根，博士，2018年毕业于浙江工业大学信息工程学院师从俞立教授和张贵军教授， 2018至2021年于密西根大学张阳实验室从事博士 后研究工作，2022年聘任为浙江工业大学运河青年学者特聘教授。主要研究方向为结构生物信息 学、计算智能及深度学习。第一作者在PNAS、Nature Computational Science、Nature Protocols、 Nucleic Acids Research、Bioinformatics、IEEE-TEVC、IEEE-TCYB等期刊发表论文15篇；授权 国家发明专利12项；承担和参与国家自然科学基金青年项目、国家重点研发等项目5项；开发了 DEMO、DEMO-EM和I-TASSER-MTD等多域蛋白质结构建模和功能预测服务器，为来自70多个国家和 地区的用户提供了超过上万次服务；相关成果获得了中国自动化学会自然科学二等奖、浙江省生 物信息学学会自然科学一等奖、浙江省优秀博士学位论文奖；入选国家高层次青年人才计划项目。

发表论文 Journal Articles

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

  • 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]

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

  • Xiaogen Zhou, Guijun Zhang. Differential evolution with underestimation-based multimutation strategy. IEEE Transactions on Cybernetics, 49(4): 1353-1364, 2019.

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

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

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

  • 周晓根, 张贵军, 郝小虎, 俞立. 一种基于局部Lipschitz下界估计支撑面的差分进化算法. 计算机学报, 39(12): 2631-2651, 2016.

  • 周晓根, 张贵军, 郝小虎. 局部抽象凸区域剖分差分进化算法. 自动化学报, 41(7): 1315-1327, 2015.

  • 周晓根, 张贵军, 梅珊, 明洁. 基于抽象凸估计选择策略的差分进化算法. 控制理论与应用, 32(03): 388-397, 2015.

  • Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, and Yang Zhang. FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, 36(12): 3749-3757, 2020.

  • Jun Liu, Xiaogen Zhou, Yang Zhang, Guijun Zhang. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics, 36(8): 2443-2450, 2020.

  • Kailong Zhao, Jun Liu, Xiaogen Zhou, Jianzhong Su, Yang Zhang, Guijun Zhang. MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics, 37(23): 4350-4356, 2021.

  • Yuhao Xia, Chunxiang Peng, Xiaogen Zhou, Guijun Zhang. A sequential niche multimodal conformational sampling algorithm for protein structure prediction. Bioinformatics, 37(23): 4357-4365, 2021.

  • Saisai Guo, Jun Liu, Xiaogen Zhou, Guijun Zhang. DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning. Bioinformatics, 38(7): 1895-1903, 2022.

  • Jun Liu, Kailong Zhao, Guangxing He, Liujing Wang, Xiaogen Zhou, Guijun Zhang. A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. Bioinformatics, 38(1): 99-107, 2022.

  • Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang. Distance-guided protein folding based on generalized descent direction. Briefings in Bioinformatics, 22(6): bbab296, 2021.

  • Minghua Hou, Chunxiang Peng, Xiaogen Zhou, Biao Zhang, Guijun Zhang. Multi contact-based folding method for de novo protein structure prediction. Briefings in Bioinformatics, 23(1): bbab463, 2022.

  • Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L. Freddolino, and Yang Zhang. LOMETS3: Integrating deep learning and profile-alignment for advanced protein template recognition and function annotation. Nucleic Acids Research, https://doi.org/10.1093/nar/gkac248, in press, 2022.

  • Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dongjun Yu, Yang Zhang. Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLOS Computational Biology, 17(3): e1008865, 2021.

  • Chunxiang Peng, Xiaogen Zhou, Guijun Zhang. De novo protein structure prediction by coupling contact with distance profile. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1): 395-406, 2022.

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

  • Jun Hu, Xiaogen Zhou, Yiheng Zhu, Dongjun Yu, Guijun Zhang. TargetDBP: accurate DNA-binding protein prediction via sequence-based multi-view feature learning. IEEE/ACM transactions on computational biology and bioinformatics, 17(4):1419-1429, 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, 18(2): 697-707, 2021.

  • Xiaohu Hao, Guijun Zhang, Xiaogen Zhou, 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, 13(5): 887-900, 2015.

  • Guijun Zhang, Laifa Ma, Xiaoqi Wang, Xiaogen Zhou. Secondary structure and contact guided differential evolution for protein structure prediction. IEEE/ACM transactions on computational biology and bioinformatics, 17(3): 1068-1081, 2020.

  • Guijun Zhang, Xiaoqi Wang, Laifa Ma, Liujing Wang, Jun Hu, Xiaogen Zhou. Two-stage distance feature-based optimization algorithm for de novo protein structure prediction. IEEE/ACM transactions on computational biology and bioinformatics, 17(6): 2119-2130, 2019.

  • Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang. Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of proteome research, 19(4): 1351-1360, 2020.

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

  • Zhangwei Li, Ke Sun, Xiaohu Hao, Jun Hu, Laifa Ma, Xiaogen Zhou, Guijun Zhang. Loop enhanced conformational resampling method for protein structure prediction. IEEE Transactions on NanoBioscience, 18(4): 567-577, 2019.

  • Wei Zheng, Yang Li, Chengxin Zhang, Xiaogen Zhou, Robin Pearce, Eric W. Bell, Xiaoqiang Huang, Yang Zhang. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12): 1734-1751, 2021.

  • Yang Li, Chengxin Zhang, Wei Zheng, Xiaogen Zhou, Eric W. Bell, Dongjun Yu, Yang Zhang. Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12): 1911-1921, 2021.

  • Pithadia, A., H. Trzeciakiewicz, E. V. Crowley, R. Pacitto, Nathaniel Safren, Xiaogen Zhou, Y. Zhang, V. Basrur, H. Paulson, and L. M. Sharkey. RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cellular and Molecular Life Sciences, 79(3): 176, 2022.

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

  • 王柳静, 张贵军, 周晓根. 基于状态估计反馈的策略自适应差分进化算法. 自动化学报, 46(4): 752-766, 2020.

发明专利 Patents

  • 周晓根, 张贵军, 彭春祥, 胡俊. 一种基于域间残基接触的多域蛋白结构组装方法, 2021.02(授权日), 中国, 授权号: ZL201910316906.7.

  • 周晓根, 张贵军, 彭春祥, 胡俊, 刘俊. 一种基于子种群协同进化的蛋白质结构预测方法. 2021.04(授权日), 中国, 授权号: ZL201810762887.6.

  • 周晓根, 张贵军, 彭春祥, 刘俊, 胡俊. 一种基于动态抽象凸下界估计的群体蛋白质结构预测方法. 2021.03(授权日), 中国, 授权号: ZL201810994503.3.

  • 周晓根, 张贵军, 彭春祥, 胡俊, 刘俊. 一种基于动态片段长度的群体蛋白质结构预测方法, 2021.04(授权日),中国, 授权号: ZL201810986058.6.

  • 周晓根, 张贵军, 彭春祥, 刘俊, 胡俊. 一种基于抽象凸估计的k-近邻蛋白质结构预测方法, 2020.06(授权日), 中国, 授权号: ZL201811000827.7.

  • 张贵军, 周晓根, 王柳静, 郝小虎, 俞旭峰, 徐东伟, 李章维. 一种基于群体Lipschitz下界估计的蛋白质结构预测方法. 2018.04 (授权日), 中国, 授权号: ZL201610219089.X.

  • 张贵军, 周晓根, 张贵军, 彭春祥, 刘俊, 胡俊, 王柳静. 一种基于简约抽象凸估计的蛋白质构象空间优化方法. 2021.06 (授权日)，中国, 授权号: ZL201810584219.9.

  • 张贵军, 周晓根, 俞旭锋, 郝小虎, 王柳静, 徐东伟, 李章维. 一种基于局部Lipschitz支撑面的双层差分进化蛋白质结构预测方法, 2018.09(授权日), 中国, 授权号: ZL201610265960.X.

  • 张贵军, 周晓根, 王柳静, 郝小虎, 俞旭锋, 李章维. 一种基于局部抽象凸支撑面的多策略群体蛋白质结构预测方法. 2019.01(授权日) , 中国, 授权号: ZL201610884824.9.

  • 张贵军, 周晓根, 郝小虎, 王柳静, 俞旭锋, 徐东伟, 李章维. 一种基于抽象凸估计的多阶段差分进化蛋白质结构预测方法. 2019.07(授权日), 中国, 授权号: ZL201610845314.0.