Short-Time Traffic Flow Forecasting Based on Projection Pursuit Auto-Regression. - Xiao-Yuan Wang; Hai-hong Liu; Zhi-Ping Liu (ICICIC (1), 2006)

Predicting gene ontology functions from protein's regional surface structures. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Luonan Chen; Xiang-Sun Zhang (BMC Bioinform., 2007)

Protein cavity clustering based on community structure of pocket similarity network. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Int. J. Bioinform. Res. Appl., 2008)

Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. - Zhi-Ping Liu; Yong Wang 001; Tieqiao Wen; Xiang-Sun Zhang; Weiming Xia; Luonan Chen (SMC, 2009)

Inferring gene regulatory networks from expression data with prior knowledge by linear programming. - Zhi-Ping Liu; Xiang-Sun Zhang; Luonan Chen (ICMLC, 2010)

Prediction of protein-RNA binding sites by a random forest method with combined features. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Bioinform., 2010)

Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. - Zhi-Ping Liu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2010)

Inferring Protein-Protein Interactions Based on Sequences and Interologs in Mycobacterium Tuberculosis. - Zhi-Ping Liu; Jiguang Wang; Yu-Qing Qiu; Ross K. K. Leung; Xiang-Sun Zhang; Stephen Kwok-Wing Tsui; Luonan Chen (ICIC (3), 2011)

Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression. - Huarong Zhou; Shigeru Saito; Guanying Piao; Zhi-Ping Liu; Jiguang Wang; Katsuhisa Horimoto; Luonan Chen (BMC Syst. Biol., 2011)

A Gaussian graphical model for identifying significantly responsive regulatory networks from time series gene expression data. - Zhi-Ping Liu; Wanwei Zhang; Katsuhisa Horimoto; Luonan Chen (ISB, 2012)

Construction and analysis of genome-wide SNP networks. - Yang Liu 100; Jin Zhou; Zhi-Ping Liu; Luonan Chen; Michael K. Ng 001 (ISB, 2012)

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. - Xiujun Zhang; Xing-Ming Zhao; Kun He 007; Le Lu 001; Yongwei Cao; Jingdong Liu; Jin-Kao Hao; Zhi-Ping Liu; Luonan Chen (Bioinform., 2012)

Identifying dysregulated pathways in cancers from pathway interaction networks. - Keqin Liu; Zhi-Ping Liu; Jin-Kao Hao; Luonan Chen; Xing-Ming Zhao (BMC Bioinform., 2012)

Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. - Zhi-Ping Liu; Jiguang Wang; Yu-Qing Qiu; Ross K. K. Leung; Xiang-Sun Zhang; Stephen Kwok-Wing Tsui; Luonan Chen (BMC Bioinform., 2012)

A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats. - Guanying Piao; Shigeru Saito; Yidan Sun; Zhi-Ping Liu; Yong Wang 001; Xiao Han; Jiarui Wu; Huarong Zhou; Luonan Chen; Katsuhisa Horimoto (BMC Syst. Biol., 2012)

Multiple-resource and multiple-depot emergency response problem considering secondary disasters. - Jianghua Zhang; Jin Li; Zhi-Ping Liu (Expert Syst. Appl., 2012)

Identifying disease genes and module biomarkers by differential interactions. - Xiaoping Liu 002; Zhi-Ping Liu; Xing-Ming Zhao; Luonan Chen (J. Am. Medical Informatics Assoc., 2012)

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. - Xiujun Zhang; Keqin Liu; Zhi-Ping Liu; Béatrice Duval; Jean-Michel Richer; Xing-Ming Zhao; Jin-Kao Hao; Luonan Chen (Bioinform., 2013)

Research and applications: An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. - Zhenshu Wen; Zhi-Ping Liu; Zhengrong Liu; Yan Zhang; Luonan Chen (J. Am. Medical Informatics Assoc., 2013)

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. - Zhi-Ping Liu; Hulin Wu; Jian Zhu; Hongyu Miao 001 (BMC Bioinform., 2014)

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. - Zhi-Ping Liu; Canglin Wu; Hongyu Miao 001; Hulin Wu (Database J. Biol. Databases Curation, 2015)

Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. - Xindong Zhang; Lin Gao 006; Zhi-Ping Liu; Luonan Chen (BMC Bioinform., 2015)

Identifying overlapping communities in social networks using multi-scale local information expansion. - Hui-Jia Li; Junhua Zhang 002; Zhi-Ping Liu; Luonan Chen; Xiang-Sun Zhang (CoRR, 2015)

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. - Guangyong Zheng; Yaochen Xu; Xiujun Zhang; Zhi-Ping Liu; Zhuo Wang; Luonan Chen; Xin-Guang Zhu (BMC Bioinform., 2016)

Prediction of protein-RNA interactions using sequence and structure descriptors. - Zhi-Ping Liu; Hongyu Miao 001 (Neurocomputing, 2016)

Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. - Zhi-Ping Liu; Shutang Liu; Ruitang Chen; Xiaopeng Huang; Ling-Yun Wu (BMC Bioinform., 2017)

Multi-dimensional data representation using linear tensor coding. - Xu Qiao; Xiaoqing Liu; Yen-Wei Chen 001; Zhi-Ping Liu (IET Image Process., 2017)

Detecting pathway biomarkers of diabetic progression with differential entropy. - Zhi-Ping Liu; Rui Gao (J. Biomed. Informatics, 2018)

Towards precise reconstruction of gene regulatory networks by data integration. - Zhi-Ping Liu (Quant. Biol., 2018)

Identifying Cancer Biomarkers from High-Throughput RNA Sequencing Data by Machine Learning. - Zishuang Zhang; Zhi-Ping Liu (ICIC (2), 2019)

iNOA: An Improvement of Network Ontology Analysis with GO Semantic Similarity. - Yaohua Chang; Zhi-Ping Liu (ICBIP, 2020)

Network-based prioritization of cancer genes by integrative ranks from multi-omics data. - Haixia Shang; Zhi-Ping Liu (Comput. Biol. Medicine, 2020)

A Semi-Supervised Learning Algorithm for Predicting MiRNA-Disease Association. - Na Yu; Zhi-Ping Liu; Rui Gao 006 (BIBM, 2021)

Inference of Gene Regulatory Network from Time Series Expression Data by Combining Local Geometric Similarity and Multivariate Regression. - Guangyi Chen; Zhi-Ping Liu (ICIC (3), 2021)

Prediction of cardiovascular diseases by integrating multi-modal features with machine learning methods. - Pengpai Li; Yongmei Hu; Zhi-Ping Liu (Biomed. Signal Process. Control., 2021)

Prioritizing Type 2 Diabetes Genes by Weighted PageRank on Bilayer Heterogeneous Networks. - Haixia Shang; Zhi-Ping Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Comparison Study of Predicting lncRNA-Protein Interactions via Representative Network Embedding Methods. - Guoqing Zhao; Pengpai Li; Zhi-Ping Liu (ICIC (2), 2022)

A connected network-regularized logistic regression model for feature selection. - Lingyu Li; Zhi-Ping Liu (Appl. Intell., 2022)

Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data. - Guangyi Chen; Zhi-Ping Liu (Bioinform., 2022)

PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning. - Pengpai Li; Zhi-Ping Liu (Bioinform., 2022)

Identifying biomarkers for breast cancer by gene regulatory network rewiring. - Yijuan Wang; Zhi-Ping Liu (BMC Bioinform., 2022)

Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods. - Lingyu Li; Wai-Ki Ching; Zhi-Ping Liu (Comput. Biol. Chem., 2022)

Predicting multiple types of MicroRNA-disease associations based on tensor factorization and label propagation. - Na Yu; Zhi-Ping Liu; Rui Gao 006 (Comput. Biol. Medicine, 2022)

Automated machine learning for secure key rate in discrete-modulated continuous-variable quantum key distribution. - Zhi-Ping Liu; Min-Gang Zhou; Wen-Bo Liu; Chen-Long Li; Jie Gu 008; Hua-Lei Yin; Zeng-Bing Chen (CoRR, 2022)

Predicting Box-Office Markets with Machine Learning Methods. - Dawei Li; Zhi-Ping Liu (Entropy, 2022)

Discovering biomarkers of hepatocellular carcinoma from single-cell RNA sequencing data by cooperative games on gene regulatory network. - Zishuang Zhang; Chenxi Sun; Zhi-Ping Liu (J. Comput. Sci., 2022)

Evaluating Gene Regulatory Network Activity From Dynamic Expression Data by Regularized Constraint Programming. - Chuan-Yuan Wang; Shiyu Xu; Zhi-Ping Liu (IEEE J. Biomed. Health Informatics, 2022)

Multi-objective Optimization-Based Approach for Detection of Breast Cancer Biomarkers. - Jiaxin Yang; Chuan-Yuan Wang; Duanchen Sun; Zhi-Ping Liu (ICIC (3), 2023)

MOFNet: A Deep Learning Framework of Integrating Multi-omics Data for Breast Cancer Diagnosis. - Chunxiao Zhang; Pengpai Li; Duanchen Sun; Zhi-Ping Liu (ICIC (3), 2023)

Quantum Neural Network for Quantum Neural Computing. - Min-Gang Zhou; Zhi-Ping Liu; Hua-Lei Yin; Chen-Long Li; Tong-Kai Xu; Zeng-Bing Chen (CoRR, 2023)

LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data. - Lingyu Li; Liangjie Sun; Guangyi Chen; Chi-Wing Wong; Wai-Ki Ching; Zhi-Ping Liu (Bioinform., 2023)

Editorial: Insights in integrative bioinformatics-2021. - Zhi-Ping Liu (Frontiers Bioinform., 2023)

ActivePPI: quantifying protein-protein interaction network activity with Markov random fields. - Chuan-Yuan Wang; Shiyu Xu; Duanchen Sun; Zhi-Ping Liu (Bioinform., 2023)

Biomarker discovery from high-throughput data by connected network-constrained support vector machine. - Lingyu Li; Zhi-Ping Liu (Expert Syst. Appl., 2023)

Predicting Drug-Target Affinity Using Protein Pocket and Graph Convolution Network. - Yunhai Li; Pengpai Li; Duanchen Sun; Zhi-Ping Liu (ISBRA (1), 2024)

LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data. - Dezhen Zhang; Shuhua Gao; Zhi-Ping Liu; Rui Gao 006 (Briefings Bioinform., 2024)

TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters. - Yanqiu Wang; Tong Wang; Yi Cao; Xu Qiao; Xianhua Han; Zhi-Ping Liu (Comput. Biol. Chem., 2024)

Discovering explainable biomarkers for breast cancer anti-PD1 response via network Shapley value analysis. - Chenxi Sun; Zhi-Ping Liu (Comput. Methods Programs Biomed., 2024)

Network Activity Evaluation Reveals Significant Gene Regulatory Architectures During SARS-CoV-2 Viral Infection From Dynamic scRNA-seq Data. - Chuan-Yuan Wang; Zhi-Ping Liu (IEEE J. Biomed. Health Informatics, 2024)

Inferring cell-type-specific gene regulatory network from cellular transcriptomics data with GeneLink+. - Wei Zhang 241; Bowen Shao; Wenrui Li; Wenbo Guo 010; Jiaxin Lyu; Guangyi Chen; Chuanyuan Wang; Zhi-Ping Liu (Briefings Bioinform., 2025)

GCNPMDA: Human microbe-disease association prediction by hierarchical graph convolutional network with layer attention. - Chuanyan Wu; Bentao Lin; Huanghe Zhang; Da Xu; Rui Gao 006; Rui Song 002; Zhi-Ping Liu; Yang De Marinis (Biomed. Signal Process. Control., 2025)

Practical quantum federated learning and its experimental demonstration. - Zhi-Ping Liu; Xiao-Yu Cao; Hao-Wen Liu; Xiao-Ran Sun; Yu Bao; Yu-Shuo Lu; Hua-Lei Yin; Zeng-Bing Chen (CoRR, 2025)