Intelligent System Optimization and Bioinformatics Laboratory      IOBIOLabs

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  • 张贵军，陈铭. WebGIS工程项目开发实践， 清华大学出版社, 2016.
  • paper
  • Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang* Distance-guided protein folding based on generalized descent direction. Briefings in Bioinformatics. DOI: bbab296, 2021.
  • Yuhao Xia, Chunxiang Peng, Xiaogen Zhou, Guijun Zhang*, A sequential niche multimodal conformational sampling algorithm for protein structure prediction. Bioinformatics. DOI: 10.1093/bioinformatics/btab500, 2021.
  • 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. DOI: 10.1093/bioinformatics/btab484, 2021.
  • Guijun Zhang*, Tengyu Xie, Xiaogen Zhou, Liujing Wang, 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.
  • Jun Hu*, Liang Rao, Yiheng Zhu, Guijun Zhang*, Dongjun Yu*, TargetDBP+: Enhancing the performance of identifying DNA-binding proteins via weighted convolutional features. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.0c00735, 2021.
  • Jun Hu*, Linlin Zhen, Yansong Bai, Kewen Zhang, Dongjun Yu*, Guijun Zhang*, Accurate prediction of protein-ATP binding residues using position-specific frequency matrix. Analytical Biochemistry. DOI: 10.1016/j.ab.2021.114241, 2021.
  • Yan Zhang#, Yaru Zhang#, Jun Hu#, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang*, Fulong Yu*, Jianzhong Su*. scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures. Bioinformatics. DOI: 10.1093/bioinformatics/btaa532, 2020.
  • Chunxiang Peng, Xiaogen Zhou, Guijun Zhang*. De novo protein structure prediction coupling contact with distance profile. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2020.
  • 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.
  • 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.
  • Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang*, Yang Zhang*. Assembling multi-domain protein structures through analogous global structural alignments. PNAS, 116(32): 15930-15938, 2019.
  • 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. DOI: 10.1109/TNB.2019.2922101, 2019
  • 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. DOI: 10.1109/TCBB. 2019.2917452, 2019.
  • Weifeng Chen, Yinyin Ren, Guijun Zhang, Lorenz T. Biegler*. A simultaneous approach for singular optimal control based on partial moving grid. AIChE Journal. DOI:10.1002/aic.16584, 2019.
  • Jun Hu, Xiao-Gen Zhou, Yi-Heng Zhu, Dong-Jun Yu*, Guijun Zhang*. TargetDBP: Accurate DNA-Binding Protein Prediction via Sequence-based Multi-View Feature Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2019.2893634, 2019. [Web Server]
  • Xiaogen Zhou,Guijun Zhang*. Differential evolution with underestimation-based multimutation strategy. IEEE Transactions on Cybernetics, 49(4): 1353-1364, 2019.
  • 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. DOI: 10.1109/TCBB.2018.2873691, 2018.
  • 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, DOI: 10.1016/j.compbiolchem.2018.02.003, 2018.
  • Xiaogen Zhou, Guijun Zhang*. Abstract convex underestimation assisted multistage differential evolution. IEEE Transactions on Cybernetics, 47(9): 2730-2741, 2017.
  • Guijun Zhang*, Xiaogen Zhou, Xufeng Yu, Xiaohu Hao. Li Yu. Enhancing protein conformational space sampling using distance profile-guided differential evolution, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(6): 1288-1301, 2017.
  • 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
  • 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, 2016.
  • Xiaogen Zhou, Guijun Zhang*, Xiaohu Hao, Li Yu. A novel differential evolution algorithm using abstract convex underestimate strategy for global optimization, Computers & Operations Research, 75(11): 132-149, 2016.
  • Xiaogen Zhou, Guijun Zhang*, Xiaohu Hao. Li Yu, Enhanced differential evolution using local Lipschitz underestimate strategy for computationally expensive optimization problems, Applied Soft Computing, 48(11): 169-181, 2016.
  • Guijun Zhang*, Li Yu, Qike Shao. Hybrid algorithm for more accurate global optimization of continuous multimodal function, Dynamics of Continuous Discrete and Impulsive Systems-Series A-Mathematical Analysis, 13(2) : 983-990, 2006.
  • Guijun Zhang*, Li Yu, Qike Shao. Continuous global optimization using enhanced differential evolution algorithm, Dynamics of Continuous Discrete and Inpulsive System-Series B-Application and Algorithms, 13(5): 2503-2508, 2006.
  • Guijun Zhang*, Tihua Wu, Rong Ye. Global optimization over linear constraint non-convex programming problem, Journal of Harbin Institute of Technology, 12(6): 650-655, 2005.
  • Guijun Zhang*, Tihua Wu, Rong Ye. Global optimization of pump configuration problem using extended crowding genetic algorithm, Chinese Journal of Mechanical Engineering, 17(2): 247-252, 2004.
  • 武楚雄, 陈驰，张贵军*. 动态路网选址-路径优化算法及实现, 控制理论与应用, 2020年，录用.
  • 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, 2018年，录用.
  • 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.
  • 张贵军*, 何洋军, 郭海锋, 冯远静, 徐建明. 基于广义凸下界估计的多模态差分进化算法, 软件学报, 24(6): 1177?1195, 2013.
  • 吴海涛, 张贵军*, 洪榛, 俞立. 进化树拓扑路网构建及多停靠点路径规划方法研究, 计算机学报, 35(5):964-971, 2012.
  • 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.
  • 邓勇跃, 张贵军*. 基于局部抽象凸支撑面的多模态优化算法, 控制理论与应用, 31(4): 458-466, 2014.
  • 张贵军*, 洪榛, 俞立, 郭海锋. 调速泵结构配置协调分解优化算法及实现, 控制理论与应用, 28(5): 659-666, 2011.
  • 张贵军*, 王信波, 俞立, 冯远静. 求解高维多模优化问题的自适应差分进化算法, 控制理论与应用, 25(3): 862-867, 2008.
  • 张贵军*, 俞立, 吴惕华. 线性约束非线性函数全局优化算法的研究, 控制理论与应用, 22(1): 1-6, 2005.
  • 张贵军*, 王柳静,周晓根, 丁情. 基于共轭增强策略的差分进化算法, 控制与决策，32(07): 1313-1318, 2017.
  • 张贵军*, 陈铭, 周晓根. 动态小生境半径两阶段多模态差分进化算法, 控制与决策, 31(07): 1185-1191, 2016.
  • 张贵军*, 周晓根. 基于抽象凸下界估计的群体全局优化算法, 控制与决策, 30(06): 1116-1120, 2015.
  • 张贵军*, 郝小虎, 周晓根, 秦传庆.动态步长蛋白质构象空间搜索方法, 吉林大学学报, 46(2): 585-594, 2016.
  • 张贵军*, 吴惕华. 三级泵优化配置问题算法设计与求解, 上海交通大学学报, 39(2): 1984-1987, 2005.
  • 张贵军*, 吴惕华. CTSP问题稳态小生境算法的研究及仿真实现, 系统仿真学报, 16(8): 1692-1696, 2004.
  • 张贵军*, 吴惕华. GIS线性矢量图形最优路径算法研究及仿真实现, 系统仿真学报, 15(4) : 551-553,2003.
  • Proceedings
  • Xiaogen Zhou, Guijun Zhang*. Double estimation of distribution guided sampling algorithm for De-novo protein structure prediction, CCC,大连, 9853-9858. 2017.
  • Xiaogen Zhou, Guijun Zhang*, Xiaohu Hao, Li Yu, Dongwei Xu. Differential Evolution with multi-stage strategies for global optimization. IEEE Congress on Evolutionary Computation, 2016 7.24~29. Canada, 2016.
  • Guijun Zhang*, Xufeng Yu, Xiaogen Zhou, Xiaohu Hao. A population-based conformational optimal algorithm using replica-exchange in ab-initio protein structure prediction, Chinese Control and Decision Conference (CCDC2016), 2016.

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