Classification of protein quaternary structure with support vector machine. - Shao-Wu Zhang 001; Quan Pan 001; Hongcai Zhang; Yun-Long Zhang; Hai-Yu Wang (Bioinform., 2003)

Prediction of Protein Subcellular Localizations Using Moment Descriptors and Support Vector Machine. - Jianyu Shi; Shao-Wu Zhang 001; Yan Liang 001; Quan Pan 001 (PRIB, 2006)

A New Hybrid Approach to Predict Subcellular Localization by Incorporating Protein Evolutionary Conservation Information. - ShaoWu Zhang 001; YunLong Zhang; JunHui Li; HuiFeng Yang; Yongmei Cheng; GuoPing Zhou (LSMS (2), 2007)

Using Decision Templates to Predict Subcellular Localization of Protein. - Jianyu Shi; Shao-Wu Zhang 001; Quan Pan 001; Yanning Zhang 001 (PRIB, 2007)

Prediction of Protein Homo-oligomer Types with a Novel Approach of Glide Zoom Window Feature Extraction. - Qi-Peng Li; Shao-Wu Zhang 001; Quan Pan 001 (ICIC (1), 2008)

Predicting Protein Quaternary Structure with Multi-scale Energy of Amino Acid Factor Solution Scores and Their Combination. - Shao-Wu Zhang 001; Wei Chen 145; Chunhui Zhao 002; Yongmei Cheng; Quan Pan 001 (ICMB, 2008)

Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types. - Qi-Peng Li; Shao-Wu Zhang 001; Quan Pan 001 (PRIB, 2008)

Finding Fuzzy Communities in Directed Networks. - Kun Zhao; Shao-Wu Zhang 001; Quan Pan 001 (ANNIIP, 2010)

Prediction of Protein-RNA interaction site using SVM-KNN algorithm with spatial information. - Wei Chen 145; Shao-Wu Zhang 001; Yongmei Cheng; Quan Pan 001 (BIBM, 2010)

Network-based modeling for analyzing the human skin microbiome. - Yingzhuo Wei; Shaowu Zhang 001; Chunhui Zhao 002; Feng Yang 001; Quan Pan 001 (BIBM Workshops, 2010)

PPLook: an automated data mining tool for protein-protein interaction. - Shao-Wu Zhang 001; Yao-Jun Li; Li C. Xia; Quan Pan 001 (BMC Bioinform., 2010)

Prediction of protein-protein interaction types using the decision templates based on multiple classier fusion. - Wei Chen 145; Shao-Wu Zhang 001; Yongmei Cheng; Quan Pan 001 (Math. Comput. Model., 2010)

Prediction of Protein-Protein Interaction Using Distance Frequency of Amino Acids Grouped with their Physicochemical Properties. - Shao-Wu Zhang 001; Yongmei Cheng; Li Luo; Quan Pan 001 (BIC-TA, 2011)

A seed-based approach to identify risk disease sub-networks in human lung cancer. - Yi-Bin Wang; Yongmei Cheng; Shao-Wu Zhang 001; Wei Chen 145 (ISB, 2012)

Unveiling the dynamics in RNA epigenetic regulations. - Jia Meng 001; Xiaodong Cui; Hui Liu 024; Lin Zhang 015; Shaowu Zhang 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Detecting seasonal marine microbial communities with symmetrical non-negative matrix factorization. - Shao-Wu Zhang 001; Fei Liu; Ze-Gang Wei; Wei Chen 145; Chen Zhou (BIBM, 2013)

Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Xiaodong Cui; Shao-Wu Zhang 001; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2014)

Differential analysis of RNA methylome with improved spatial resolution. - Yu-Chen Zhang; Shao-Wu Zhang 001; Lian Liu; Lin Zhang 015; Hui Liu 024; Xiaodong Cui; Yufei Huang 001; Jia Meng 001 (GlobalSIP, 2014)

Supervised method for periodontitis phenotypes prediction based on microbial composition using 16S rRNA sequences. - Wei Chen 145; Yongmei Cheng; Shao-Wu Zhang 001; Quan Pan 001 (Int. J. Comput. Biol. Drug Des., 2014)

Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates. - Xiaodong Cui; Zhen Wei; Lin Zhang 015; Hui Liu 024; Lei Sun; Shaowu Zhang 001; Yufei Huang 001; Jia Meng 001 (BIBM, 2015)

Modeling of replicates variances for detecting RNA methylation site in MERIP-SEQ data. - Xiaodong Cui; Jia Meng 001; Shaowu Zhang 001; Yufei Huang 001 (ChinaSIP, 2015)

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data. - Xiaodong Cui; Jia Meng 001; Shaowu Zhang 001; Yidong Chen 002; Yufei Huang 001 (Bioinform., 2016)

Inference of Gene Regulatory Network Based on Local Bayesian Networks. - Fei Liu; Shao-Wu Zhang 001; Weifeng Guo; Ze-Gang Wei; Luonan Chen (PLoS Comput. Biol., 2016)

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. - Song-Yao Zhang; Shao-Wu Zhang 001; Lian Liu; Jia Meng 001; Yufei Huang 001 (PLoS Comput. Biol., 2016)

Exploring the interaction patterns among taxa and environments from marine metagenomic data. - Ze-Gang Wei; Shao-Wu Zhang 001; Fang Jing (Quant. Biol., 2016)

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. - Lian Liu; Shao-Wu Zhang 001; Yufei Huang 001; Jia Meng 001 (BMC Bioinform., 2017)

A Machine Learning Approach for Uncovering N6-methyladenosine-Disease Association. - Songyao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Yufei Huang 001 (BCB, 2018)

Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. - Fang Jing; Shao-Wu Zhang 001; Zhen Cao; Shihua Zhang (ISBRA, 2018)

Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. - Weifeng Guo; Shao-Wu Zhang 001; Li-Li Liu; Fei Liu; Qianqian Shi; Lei Zhang; Ying Tang; Tao Zeng 003; Luonan Chen (Bioinform., 2018)

NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model. - Ze-Gang Wei; Shao-Wu Zhang 001 (BMC Bioinform., 2018)

trumpet: transcriptome-guided quality assessment of m6A-seq data. - Teng Zhang; Shao-Wu Zhang 001; Lin Zhang 015; Jia Meng 001 (BMC Bioinform., 2018)

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. - Hui Liu 024; Huaizhi Wang; Zhen Wei; Songyao Zhang; Gang Hua 002; Shao-Wu Zhang 001; Lin Zhang 015; Shou-Jiang Gao; Jia Meng 001; Xing Chen 001; Yufei Huang 001 (Nucleic Acids Res., 2018)

FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. - Song-Yao Zhang; Shao-Wu Zhang 001; Xiao-Nan Fan 001; Teng Zhang; Jia Meng 001; Yufei Huang 001 (Bioinform., 2019)

Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. - Xiao-Nan Fan 001; Shao-Wu Zhang 001; Song-Yao Zhang; Kunju Zhu; Songjian Lu (BMC Bioinform., 2019)

Prediction of drug-target interaction by integrating diverse heterogeneous information source with multiple kernel learning and clustering methods. - Xiao-Ying Yan; Shao-Wu Zhang 001; Chang-Run He (Comput. Biol. Chem., 2019)

LPI-BLS: Predicting lncRNA-protein interactions with a broad learning system-based stacked ensemble classifier. - Xiao-Nan Fan 001; Shao-Wu Zhang 001 (Neurocomputing, 2019)

A novel network control model for identifying personalized driver genes in cancer. - Weifeng Guo; Shao-Wu Zhang 001; Tao Zeng 003; Yan Li 111; Jianxi Gao; Luonan Chen (PLoS Comput. Biol., 2019)

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Song-Yao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (PLoS Comput. Biol., 2019)

Identification of Alzheimer's disease based on wavelet transformation energy feature of the structural MRI image and NN classifier. - Jinwang Feng; Shao-Wu Zhang 001; Luonan Chen; Alzheimer's Disease Neuroimaging Initiative (Artif. Intell. Medicine, 2020)

Network control principles for identifying personalized driver genes in cancer. - Weifeng Guo; Shaowu Zhang 001; Tao Zeng 003; Tatsuya Akutsu; Luonan Chen (Briefings Bioinform., 2020)

DPDDI: a deep predictor for drug-drug interactions. - Yue-Hua Feng; Shaowu Zhang 001; Jian-Yu Shi (BMC Bioinform., 2020)

Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. - Fang Jing; Shao-Wu Zhang 001; Shihua Zhang (BMC Bioinform., 2020)

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions. - Ze-Gang Wei; Shao-Wu Zhang 001; Fei Liu (BMC Bioinform., 2020)

Resilience function uncovers the critical transitions in cancer initiation. - Yan Li 111; Shao-Wu Zhang 001 (Briefings Bioinform., 2021)

Identifying driver genes for individual patients through inductive matrix completion. - Tong Zhang; Shao-Wu Zhang 001; Yan Li 111 (Bioinform., 2021)

Alzheimer's disease classification using features extracted from nonsubsampled contourlet subband-based individual networks. - Jinwang Feng; Shaowu Zhang 001; Luonan Chen; Jie Xia (Neurocomputing, 2021)

Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. - Weifeng Guo; Xiangtian Yu; Qianqian Shi; Jing Liang 005; Shao-Wu Zhang 001; Tao Zeng 003 (PLoS Comput. Biol., 2021)

An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. - Fang Jing; Shao-Wu Zhang 001; Zhen Cao; Shihua Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation. - Song-Yao Zhang; Shaowu Zhang 001; Yujiao Tang; Xiaonan Fan 001; Jia Meng 001 (Bioinform., 2021)

Interpretable prediction of drug-cell line response by triple matrix factorization. - Xiao-Ying Yan; Shaowu Zhang 001; Siu-Ming Yiu; Jian-Yu Shi (Quant. Biol., 2021)

m 6 Aexpress-BHM: predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model. - Teng Zhang; Shao-Wu Zhang 001; Jian Feng; Bei Zhang (Briefings Bioinform., 2022)

Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network. - Shao-Wu Zhang 001; Zhen-Nan Wang; Yan Li 111; Weifeng Guo (BMC Bioinform., 2022)

Detection of Alzheimer's disease using features of brain region-of-interest-based individual network constructed with the sMRI image. - Jinwang Feng; ShaoWu Zhang 001; Luonan Chen; Chunman Zuo; Alzheimer's Disease Neuroimaging Initiative (Comput. Medical Imaging Graph., 2022)

Extracting ROI-Based Contourlet Subband Energy Feature From the sMRI Image for Alzheimer's Disease Classification. - Jinwang Feng; Shaowu Zhang 001; Luonan Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network. - Fang Jing; Shaowu Zhang 001; Shihua Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data. - Shao-Wu Zhang 001; Jing-Yu Xu 005; Tong Zhang (Genom. Proteom. Bioinform., 2022)

A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions. - Yue-Hua Feng; Shao-Wu Zhang 001; Yi-Yang Feng; Qing-Qing Zhang; Ming-Hui Shi; Jian-Yu Shi (Briefings Bioinform., 2023)

A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes. - Tong Zhang; Shao-Wu Zhang 001; Ming-Yu Xie; Yan Li 111 (Briefings Bioinform., 2023)

Few-Shot Drug Synergy Prediction With a Prior-Guided Hypernetwork Architecture. - Qing-Qing Zhang; Shaowu Zhang 001; Yue-Hua Feng; Jian-Yu Shi (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer. - Yan Li 111; Shao-Wu Zhang 001; Ming-Yu Xie; Tong Zhang (Briefings Bioinform., 2023)

Diagnosis of Alzheimer's disease by joining dual attention CNN and MLP based on structural MRIs, clinical and genetic data. - Yan-Rui Qiang; Shao-Wu Zhang 001; Jia-Ni Li; Yan Li 111; Qin-Yi Zhou (Artif. Intell. Medicine, 2023)

A novel cross-layer dual encoding-shared decoding network framework with spatial self-attention mechanism for hippocampus segmentation. - Jia-Ni Li; Shaowu Zhang 001; Yan-Rui Qiang; Qin-Yi Zhou (Comput. Biol. Medicine, 2023)

MSCLK: Multi-scale fully separable convolution neural network with large kernels for early diagnosis of Alzheimer's disease. - Run-Feng Tian; Jia-Ni Li; Shaowu Zhang 001 (Expert Syst. Appl., 2024)

Identifying cooperating cancer driver genes in individual patients through hypergraph random walk. - Tong Zhang; Shao-Wu Zhang 001; Ming-Yu Xie; Yan Li 111 (J. Biomed. Informatics, 2024)