主要论文(#为第一作者,*为通信作者)
[1] Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang(张贵军)*, Yang Zhang*. Assembling multidomain protein structures through analogous global structural alignments. PNAS, 116(32): 15930-15938, 2019.
[2] Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang(张贵军), Yang Zhang*. I-TASSER-MTD: A deep-learning based platform for multi-domain protein structure and function prediction. Nature Protocols, in press, 2022.
[3] Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang(张贵军), Yang Zhang*. Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature Computational Science, in press, 2022.
[4] Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li*, Guijun Zhang(张贵军)*. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications Biology. In press, 2023.
[5] Xiaogen Zhou#, Chunxiang Peng#, Wei Zheng, Yang Li, Guijun Zhang(张贵军)*, Yang Zhang*. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research, in press, 2022.
[6] Chunxiang Peng#, Xiaogen Zhou#, Yuhao Xia, Jun Liu, Minghua Hou, Guijun Zhang(张贵军)*. Structural analogue-based protein structure domain assembly assisted by deep learning. Bioinformatics, In press, 2022.
[7] Jun Liu, Kailong Zhao, Guangxing He, Liujing Wang, Xiaogen Zhou, Guijun Zhang(张贵军)*. A de novo protein structure prediction by iterative partition sampling, topology adjustment, and residue-level distance deviation optimization. Bioinformatics. 38(1): 99-107, 2022.
[8] Jun Liu, Xiaogen Zhou, Yang Zhang*, Guijun Zhang(张贵军)*. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics. 36(8): 2443–2450, 2020.
[9] Saisai Guo#, Jun Liu#, Xiaogen Zhou, Guijun Zhang(张贵军)* . DeepUMQA: Ultrafast shape recognition-based protein model quality assessment using deep learning. Bioinformatics. 38(7): 1895-1903, 2022.
[10] Kailong Zhao, Jun Liu, Xiaogen Zhou, Jianzhong Su*, Yang Zhang*, Guijun Zhang(张贵军)*. MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics. 37(23): 4350-4356, 2021.
[11] Yuhao Xia, Chunxiang Peng, Xiaogen Zhou, Guijun Zhang(张贵军)*. A sequential niche multimodal conformational sampling algorithm for protein structure prediction. Bioinformatics. 37(23): 4357-4365, 2021.
[12] Rao Liang, Ningxin Jia, Jun Hu*, Dongjun Yu*, Guijun Zhang(张贵军)*. ATPdock: a template-based method for ATP-specific protein-ligand docking. Bioinformatics. DOI: 10.1093/bioinformatics/btab667, 2021.
[13] Yan Zhang#, Yaru Zhang#, Jun Hu#, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang(张贵军)*, Fulong Yu*, Jianzhong Su*. scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures. Bioinformatics. DOI: 10.1093/bioinformatics/btaa532, 2020.
[14] Fengqi Ge, Chunxiang Peng, Xinyue Cui, Yuhao Xia, Guijun Zhang(张贵军)*. Inter-domain distance prediction based on deep learning for domain assembly. Briefings in Bioinformatics, In press, 2023.
[15] Jun Liu, Kailong Zhao, Guijun Zhang(张贵军)*. Improved model quality assessment using sequence and structural information by enhanced deep neural networks. Briefings in Bioinformatics, In press, 2022.
[16] Qiongqiong Feng#, Minghua Hou#, Jun Liu, Kailong Zhao, Guijun Zhang(张贵军)* . Construct a variable-length fragment library for de novo protein structure prediction. Briefings in Bioinformatics. DOI: 10.1093/bib/bbac086, 2022.
[17] Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen*, Guijun Zhang(张贵军)*. Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. Briefings in Bioinformatics. DOI: 10.1093/bib/bbac026, 2022.
[18] Minghua Hou, Chunxiang Peng, Xiaogen Zhou, Biao Zhang, Guijun Zhang(张贵军)*. Multi contact-based folding method for de novo protein structure prediction. Briefings in Bioinformatics. DOI: 10.1093/bib/bbab463, 2021.
[19] Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang(张贵军)*. Distance-guided protein folding based on generalized descent direction. Briefings in Bioinformatics. 22(6): bbab296, DOI: 10.1093/bib/bbab296, 2021.
[20] Chunxiang Peng, Xiaogen Zhou, Guijun Zhang(张贵军)*. De novo protein structure prediction by coupling contact with distance profile. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1): 395-406, 2022.
[21] Guijun Zhang(张贵军)*, 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.
[22] Jun Hu, Yansong Bai, Linlin Zheng, Ningxin Jia, Dongjun Yu*, Guijun Zhang(张贵军)*. Protein-DNA binding residue prediction via bagging strategy and sequence-based cube-format feature. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB.2021.3123828, 2021.
[23] Guijun Zhang(张贵军)*, 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, 2020.
[24] Guijun Zhang(张贵军)*, 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.
[25] Jun Hu, Xiaogen Zhou, Yihen Zhu, Dongjun Yu*, Guijun Zhang(张贵军)*. 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, 2020.
[26] Zhongze Yu#, Chunxiang Peng#, Jun Liu, Biao Zhang, Xiaogen Zhou, Guijun Zhang(张贵军)*. DomBpred: protein domain boundary prediction based on domain-residue clustering using inter-residue distance. IEEE/ACM Transactions on Computational Biology and Bioinformatics, In press, 2022.
[27] Guijun Zhang(张贵军)*, 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
[28] Xiaohu Hao, Guijun Zhang(张贵军)*, 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
[29] Zhangwei Li, Ke Sun, Xiaohu Hao, Jun Hu, Laifa Ma, Xiaogen Zhou, Guijun Zhang(张贵军)*. Loop enhanced conformational resampling method for protein structure prediction. IEEE Transactions on NanoBioscience. 18(4): 567-577. 2019.
[30] Xiaohu Hao, Guijun Zhang (张贵军)*, 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
[31] Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang*, Guijun Zhang(张贵军)*. Underestimation-assisted global-local cooperative differential evolution and the application to protein structure prediction. IEEE Transactions on Evolutionary Computation. 24(3): 536-550, 2020.
[32] Xiaogen Zhou, Guijun Zhang(张贵军)*. Differential evolution with underestimation- based multimutation strategy. IEEE Transactions on Cybernetics, 49(4): 1353-1364, 2019.
[33] Xiaogen Zhou, Guijun Zhang(张贵军)*. Abstract convex underestimation assisted multistage differential evolution. IEEE Transactions on Cybernetics, 47(9): 2730-2741, 2017
[34] Jun Hu*, Wenwu Zeng, Ningxin Jia, Muhammad Arif, Dongjun Yu*, Guijun Zhang(张贵军)*. Improving DNA-Binding protein prediction using three-part sequence-order feature extraction and a deep neural network algorithm. Journal of Chemical Information and Modeling. In press, 2023.
[35] Jun Hu*, Liang Rao, Yiheng Zhu, Guijun Zhang(张贵军)*, 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.
[36] 张贵军*, 侯铭桦, 彭春祥, 刘俊. 多结构域蛋白质结构预测方法综述. 电子科技大学学报(自科版). In press, 2022.
[37] 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
[38] 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.
[39] 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.
[40] 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.
[41] 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.
[42] 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, 37(11): 2398-2412, 2020.
[43] 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.
[44] 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.
[45] 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
[46] 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.
[47] 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.
[48] 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
[49] 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.
[50] 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.
奖励:
1. 蛋白质多结构域折叠机理及全链建模方法,中国自动化学会自然科学二等奖,完成人:张贵军,周晓根,张彪,2022.11.24
2. 蛋白质构象空间优化及多域蛋白质建模方法,浙江省生物信息学学会自然科学一等奖,完成人:张贵军,周晓根,张彪,2022.12.4
3. 蛋白质结构预测大赛CASP15复合物界面接触残基精度评估赛道冠军(第一名),2022.12.10,
4. 模型质量评估算法DeepUMQA,获得国际CAMEO竞赛年度冠军