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Journal Articles
- 2024
[j63]Chunxiang Peng, Fang Liang, Yuhao Xia, Kai-Long Zhao, Minghua Hou, Gui-Jun Zhang:
Recent Advances and Challenges in Protein Structure Prediction. J. Chem. Inf. Model. 64(1): 76-95 (2024)- 2023
- [j62]Jun Liu, Kai-Long Zhao, Guijun Zhang
:
Improved model quality assessment using sequence and structural information by enhanced deep neural networks. Briefings Bioinform. 24(1) (2023) - [j61]Fengqi Ge, Chunxiang Peng, Xinyue Cui, Yuhao Xia, Guijun Zhang:
Inter-domain distance prediction based on deep learning for domain assembly. Briefings Bioinform. 24(3) (2023) - [j60]Guang-Xing He, Jun Liu, Dong Liu, Guijun Zhang:
GraphGPSM: a global scoring model for protein structure using graph neural networks. Briefings Bioinform. 24(4) (2023) - [j59]Dong Liu, Biao Zhang, Jun Liu, Hui Li, Le Song, Guijun Zhang:
Assessing protein model quality based on deep graph coupled networks using protein language model. Briefings Bioinform. 25(1) (2023) - [j58]Jun Liu, Dong Liu, Gui-Jun Zhang:
DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes. Bioinform. 39(10) (2023) - [j57]Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang:
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. J. Chem. Inf. Model. 63(3): 1044-1057 (2023) - [j56]Jun Hu, Yu-Xuan Tang, Yu Zhou, Zhe Li, Bing Rao, Gui-Jun Zhang:
Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism. J. Chem. Inf. Model. 63(17): 5689-5700 (2023) - [j55]Hai-Tao Zhu, Yuhao Xia, Gui-Jun Zhang:
E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning. J. Chem. Inf. Model. 63(20): 6451-6461 (2023) - [j54]Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang:
Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS Comput. Biol. 19(9) (2023) - [j53]Lai-Zhen Luo, Yu Xia, Gui-Jun Zhang:
Mutually unbiased maximally entangled bases in Cdøtimes Cd with d an odd prime power. Quantum Inf. Process. 22(11): 415 (2023) - [j52]Zhong-Ze Yu, Chunxiang Peng, Jun Liu, Biao Zhang, Xiao-Gen Zhou, Gui-Jun Zhang:
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance. IEEE ACM Trans. Comput. Biol. Bioinform. 20(2): 912-922 (2023) - 2022
- [j51]Minghua Hou, Chunxiang Peng, Xiaogen Zhou, Biao Zhang, Guijun Zhang:
Multi contact-based folding method for de novo protein structure prediction. Briefings Bioinform. 23(1) (2022) - [j50]Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Gui-Jun Zhang:
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. Briefings Bioinform. 23(2) (2022) - [j49]Qiongqiong Feng, Minghua Hou, Jun Liu, Kai-Long Zhao, Guijun Zhang:
Construct a variable-length fragment library for de novo protein structure prediction. Briefings Bioinform. 23(3) (2022) - [j48]Liang Rao, Ning-Xin Jia, Jun Hu, Dong-Jun Yu, Gui-Jun Zhang:
ATPdock: a template-based method for ATP-specific protein-ligand docking. Bioinform. 38(2): 556-558 (2022) - [j47]Sai-Sai Guo, Jun Liu, Xiao-Gen Zhou, Gui-Jun Zhang:
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning. Bioinform. 38(7): 1895-1903 (2022) - [j46]Chunxiang Peng, Xiao-Gen Zhou, Yuhao Xia, Jun Liu, Minghua Hou, Gui-Jun Zhang:
Structural analogue-based protein structure domain assembly assisted by deep learning. Bioinform. 38(19): 4513-4521 (2022) - [j45]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 Res. 50(W1): 235-245 (2022) - [j44]Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang:
Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nat. Comput. Sci. 2(4): 265-275 (2022) - [j43]Chunxiang Peng, Xiao-Gen Zhou, Gui-Jun Zhang:
De novo Protein Structure Prediction by Coupling Contact With Distance Profile. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 395-406 (2022) - [j42]Jun Hu, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang:
Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3635-3645 (2022) - 2021
- [j41]Liujing Wang, Xiaogen Zhou, Tengyu Xie, Jun Liu, Guijun Zhang:
Adaptive Differential Evolution With Information Entropy-Based Mutation Strategy. IEEE Access 9: 146783-146796 (2021) - [j40]Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang:
Distance-guided protein folding based on generalized descent direction. Briefings Bioinform. 22(6) (2021) - [j39]Kai-Long Zhao, Jun Liu, Xiao-Gen Zhou, Jianzhong Su, Yang Zhang, Gui-Jun Zhang:
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinform. 37(23): 4350-4356 (2021) - [j38]Yuhao Xia, Chunxiang Peng, Xiao-Gen Zhou, Gui-Jun Zhang:
A sequential niche multimodal conformational sampling algorithm for protein structure prediction. Bioinform. 37(23): 4357-4365 (2021) - [j37]Jun Liu, Kai-Long Zhao, Guang-Xing He, Liu-Jing Wang, Xiao-Gen Zhou, Gui-Jun Zhang:
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. Bioinform. 38(1): 99-107 (2021) - [j36]Lin Liu, Yapeng Zhou, Haikui Yin, Ruiqiang Zhang, Ying Ma, Guijun Zhang, Pengfei Zhao, Jinxiong Feng:
Improving Land Use Planning through the Evaluation of Ecosystem Services: One Case Study of Quyang County. Complex. 2021: 3486138:1-3486138:13 (2021) - [j35]Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu:
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. J. Chem. Inf. Model. 61(1): 505-515 (2021) - [j34]Zhangwei Li, Anshun Hu, Xiaofei Wang, Jun Hu, Guijun Zhang:
Learning to capture dependencies between global features of different convolution layers. J. Vis. Commun. Image Represent. 81: 103360 (2021) - [j33]Gui-Jun Zhang, Tengyu Xie, Xiao-Gen Zhou, Liu-Jing Wang, Jun Hu:
Protein Structure Prediction Using Population-Based Algorithm Guided by Information Entropy. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 697-707 (2021) - 2020
- [j32]Jun Liu, Xiao-Gen Zhou, Yang Zhang, Gui-Jun Zhang:
CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinform. 36(8): 2443-2450 (2020) - [j31]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. Bioinform. 36(14): 4217-4219 (2020) - [j30]Guijun Zhang:
Automatic generation of Chinese abstract based on vocabulary and LSTM neural network. Int. J. Wirel. Mob. Comput. 19(3): 241-248 (2020) - [j29]Tengyu Xie, Xiaogen Zhou, Jun Hu, Guijun Zhang:
基于接触图残基对距离约束的蛋白质结构预测算法 (Contact Map-based Residue-pair Distances Restrained Protein Structure Prediction Algorithm). 计算机科学 47(1): 59-65 (2020) - [j28]Gui-Jun Zhang, Lai-Fa Ma, Xiao-Qi Wang, Xiaogen Zhou:
Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 17(3): 1068-1081 (2020) - [j27]Jun Hu, Xiaogen Zhou, Yi-Heng Zhu, Dong-Jun Yu, Gui-Jun Zhang:
TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 17(4): 1419-1429 (2020) - [j26]Gui-Jun Zhang, Xiao-Qi Wang, Lai-Fa Ma, Liu-Jing Wang, Jun Hu, Xiao-Gen Zhou:
Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 17(6): 2119-2130 (2020) - [j25]Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Gui-Jun Zhang:
Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. IEEE Trans. Evol. Comput. 24(3): 536-550 (2020) - 2019
- [j24]Zhangwei Li, Xiaohu Hao, Guijun Zhang:
蛋白质结构从头预测多级个体筛选进化算法 (Multi-layer Screening Based Evolution Algorithm for De Novo Protein Structure Prediction). 计算机科学 46(6A): 80-84 (2019) - [j23]Jing Zheng, Xiao Fu, Guijun Zhang:
Research on exchange rate forecasting based on deep belief network. Neural Comput. Appl. 31(S-1): 573-582 (2019) - [j22]Yongdong Wang, Dongwei Xu, Peng Peng, Qi Xuan, Gui-jun Zhang:
Analysis of Hospitalizing Behaviors Based on Big Trajectory Data. IEEE Trans. Comput. Soc. Syst. 6(4): 692-701 (2019) - [j21]Xiaogen Zhou, Gui-Jun Zhang:
Differential Evolution With Underestimation-Based Multimutation Strategy. IEEE Trans. Cybern. 49(4): 1353-1364 (2019) - 2018
- [j20]Xiao-hu Hao, Gui-jun Zhang, Xiaogen Zhou:
Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction. Comput. Biol. Chem. 73: 105-119 (2018) - [j19]Guijun Zhang, Qing Ding, Liujing Wang, Xiaogen Zhou:
柔性车间生产排产调度优化方法 (Optimization Method of Production Scheduling in Flexible Job). 计算机科学 45(2): 269-275 (2018) - [j18]Guijun Zhang, Wen Wang, Xiaogen Zhou, Liujing Wang:
基于动态策略的差分进化柔性车间优化调度 (Dynamic Strategy-based Differential Evolution for Flexible Job Shop Scheduling Optimization). 计算机科学 45(10): 240-245 (2018) - [j17]Yi-Fan Han, Gui-Jun Zhang, Xin-Lei Yong, Lingshan Xu, Yuan-Hong Tao:
Mutually unbiased special entangled bases with Schmidt number 2 in \({\mathbb {C}}^3 \otimes {\mathbb {C}}^{4k}\). Quantum Inf. Process. 17(3): 58 (2018) - [j16]Gui-Jun Zhang, Yuan-Hong Tao, Yi-Fan Han, Xin-Lei Yong, Shao-Ming Fei:
Unextendible maximally entangled bases in \({\mathbb {C}}^{pd}\otimes {\mathbb {C}}^{qd}\). Quantum Inf. Process. 17(11): 318 (2018) - 2017
- [j15]Zhangwei Li, Xiaohu Hao, Guijun Zhang:
基于副本交换的局部增强差分进化蛋白质结构从头预测方法 (Replica Exchange Based Local Enhanced Differential Evolution Searching Method in Ab-initio Protein Structure Prediction). 计算机科学 44(5): 211-217 (2017) - [j14]Gui-Jun Zhang, Xiaogen Zhou, Xufeng Yu, Xiao-hu Hao, Li Yu:
Enhancing Protein Conformational Space Sampling Using Distance Profile-Guided Differential Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 14(6): 1288-1301 (2017) - [j13]Xiaogen Zhou, Gui-Jun Zhang:
Abstract Convex Underestimation Assisted Multistage Differential Evolution. IEEE Trans. Cybern. 47(9): 2730-2741 (2017) - 2016
- [j12]Xiaogen Zhou, Gui-jun Zhang, Xiao-hu Hao, Dongwei Xu, Li Yu:
Enhanced differential evolution using local Lipschitz underestimate strategy for computationally expensive optimization problems. Appl. Soft Comput. 48: 169-181 (2016) - [j11]Xiaogen Zhou, Gui-jun Zhang, Xiao-hu Hao, Li Yu:
A novel differential evolution algorithm using local abstract convex underestimate strategy for global optimization. Comput. Oper. Res. 75: 132-149 (2016) - [j10]Guijun Zhang, Huadong Xia, Xiaogen Zhou, Beijin Zhang:
一种配电网络差分禁忌线路规划方法 (Hybrid Differential Evolution Based on Tabu Search Algorithm for Distribution Network Line Planning). 计算机科学 43(10): 248-255 (2016) - [j9]Xiao-hu Hao, Gui-jun 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 Trans. Comput. Biol. Bioinform. 13(5): 887-900 (2016) - 2015
- [j8]Xiaohu Hao, Guijun Zhang, Xiaogen Zhou, Zhenghua Cheng, Qipeng Zhang:
一种基于片段组装的蛋白质构象空间优化算法 (Protein Conformational Space Optimization Algorithm Based on Fragment-assembly). 计算机科学 42(3): 237-240 (2015) - [j7]Jie Ming, Guijun Zhang, Yudong Liu:
多模式公交组合调度优化模型 (Combinatorial Optimization Model of Multi-modal Transit Scheduling). 计算机科学 42(9): 263-267 (2015) - [j6]Hui Dong, Xiaohu Hao, Guijun Zhang:
蛋白质构象空间局部增强差分进化搜索方法 (Local Enhancement Differential Evolution Searching Method for Protein Conformational Space). 计算机科学 42(Z11): 22-26 (2015) - [j5]Zhangwei Li, Xiaogen Zhou, Guijun Zhang:
一种动态自适应差分进化算法 (Dynamic Adaptive Differential Evolution Algorithm). 计算机科学 42(Z6): 52-56 (2015) - [j4]Xianpao Chen, Guijun Zhang, Chuanqing Qin, Xiaohu Hao:
基于Monte Carlo局部增强的多模态优化算法 (Local Monte Carlo Search Approach to Multimodal Problem in Protein Conformation Space Optimization). 计算机科学 42(Z6): 61-66 (2015) - 2013
- [j3]Jianming Xu, Yurong Nan, Guijun Zhang, Linlin Ou, Hongjie Ni:
Delay-dependent H∞ Control for Uncertain 2-D Discrete Systems with State Delay in the Roesser Model. Circuits Syst. Signal Process. 32(3): 1097-1112 (2013) - [j2]Gaofeng Zou, Longmei Chen, Wei Liu, Xiaoxin Hong, Guijun Zhang, Ziyi Zhang:
Measurement and evaluation of Chinese regional energy efficiency based on provincial panel data. Math. Comput. Model. 58(5-6): 1000-1009 (2013) - 2007
- [j1]Yuanjing Feng, Li Yu, Gui-Jun Zhang:
Ant colony pattern search algorithms for unconstrained and bound constrained optimization. Appl. Math. Comput. 191(1): 42-56 (2007)
Conference and Workshop Papers
- 2019
- [c2]Chunxiang Peng, Xiaogen Zhou, Guijun Zhang:
Multi-subpopulation Algorithm with Ensemble Mutation Strategies for Protein Structure Prediction. BIC-TA (1) 2019: 255-268 - 2016
- [c1]Xiaogen Zhou, Gui-Jun Zhang, Xiao-hu Hao, Li Yu, Dongwei Xu:
Differential evolution with multi-stage strategies for global optimization. CEC 2016: 2550-2557
Informal and Other Publications
- 2022
- [i2]Wentao Kang, Guijun Zhang, Xiao Fu:
A Noise-Robust Loss for Unlabeled Entity Problem in Named Entity Recognition. CoRR abs/2208.02934 (2022) - 2021
- [i1]Xiao Fu, Guijun Zhang:
A More Efficient Chinese Named Entity Recognition base on BERT and Syntactic Analysis. CoRR abs/2101.11423 (2021)
Coauthor Index
Xiaogen Zhou
aka: Xiao-Gen Zhou
aka: Xiao-Gen Zhou
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