发表论文 Journal Articles
2023

  • Jun Liu, Dong Liu, Guijun Zhang.
    DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes.
    Bioinformatics, In press, 2023.

  • Haitao Zhu, Yuhao Xia, Guijun Zhang.
    E2EDA: Protein domain assembly based on end-to-end deep learning.
    Journal of Chemical Information and Modeling, In press, 2023.

  • 刘栋，崔新月，王浩东，张贵军.
    蛋白质结构模型质量评估方法综述.
    物理学报, 录用, 2023.

  • Kailong Zhao, Fang Liang, Yuhao Xia, Minghua Hou, Guijun Zhang.
    Recent advances in protein folding pathway prediction through computational methods.
    Current Medicinal Chemistry, in press, 2023.

  • Jun Hu, Yuxuan Tang, Yu Zhou, Zhe Li, Bing Rao, Guijun Zhang.
    Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism.
    Journal of Chemical Information and Modeling, 2023.

  • Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang.
    Pathfinder: protein folding pathway prediction based on conformational sampling.
    PLOS Computational Biology, in press, 2023.

  • Jun Liu, Dong Liu, Guangxing He, Guijun Zhang.
    Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15.
    PROTEINS: Structure, Function, and Bioinformatics, 2023.

  • Guangxing He, Jun Liu, Dong Liu, Guijun Zhang.
    GraphGPSM: a global scoring model for protein structure using graph neural networks.
    Briefings in Bioinformatics, bbad219, 2023.

  • Jun Hu, Ming Dong, Yuxuan Tang, Guijun Zhang.
    Improving protein-protein interaction site prediction using deep residual neural network.
    Analytical Biochemistry, 115132, 2023.

  • Fengqi Ge, Chunxiang Peng, Xinyue Cui, Yuhao Xia, Guijun Zhang.
    Inter-domain distance prediction based on deep learning for domain assembly.
    Briefings in Bioinformatics, bbad100, 2023.

  • Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li, Guijun Zhang.
    Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.
    Communications Biology, 6: 243, 2023.

  • Jun Hu, Wenwu Zeng, Ningxin Jia, Muhammad Arif, Dongjun Yu, Guijun Zhang.
    Improving DNA-Binding protein prediction using three-part sequence-order feature extraction and a deep neural network algorithm.
    Journal of Chemical Information and Modeling, 63(3): 1044-1057, 2023.

2022

  • Jun Liu, Kailong Zhao, Guijun Zhang.
    Improved model quality assessment using sequence and structural information by enhanced deep neural networks.
    Briefings in Bioinformatics, 24(1): bbac507, 2022.

  • Chunxiang Peng, Xiaogen Zhou, Yuhao Xia, Jun Liu, Minghua Hou, Guijun Zhang.
    Structural analogue-based protein structure domain assembly assisted by deep learning.
    Bioinformatics, 38(19): 4513-4521, 2022.

  • 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), 51(06):820-829, 2022.

  • Zhongze Yu, Chunxiang Peng, Jun Liu, Biao Zhang, Xiaogen Zhou, Guijun Zhang.
    DomBpred: protein domain boundary prediction based on domain-residue clustering using inter-residue distance.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022.

  • 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, 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(10): 2326-2353, 2022. [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]

  • Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Guijun Zhang.
    Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.
    Briefings in Bioinformatics, 23(2): bbac026, 2022.

  • Qiongqiong Feng, Minghua Hou, Jun Liu, Kailong Zhao, Guijun Zhang.
    Construct a variable-length fragment library for de novo protein structure prediction.
    Briefings in Bioinformatics, 23(3): bbac086, 2022.

  • 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.

  • Rao Liang, Ningxin Jia, Jun Hu, Dongjun Yu, Guijun Zhang.
    ATPdock: a template-based method for ATP-specific protein-ligand docking.
    Bioinformatics. 38(2), 556-558, 2022.

  • 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.

  • 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.

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, 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.

  • 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.

  • 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, 61(1): 605-515, 2021

  • Jun Hu, Yansong Bai, Linlin Zheng, Ningxin Jia, Dongjun Yu, Guijun Zhang.
    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, in press, 2021.

  • Xueqiang Fan, Jun Hu, Ningxin Jia, Dongjun Yu, Guijun Zhang.
    Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework.
    Analytical Biochemistry, 631: 114358, 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, 626: 114241, 2021.

  • Liujing Wang, Xiaogen Zhou, Tengyu Xie, Jun Liu, Guijun Zhang.
    Information entropy-based mutation strategy adaptive differential evolution.
    IEEE Access, 9: 146783-146796, 2021.

  • 张贵军, 刘俊, 赵凯龙.
    基于片段组装的蛋白质结构预测方法综述.
    数据采集与处理, 36(4): 629-638, 2021.

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.

  • 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, 36(24): 4217-4219, 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.

  • 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, 2020.

  • Jun Hu, Xiaogen Zhou, Yihen 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, 2020.

  • 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.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Qi Xuan, Guijun Zhang.
    An urban commuters' OD hybrid prediction method based on big GPS data.
    Chaos, 30(9): 093128-1~9, 2020.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Guijun Zhang.
    Analysis of road travel behavior based on big trajectory data.
    IET Intelligent Transport Systems, 14(12): 1691-1703, 2020.

  • Jun Hu, Liang Rao, Xueqiang Fan, Guijun Zhang.
    Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model.
    Analytical Biochemistry, 604: 1-8, 2020.

  • 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.

  • 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.

2019
  • 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(32): 15930-15938, 2019. [Web Server]

  • Xiaogen Zhou, Guijun Zhang.
    Differential evolution with underestimation-based multimutation strategy.
    IEEE Transactions on Cybernetics, 49(4): 1353-1364, 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, 18(4): 567-577, 2019.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Guijun Zhang, Xuemei Xiao.
    Kernel PCA for road traffic data non-linear feature extraction.
    IET Intelligent Transport Systems, 13(8): 1291-1298, 2019.

  • Weifeng Chen, Yinyin Ren, Guijun Zhang, Lorenz T. Biegler.
    A simultaneous approach for singular optimal control based on partial moving grid.
    AIChE Journal, 65(6): e16584, 2019.

2012-2018
  • 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, 73: 105-119, 2018.

  • Yongdong Wang, Dongwei Xu, YunLu, Junyan Shen, Guijun Zhang.
    Compression algorithm of road traffic data in time series based on temporal correlation.
    IET Intelligent Transport Systems, 12(3): 177-185, 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.

  • Dongwei Xu, Yongdong Wang, Liming Jia, Guijun Zhang, Haifeng Guo.
    Compression Algorithm of Road Traffic Spatial Data Based on LZW Encoding.
    Journal of Advanced Transportation, 2017: 8182690, 2017.

  • 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.

  • 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.

  • 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.

  • 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, 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.

  • 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.