Improvement of the Needleman-Wunsch Algorithm. - Zhihua Du; Feng Lin (Rough Sets and Current Trends in Computing, 2004)

A hierarchical clustering algorithm for MIMD architecture. - Zhihua Du; Feng Lin (Comput. Biol. Chem., 2004)

Pattern-constrained multiple polypeptide sequence alignment. - Zhihua Du; Feng Lin (Comput. Biol. Chem., 2005)

Reconstruction of large phylogenetic trees: A parallel approach. - Zhihua Du; Feng Lin; Usman W. Roshan (Comput. Biol. Chem., 2005)

A novel parallelization approach for hierarchical clustering. - Zhihua Du; Feng Lin (Parallel Comput., 2005)

High performance computing for computational biology - Zhihua Du (2005)

Parallel Computing for Optimal Genomic Sequence Alignment. - Zhihua Du; Zhen Ji; Feng Lin (FSKD, 2006)

pNJTree: A parallel program for reconstruction of neighbor-joining tree and its application in ClustalW. - Zhihua Du; Feng Lin (Parallel Comput., 2006)

A New Algorithm for Reconstruction of Phylogenetic Tree. - Zhihua Du; Zhen Ji (AIRS, 2008)

Gene clustering using an evolutionary algorithm. - Zhihua Du; Yiwei Wang; Zhen Ji (IEEE Congress on Evolutionary Computation, 2008)

PK-means: A new algorithm for gene clustering. - Zhihua Du; Yiwei Wang; Zhen Ji (Comput. Biol. Chem., 2008)

Coloring and the Lovász Local Lemma. - Xing Chen; Zhihua Du; Jixiang Meng (Appl. Math. Lett., 2010)

Orthogonal trigonometric polynomials: Riemann-Hilbert analysis and relations with OPUC. - Zhihua Du; Jinyuan Du (Asymptot. Anal., 2012)

Efficiency-Aware Workload Optimizations of Heterogeneous Cloud Computing for Capacity Planning in Financial Industry. - Keke Gai; Zhihua Du; Meikang Qiu; Hui Zhao 002 (CSCloud, 2015)

A double-module immune algorithm for multi-objective optimization problems. - Zhengping Liang; Ruizhen Song; Qiuzhen Lin; Zhihua Du; Jianyong Chen; Zhong Ming 001; Jianping Yu (Appl. Soft Comput., 2015)

A novel multi-objective particle swarm optimization with multiple search strategies. - Qiuzhen Lin; Jianqiang Li 001; Zhihua Du; Jianyong Chen; Zhong Ming 001 (Eur. J. Oper. Res., 2015)

A novel hybrid differential evolution algorithm with modified CoDE and JADE. - Genghui Li; Qiuzhen Lin; Laizhong Cui; Zhihua Du; Zhengping Liang; Jianyong Chen; Nan Lu; Zhong Ming 001 (Appl. Soft Comput., 2016)

A novel multiple rule sets data classification algorithm based on ant colony algorithm. - Zhengping Liang; Jiangtao Sun; Qiuzhen Lin; Zhihua Du; Jianyong Chen; Zhong Ming 001 (Appl. Soft Comput., 2016)

A novel artificial bee colony algorithm with depth-first search framework and elite-guided search equation. - Laizhong Cui; Genghui Li; Qiuzhen Lin; Zhihua Du; Weifeng Gao; Jianyong Chen; Nan Lu (Inf. Sci., 2016)

Adaptive composite operator selection and parameter control for multiobjective evolutionary algorithm. - Qiuzhen Lin; Zhiwang Liu; Qiao Yan; Zhihua Du; Carlos A. Coello Coello; Zhengping Liang; Wenjun Wang 003; Jianyong Chen (Inf. Sci., 2016)

A novel adaptive hybrid crossover operator for multiobjective evolutionary algorithm. - Qingling Zhu; Qiuzhen Lin; Zhihua Du; Zhengping Liang; Wenjun Wang 003; Zexuan Zhu; Jianyong Chen; Peizhi Huang; Zhong Ming 001 (Inf. Sci., 2016)

A novel adaptive control strategy for decomposition-based multiobjective algorithm. - Qiuzhen Lin; Chaoyu Tang; Yueping Ma; Zhihua Du; Jianqiang Li 001; Jianyong Chen; Zhong Ming 001 (Comput. Oper. Res., 2017)

Quantitative Analysis of Blood Flow in Cerebral Venous Sinus With Stenosis by Patient-Specific CFD Modeling. - Xin Liu 023; Zhihua Du; Tao Han 004; Dhanjoo N. Ghista; Shi Lin; Vicky Wang; Jun Wang; Heye Zhang; Zhigeng Pan (IEEE Access, 2019)

DeepAdd: Protein function prediction from k-mer embedding and additional features. - Zhihua Du; Yufeng He; Jianqiang Li 001; Vladimir N. Uversky (Comput. Biol. Chem., 2020)

GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions. - Zhihua Du; Yang-Han Wu; Yu-An Huang; Jie Chen 027; Gui-Qing Pan; Lun Hu; Zhu-Hong You; Jian-Qiang Li 001 (Briefings Bioinform., 2022)

Inference of gene regulatory networks based on the Light Gradient Boosting Machine. - Zhihua Du; Xing Zhong; Fangzhong Wang; Vladimir N. Uversky (Comput. Biol. Chem., 2022)

MDCS with fully encoding the information of local shape description for 3D Rigid Data matching. - Zhihua Du; Yong Zuo; Jifang Qiu; Xiang Li 042; Yan Li 073; Hongxiang Guo; Xiaobin Hong 001; Jian Wu 010 (Image Vis. Comput., 2022)

DeepCLD: An Efficient Sequence-Based Predictor of Intrinsically Disordered Proteins. - Min Fang; Yufeng He; Zhihua Du; Vladimir N. Uversky (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Information Freshness and Energy Harvesting Tradeoff in Network-Coded Broadcasting. - Quanjia Ren; Tse-Tin Chan; Haoyuan Pan; Kin-Hon Ho; Zhihua Du (IEEE Wirel. Commun. Lett., 2022)

TFBSnet: A deep learning-based tool for predicting transcription factor binding site from DNA sequences. - Zhihua Du; Tianyou Huang; Jian-Qiang Li 001; Vladimir N. Uversky (BIBM, 2023)

A Deep Transfer Fusion Model for Recognition of Acute Lymphoblastic Leukemia with Few Samples. - Zhihua Du; Xin Xia; Min Fang; Li Yu; Jianqiang Li 001 (ICIC (2), 2023)

GeneSpider: Inferring Gene Regulation Relationships Through Graph Neural Network from Single-Cell RNA Sequence Data. - Zhihua Du; Xing Zhong; Min Fang; Jianqiang Li 001 (ICIC (3), 2023)

Knowledge graph embedding for profiling the interaction between transcription factors and their target genes. - Yang-Han Wu; Yu-An Huang; Jian-Qiang Li 001; Zhu-Hong You; Peng-Wei Hu 001; Lun Hu; Victor C. M. Leung; Zhihua Du (PLoS Comput. Biol., 2023)

Predicting TF Proteins by Incorporating Evolution Information Through PSSM. - Zhihua Du; Tianyou Huang; Vladimir N. Uversky; Jianqiang Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Improving Information Freshness via Backbone-Assisted Cooperative Access Points. - Haoyuan Pan; Yu Zhou 044; Tse-Tin Chan; Ming Tang; Jianqiang Li 001; Zhihua Du (IEEE Internet Things J., 2023)

MInet: A Novel Network Model for Point Cloud Processing by Integrating Multi-Modal Information. - Yuhao Wang; Yong Zuo; Zhihua Du; Xiaohan Song; Tian Luo; Xiaobin Hong 001; Jian Wu 010 (Sensors, 2023)

Prokaryotic virus host prediction with graph contrastive augmentaion. - Zhihua Du; Jun-Peng Zhong; Yun Liu; Jianqiang Li 001 (PLoS Comput. Biol., 2023)

Enhancing Gene Cluster Identification and Classification in Bacterial Genomes Through Synonym Replacement and Deep Learning. - Zhihua Du; Ningyu Zhong; Jianqiang Li 001 (BIBM, 2024)

AneuGuide™ software-assisted vs. manual measurements in sizing for pipeline embolization device: An agreement study. - Bin Lv; Mingguang Sun; Yejie Shan; Xiangyu Cao; Zhihua Du; Xinfeng Liu; Rongju Zhang; Xiaochang Leng; Jens Fiehler; Adnan H. Siddiqui; Jianping Xiang; Jun Wang (Comput. Biol. Medicine, 2024)

Hybrid Bayesian Optimization-Based Graphical Discovery for Methylation Sites Prediction. - Ling-Yan Gu; Ting-Bo Chen; Jianqiang Li 001; Yu-An Huang; Zhihua Du; Victor C. M. Leung; Jie Chen 027 (IEEE J. Biomed. Health Informatics, 2024)

ProtPhage: a deep learning framework for phage viral protein identification and functional annotation. - Yuehua Ou; Qiyi Chen; Ningyu Zhong; Zhihua Du (Briefings Bioinform., 2025)

NASNet-DTI: accurate drug-target interaction prediction using heterogeneous graphs and node adaptation. - Ningyu Zhong; Zhihua Du (Briefings Bioinform., 2025)

Multi-view attention graph convolutional networks for the host prediction of phages. - Lijia Ma; Peng Gao; Wenxiang Zhou; Qiuzhen Lin; Yuan Bai; Min Fang; Zhihua Du; Jianqiang Li 001 (Knowl. Based Syst., 2025)

MPDA: a data augmentation approach to improve deep learning for software vulnerability detection. - Feiqiao Mao; Yingxiang Yuan; Xingyang Du; Li Gao; Zhihua Du (Empir. Softw. Eng., 2025)