RNA Secondary Structure Prediction Based on Forest Representation and Genetic Algorithm. - Taotao Zhang; Maozu Guo 001; Quan Zou 001 (ICNC (4), 2007)

An Improved Diverse Density Algorithm for Multiple Overlapped Instances. - Lei Xu 047; Maozu Guo 001; Quan Zou 001; Yang Liu 006; Haifeng Li (ICNC (3), 2008)

A Novel Comparative Sequence Analysis Method for ncRNA Secondary Structure Prediction without Multiple Sequence Alignment. - Quan Zou 001; Maozu Guo 001; Yang Liu 006; Zhi-An Xing (ICNC (5), 2008)

Interest filter vs. interest operator: Face recognition using Fisher linear discriminant based on interest filter representation. - Tuo Zhao; Zhizheng Liang; David Zhang 001; Quan Zou 001 (Pattern Recognit. Lett., 2008)

Novel H/ACA Box snoRNA Mining and Secondary Structure Prediction Algorithms. - Quan Zou 001; Maozu Guo 001; Chunyu Wang 002; Yingpeng Han; Wenbin Li (RSKT, 2009)

Predicting RNA secondary structure based on the class information and Hopfield network. - Quan Zou 001; Tuo Zhao; Yang Liu 006; Maozu Guo 001 (Comput. Biol. Medicine, 2009)

Automatic extraction of ocean internal waves based on multi-scale fusion and elliptical tracking region method. - Qicong Wang; Shaoling Shang; QingKai Zhen; Yan Li; Quan Zou 001 (ICIMCS, 2010)

TiSGeD: a database for tissue-specific genes. - Sheng-Jian Xiao; Chi Zhang; Quan Zou 001; Zhi-Liang Ji (Bioinform., 2010)

DuplexFinder: Predicting the miRNA - miRNA* duplex from the animal precursors. - Quan Zou 001; Maozu Guo 001; Yang Liu 006; Ping Xuan (Int. J. Bioinform. Res. Appl., 2010)

Maintaining Internal Consistency of Report for Real-Time OLAP with Layer-Based View. - Ziyu Lin; Yongxuan Lai; Chen Lin 001; Yi Xie 004; Quan Zou 001 (APWeb, 2011)

Performance Optimization of Analysis Rules in Real-Time Active Data Warehouses. - Ziyu Lin; Dongzhan Zhang; Chen Lin 001; Yongxuan Lai; Quan Zou 001 (APWeb, 2012)

Location and Route Tracking in University from Photos without GPS Information. - Mingxia Lin; Shi-chang Hu; Cuihua Li; Taisong Jin; Quan Zou 001 (PCM, 2012)

PaGeFinder: quantitative identification of spatiotemporal pattern genes. - Jian-Bo Pan; Shi-chang Hu; Hao Wang; Quan Zou 001; Zhi-Liang Ji (Bioinform., 2012)

Identify content quality in online social networks. - Chen Lin 001; Zhenhua Huang 001; Fan Yang 010; Quan Zou 001 (IET Commun., 2012)

Hybrid pseudo-relevance feedback for microblog retrieval. - Chen Lin 001; Chun Lin; Ziyu Lin; Quan Zou 001 (J. Inf. Sci., 2013)

Survey of MapReduce frame operation in bioinformatics. - Quan Zou 001; Xu-Bin Li; Wen-Rui Jiang; Ziyu Lin; Gui-Lin Li; Ke Chen (Briefings Bioinform., 2014)

Using distances between Top-n-gram and residue pairs for protein remote homology detection. - Bin Liu 014; Jinghao Xu; Quan Zou 001; Ruifeng Xu 001; Xiaolong Wang 001; Qingcai Chen (BMC Bioinform., 2014)

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification. - Li Song; Dapeng Li; Xiangxiang Zeng; Yunfeng Wu; Li Guo; Quan Zou 001 (BMC Bioinform., 2014)

miRClassify: An advanced web server for miRNA family classification and annotation. - Quan Zou 001; Yaozong Mao; Lingling Hu; Yunfeng Wu; Zhi-Liang Ji (Comput. Biol. Medicine, 2014)

LibD3C: Ensemble classifiers with a clustering and dynamic selection strategy. - Chen Lin 001; Wenqiang Chen; Cheng Qiu; Yunfeng Wu; Sridhar Krishnan 001; Quan Zou 001 (Neurocomputing, 2014)

Decision Tree Classification Model for Popularity Forecast of Chinese Colleges. - Xiangxiang Zeng; Sisi Yuan; You Li; Quan Zou 001 (J. Appl. Math., 2014)

Improved and Promising Identificationof Human MicroRNAs by Incorporatinga High-Quality Negative Set. - Leyi Wei; Minghong Liao; Yue Gao 002; Rongrong Ji; Zengyou He; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Selective ensemble learning with parallel optimization and hierarchical selection. - Jiasheng Guo; Jian-Cang Zeng; Jin-Xiu Chen; Quan Zou 001 (ICMLC, 2015)

HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy. - Quan Zou 001; Qinghua Hu; Maozu Guo 001; Guohua Wang (Bioinform., 2015)

Identification of cytokine via an improved genetic algorithm. - Xiangxiang Zeng; Sisi Yuan; Xianxian Huang; Quan Zou 001 (Frontiers Comput. Sci., 2015)

Asynchronous spiking neural P systems with rules on synapses. - Tao Song 001; Quan Zou 001; Xiangrong Liu; Xiangxiang Zeng (Neurocomputing, 2015)

Latent factor model with heterogeneous similarity regularization for predicting gene-disease associations. - Xiangxiang Zeng; Ningxiang Ding; Quan Zou 001 (BIBM, 2016)

Multiple sequence alignment and reconstructing phylogenetic trees with Hadoop. - Quan Zou 001 (BIBM, 2016)

HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop. - Quan Zou 001; Shixiang Wan; Xiangxiang Zeng (BIBM, 2016)

BDSCyto: An Automated Approach for Identifying Cytokines Based on Best Dimension Searching. - Quan Zou 001; Shixiang Wan; Bing Han 003; Zhihui Zhan (PRICAI, 2016)

Finding the Best Classification Threshold in Imbalanced Classification. - Quan Zou 001; Sifa Xie; Ziyu Lin; Meihong Wu; Ying Ju (Big Data Res., 2016)

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. - Xiangxiang Zeng; Xuan Zhang 010; Quan Zou 001 (Briefings Bioinform., 2016)

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. - Quan Zou 001; Shixiang Wan; Ying Ju; Jijun Tang; Xiangxiang Zeng (BMC Syst. Biol., 2016)

Annotation-retrieval reinforcement by visual cognition modeling on manifold. - Zhiqiang Zeng; Hua Shi; Yun Wu; Quan Zou 001 (Neurocomputing, 2016)

Hierarchical support vector machine based structural classification with fused hierarchies. - Shuo Zhao; Yahong Han; Quan Zou 001; Qinghua Hu (Neurocomputing, 2016)

Advanced learning for large-scale heterogeneous computing. - Quan Zou 001; Wei Liu 005; Michele Merler; Rongrong Ji (Neurocomputing, 2016)

A novel features ranking metric with application to scalable visual and bioinformatics data classification. - Quan Zou 001; Jian-Cang Zeng; Liujuan Cao; Rongrong Ji (Neurocomputing, 2016)

Iteratively collective prediction of disease-gene associations through the incomplete network. - Xiangyi Meng; Quan Zou 001; Alfonso Rodríguez-Patón; Xiangxiang Zeng (BIBM, 2017)

Learning Planning and Recommendation Based on an Adaptive Architecture on Data Graph, Information Graph and Knowledge Graph. - Lixu Shao; Yucong Duan; Zhangbing Zhou; Quan Zou 001; Honghao Gao (CollaborateCom, 2017)

Wavelet-based single image super-resolution with an overall enhancement procedure. - Zongqing Lu 001; Quan Zou 001; Fei Zhou 001; Qingmin Liao (ICASSP, 2017)

A Pay as You Use Resource Security Provision Approach Based on Data Graph, Information Graph and Knowledge Graph. - Lixu Shao; Yucong Duan; Lizhen Cui; Quan Zou 001; Xiaobing Sun 001 (IDEAL, 2017)

Specifying architecture of knowledge graph with data graph, information graph, knowledge graph and wisdom graph. - Yucong Duan; Lixu Shao; Gongzhu Hu; Zhangbing Zhou; Quan Zou 001; Zhaoxin Lin (SERA, 2017)

Bidirectional value driven design between economical planning and technical implementation based on data graph, information graph and knowledge graph. - Lixu Shao; Yucong Duan; Xiaobing Sun 001; Quan Zou 001; Rongqi Jing; Jiami Lin (SERA, 2017)

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing. - Shixiang Wan; Quan Zou 001 (Algorithms Mol. Biol., 2017)

Machine learning and graph analytics in computational biomedicine. - Quan Zou 001; Lei Chen 007; Tao Huang 004; Zhenguo Zhang; Yungang Xu (Artif. Intell. Medicine, 2017)

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment. - Xi Chen; Chen Wang 004; Shanjiang Tang; Ce Yu; Quan Zou 001 (BMC Bioinform., 2017)

Reconstructing evolutionary trees in parallel for massive sequences. - Quan Zou 001; Shixiang Wan; Xiangxiang Zeng; Zhanshan (Sam) Ma (BMC Syst. Biol., 2017)

HPSLPred: An Ensemble Multi-label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source. - Shixiang Wan; Quan Zou 001 (CoRR, 2017)

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information. - Leyi Wei; Jijun Tang; Quan Zou 001 (Inf. Sci., 2017)

Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework. - Wenhe Su; Xiangke Liao; Yutong Lu; Quan Zou 001; Shaoliang Peng (J. Comput. Biol., 2017)

基于分层筛选和动态更新的并行选择集成算法 (Selective Ensemble Learning Algorithm Based on Hierarchical Selection and Dynamic Updating in Parallel). - Meihong Wu; Jiasheng Guo; Ying Ju; Ziyu Lin; Quan Zou 001 (计算机科学, 2017)

A comprehensive overview and evaluation of circular RNA detection tools. - Xiangxiang Zeng; Wei Lin; Maozu Guo 001; Quan Zou 001 (PLoS Comput. Biol., 2017)

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources. - Yuansheng Liu; Xiangxiang Zeng; Zengyou He; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Prediction and Validation of Disease Genes Using HeteSim Scores. - Xiangxiang Zeng; Yuanlu Liao; Yuansheng Liu; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Towards Cost Effective Privacy Provision for Typed Resources in IoT Environment (S). - Yucong Duan; Zhengyang Song; Xiaoxian Yang; Quan Zou 001; Xiaobing Sun 001; Xinyue Zhang (SEKE, 2018)

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique. - Cangzhi Jia; Yun Zuo 001; Quan Zou 001 (Bioinform., 2018)

Tumor origin detection with tissue-specific miRNA and DNA methylation markers. - Wei Tang; Shixiang Wan; Zhen Yang; Andrew E. Teschendorff; Quan Zou 001 (Bioinform., 2018)

Prediction of potential disease-associated microRNAs using structural perturbation method. - Xiangxiang Zeng; Li Liu; Linyuan Lü; Quan Zou 001 (Bioinform., 2018)

Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture. - Shaoliang Peng; Minxia Cheng; Kaiwen Huang; Yingbo Cui 001; Zhiqiang Zhang; Runxin Guo; Xiaoyu Zhang 008; Shunyun Yang; Xiangke Liao; Yutong Lu; Quan Zou 001; Benyun Shi (BMC Bioinform., 2018)

cmFSM: a scalable CPU-MIC coordinated drug-finding tool by frequent subgraph mining. - Shunyun Yang; Runxin Guo; Rui Liu; Xiangke Liao; Quan Zou 001; Benyun Shi; Shaoliang Peng (BMC Bioinform., 2018)

70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features. - Wenying He; Cangzhi Jia; Yucong Duan; Quan Zou 001 (BMC Syst. Biol., 2018)

Prediction of human protein subcellular localization using deep learning. - Leyi Wei; Yijie Ding; Ran Su; Jijun Tang; Quan Zou 001 (J. Parallel Distributed Comput., 2018)

Identifying Cleavage Sites of Gelatinases A and B by Integrating Feature Computing Models. - Quan Zou 001; Chi-Wei Chen; Hao-Chen Chang; Yen-Wei Chu (J. Univers. Comput. Sci., 2018)

Processing Optimization of Typed Resources with Synchronized Storage and Computation Adaptation in Fog Computing. - Zhengyang Song; Yucong Duan; Shixiang Wan; Xiaobing Sun 001; Quan Zou 001; Honghao Gao; Donghai Zhu (Wirel. Commun. Mob. Comput., 2018)

Grouped Correlational Generative Adversarial Networks for Discrete Electronic Health Records. - Fan Yang 010; Zhongping Yu; Yunfan Liang; Xiaolu Gan; Kaibiao Lin; Quan Zou 001; Yifeng Zeng (BIBM, 2019)

A Prototype System using Location-based Twitter Data for Disaster Management. - Quan Zou 001 (IGARSS, 2019)

Prediction of Thermophilic Proteins Using Voting Algorithm. - Jing Li; Pengfei Zhu; Quan Zou 001 (IWBBIO (1), 2019)

Exploiting Discriminative Regions of Brain Slices Based on 2D CNNs for Alzheimer's Disease Classification. - Fujia Ren; Chenhui Yang; Qi Qiu; Nianyin Zeng; Chunting Cai; Chaoqun Hou; Quan Zou 001 (IEEE Access, 2019)

4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction. - Wenying He; Cangzhi Jia; Quan Zou 001 (Bioinform., 2019)

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species. - Leyi Wei; Shasha Luan; Luis Augusto Eijy Nagai; Ran Su; Quan Zou 001 (Bioinform., 2019)

Iterative feature representations improve N4-methylcytosine site prediction. - Leyi Wei; Ran Su; Shasha Luan; Zhijun Liao; Balachandran Manavalan; Quan Zou 001; Xiaolong Shi (Bioinform., 2019)

PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning. - Leyi Wei; Chen Zhou; Ran Su; Quan Zou 001 (Bioinform., 2019)

Identifying protein-protein interface via a novel multi-scale local sequence and structural representation. - Fei Guo 001; Quan Zou 001; Guang Yang; Dan Wang; Jijun Tang; Junhai Xu (BMC Bioinform., 2019)

A novel collaborative filtering model for LncRNA-disease association prediction based on the Naïve Bayesian classifier. - Jingwen Yu; Zhanwei Xuan; Xiang Feng; Quan Zou 001; Lei Wang 069 (BMC Bioinform., 2019)

Taxonomy dimension reduction for colorectal cancer prediction. - Kaiyang Qu; Feng Gao; Fei Guo 001; Quan Zou 001 (Comput. Biol. Chem., 2019)

Multi-objective optimization and data analysis in informationization. - Kelvin Kian Loong Wong; Zhihua Liu; Quan Zou 001 (Computing, 2019)

Integration of deep feature representations and handcrafted features to improve the prediction of N6-methyladenosine sites. - Leyi Wei; Ran Su; Bing Wang; Xiuting Li; Quan Zou 001; Xing Gao 004 (Neurocomputing, 2019)

Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang. - Xiangxiang Zeng; Wei Lin; Maozu Guo 001; Quan Zou 001 (PLoS Comput. Biol., 2019)

Fast Prediction of Protein Methylation Sites Using a Sequence-Based Feature Selection Technique. - Leyi Wei; Pengwei Xing; Gaotao Shi; Zhiliang Ji; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Meta-Path Methods for Prioritizing Candidate Disease miRNAs. - Xuan Zhang 010; Quan Zou 001; Alfonso Rodríguez-Patón; Xiangxiang Zeng (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Advanced Machine Learning Techniques for Bioinformatics. - Quan Zou 001; Qi Liu 019 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

GRRFNet: Guided Regularized Random Forest-based Gene Regulatory Network Inference Using Data Integration. - Yongqing Zhang; Qingyuan Chen; Dongrui Gao; Quan Zou 001 (BIBM, 2020)

Reference-Based Sequence Classification. - Zengyou He; Guangyao Xu; Chaohua Sheng; Bo Xu 008; Quan Zou 001 (IEEE Access, 2020)

Computational methods for identifying the critical nodes in biological networks. - Xiangrong Liu; Zengyan Hong; Juan Liu 003; Yuan Lin; Alfonso Rodríguez-Patón; Quan Zou 001; Xiangxiang Zeng (Briefings Bioinform., 2020)

HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search. - Bin Liu 014; Shuangyan Jiang; Quan Zou 001 (Briefings Bioinform., 2020)

Clustering and classification methods for single-cell RNA-sequencing data. - Ren Qi; Anjun Ma; Qin Ma 003; Quan Zou 001 (Briefings Bioinform., 2020)

Critical evaluation of web-based prediction tools for human protein subcellular localization. - Yinan Shen; Yijie Ding; Jijun Tang; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2020)

Transcription factors-DNA interactions in rice: identification and verification. - Zijie Shen; Yuan Lin; Quan Zou 001 (Briefings Bioinform., 2020)

Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools. - Ran Su; Jie Hu; Quan Zou 001; Balachandran Manavalan; Leyi Wei (Briefings Bioinform., 2020)

Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. - Leyi Wei; Jie Hu; Fuyi Li; Jiangning Song; Ran Su; Quan Zou 001 (Briefings Bioinform., 2020)

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods. - Xiangxiang Zeng; Yue Zhong; Wei Lin; Quan Zou 001 (Briefings Bioinform., 2020)

Sequence clustering in bioinformatics: an empirical study. - Quan Zou 001; Gang Lin; Xingpeng Jiang; Xiangrong Liu; Xiangxiang Zeng (Briefings Bioinform., 2020)

mAML: an automated machine learning pipeline with a microbiome repository for human disease classification. - Fenglong Yang; Quan Zou 001 (Database J. Biol. Databases Curation, 2020)

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. - Xiangzheng Fu; Lijun Cai; Xiangxiang Zeng; Quan Zou 001 (Bioinform., 2020)

Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites. - Zijie Shen; Quan Zou 001 (Bioinform., 2020)

PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning. - Yu P. Zhang; Quan Zou 001 (Bioinform., 2020)

CWLy-SVM: A support vector machine-based tool for identifying cell wall lytic enzymes. - Chaolu Meng; Fei Guo 001; Quan Zou 001 (Comput. Biol. Chem., 2020)

Exploration of the correlation between GPCRs and drugs based on a learning to rank algorithm. - Xiaoqing Ru; Lida Wang; Lihong Li 005; Hui Ding 005; Xiucai Ye; Quan Zou 001 (Comput. Biol. Medicine, 2020)

Protein Complexes Identification with Family-Wise Error Rate Control. - Zengyou He; Can Zhao 007; Hao Liang; Bo Xu 008; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

DeepAVP: A Dual-Channel Deep Neural Network for Identifying Variable-Length Antiviral Peptides. - Jiawei Li 018; Yuqian Pu; Jijun Tang; Quan Zou 001; Fei Guo 001 (IEEE J. Biomed. Health Informatics, 2020)

Membrane Protein Identification via Multi-view Graph Regularized k-Local Hyperplane Distance Nearest Neighbor Model. - Mengwei Sun; Yuqing Qian; Yijie Ding; Jijun Tang; Quan Zou 001 (BIBM, 2021)

By hybrid neural networks for prediction and interpretation of transcription factor binding sites based on multi-omics. - Yongqing Zhang; Zixuan Wang; Yuhang Liu; Libo Lu; Xiaoyao Tan; Quan Zou 001 (BIBM, 2021)

News Popularity Prediction with Local-Global Long-Short-Term Embedding. - Shuai Fan 007; Chen Lin 001; Hui Li 057; Quan Zou 001 (WISE (2), 2021)

IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis. - Feifei Cui; Quan Zou 001; Qin Ma 003; Leyi Wei; Jijun Tang; Dariusz Mrozek (IEEE Access, 2021)

Instance-Based Classification Through Hypothesis Testing. - Zengyou He; Chaohua Sheng; Yan Liu 085; Quan Zou 001 (IEEE Access, 2021)

Molecular design in drug discovery: a comprehensive review of deep generative models. - Yu Cheng; Yongshun Gong; Yuansheng Liu; Bosheng Song; Quan Zou 001 (Briefings Bioinform., 2021)

A comprehensive review of the imbalance classification of protein post-translational modifications. - Lijun Dou; Fenglong Yang; Lei Xu 047; Quan Zou 001 (Briefings Bioinform., 2021)

MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction. - Wenying He; Jijun Tang; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2021)

DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences. - Jiawei Li 018; Yuqian Pu; Jijun Tang; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2021)

EP3: an ensemble predictor that accurately identifies type III secreted effectors. - Jing Li; Leyi Wei; Fei Guo 001; Quan Zou 001 (Briefings Bioinform., 2021)

SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning. - Jing Li; Lichao Zhang; Shida He; Fei Guo 001; Quan Zou 001 (Briefings Bioinform., 2021)

Anticancer peptides prediction with deep representation learning features. - Zhibin Lv; Feifei Cui; Quan Zou 001; Lichao Zhang; Lei Xu 047 (Briefings Bioinform., 2021)

A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data. - Ren Qi; Jin Wu; Fei Guo 001; Lei Xu 047; Quan Zou 001 (Briefings Bioinform., 2021)

Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transition. - Yushan Qiu; Wai-Ki Ching; Quan Zou 001 (Briefings Bioinform., 2021)

Prediction of RNA-binding protein and alternative splicing event associations during epithelial-mesenchymal transition based on inductive matrix completion. - Yushan Qiu; Wai-Ki Ching; Quan Zou 001 (Briefings Bioinform., 2021)

Application of learning to rank in bioinformatics tasks. - Xiaoqing Ru; Xiucai Ye; Tetsuya Sakurai; Quan Zou 001 (Briefings Bioinform., 2021)

Revisiting genome-wide association studies from statistical modelling to machine learning. - Shanwen Sun; BenZhi Dong; Quan Zou 001 (Briefings Bioinform., 2021)

The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis. - Furong Tang; Lichao Zhang; Lei Xu 047; Quan Zou 001; Hailin Feng (Briefings Bioinform., 2021)

Machine learning for phytopathology: from the molecular scale towards the network scale. - Yansu Wang; Murong Zhou; Quan Zou 001; Lei Xu 047 (Briefings Bioinform., 2021)

VPTMdb: a viral posttranslational modification database. - Yujia Xiang; Quan Zou 001; Lilin Zhao (Briefings Bioinform., 2021)

An in silico approach to identification, categorization and prediction of nucleic acid binding proteins. - Lei Xu 047; Shanshan Jiang; Jin Wu; Quan Zou 001 (Briefings Bioinform., 2021)

DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data. - Fenglong Yang; Quan Zou 001 (Briefings Bioinform., 2021)

GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. - Fenglong Yang; Quan Zou 001; Bo Gao (Briefings Bioinform., 2021)

Critical downstream analysis steps for single-cell RNA sequencing data. - Zilong Zhang; Feifei Cui; Chen Lin 001; Lingling Zhao; Chunyu Wang 002; Quan Zou 001 (Briefings Bioinform., 2021)

High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method. - Yongqing Zhang; Zixuan Wang; Yuanqi Zeng; Jiliu Zhou; Quan Zou 001 (Briefings Bioinform., 2021)

A comprehensive overview and critical evaluation of gene regulatory network inference technologies. - Mengyuan Zhao; Wenying He; Jijun Tang; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2021)

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers. - Yuansheng Liu; Xiaocai Zhang; Quan Zou 001; Xiangxiang Zeng (Bioinform., 2021)

Identification of sub-Golgi protein localization by use of deep representation learning features. - Zhibin Lv; Pingping Wang; Quan Zou 001; Qinghua Jiang (Bioinform., 2021)

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method. - Shanwen Sun; Lei Xu 047; Quan Zou 001; Guohua Wang (Bioinform., 2021)

DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA. - Chao Wang 043; Ying Ju; Quan Zou 001; Chen Lin 001 (Bioinform., 2021)

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques. - Yun Zuo 001; Jianyuan Lin; Xiangxiang Zeng; Quan Zou 001; Xiangrong Liu (BMC Bioinform., 2021)

Computational biology and chemistry Special section editorial: Computational analyses for miRNA. - Feifei Cui; Murong Zhou; Quan Zou 001 (Comput. Biol. Chem., 2021)

Using a low correlation high orthogonality feature set and machine learning methods to identify plant pentatricopeptide repeat coding gene/protein. - Changli Feng; Quan Zou 001; Donghua Wang (Neurocomputing, 2021)

A Convolutional Neural Network Using Dinucleotide One-hot Encoder for identifying DNA N6-Methyladenine Sites in the Rice Genome. - Zhibin Lv; Hui Ding 005; Lei Wang 069; Quan Zou 001 (Neurocomputing, 2021)

Prediction of drug-target interactions based on multi-layer network representation learning. - Yifan Shang; Lin Gao 006; Quan Zou 001; Liang Yu 002 (Neurocomputing, 2021)

iPro2L-PSTKNC: A Two-Layer Predictor for Discovering Various Types of Promoters by Position Specific of Nucleotide Composition. - Yinuo Lyu; Wenying He; Shuhao Li; Quan Zou 001; Fei Guo 001 (IEEE J. Biomed. Health Informatics, 2021)

rBPDL: Predicting RNA-Binding Proteins Using Deep Learning. - Mengting Niu; Jin Wu; Quan Zou 001; Zhendong Liu; Lei Xu 047 (IEEE J. Biomed. Health Informatics, 2021)

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation. - Lijun Cai; Li Wang 145; Xiangzheng Fu; Chenxing Xia; Xiangxiang Zeng; Quan Zou 001 (Briefings Bioinform., 2021)

Kernel Risk Sensitive Loss-based Echo State Networks for Predicting Therapeutic Peptides with Sparse Learning. - Xiaoyi Guo; Yuqing Qian; Prayag Tiwari; Quan Zou 001; Yijie Ding (BIBM, 2022)

Single-cell TF-DNA binding prediction and analysis based on transfer learning framework. - Zixuan Wang; Yongqing Zhang; Yun Yu; Maocheng Wang; Yuhang Liu; Quan Zou 001 (BIBM, 2022)

Predicting cell type-specific effects of variants on TF-DNA binding by meta-learning. - Yongqing Zhang; Yuhang Liu; Zixuan Wang; Maocheng Wang; Shuwen Xiong; Quan Zou 001 (BIBM, 2022)

GATSDCD: Prediction of circRNA-Disease Associations Based on Singular Value Decomposition and Graph Attention Network. - Mengting Niu; Abd El-Latif Hesham; Quan Zou 001 (ICIC (2), 2022)

NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences. - Chunyan Ao; Quan Zou 001; Liang Yu 002 (Briefings Bioinform., 2022)

Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization. - Yijie Ding; Jijun Tang; Fei Guo 001; Quan Zou 001 (Briefings Bioinform., 2022)

Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides. - Xiaoyi Guo; Yizhang Jiang; Quan Zou 001 (Briefings Bioinform., 2022)

DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network. - Jhabindra Khanal; Hilal Tayara; Quan Zou 001; Kil To Chong 001 (Briefings Bioinform., 2022)

A novel fast multiple nucleotide sequence alignment method based on FM-index. - Huan Liu 024; Quan Zou 001; Yun Xu (Briefings Bioinform., 2022)

Characterizing viral circRNAs and their application in identifying circRNAs in viruses. - Mengting Niu; Ying Ju; Chen Lin 001; Quan Zou 001 (Briefings Bioinform., 2022)

Identification of drug-side effect association via restricted Boltzmann machines with penalized term. - Yuqing Qian; Yijie Ding; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2022)

Distant metastasis identification based on optimized graph representation of gene interaction patterns. - Ran Su; Yingying Zhu; Quan Zou 001; Leyi Wei (Briefings Bioinform., 2022)

A comparison of deep learning-based pre-processing and clustering approaches for single-cell RNA sequencing data. - Jiacheng Wang 009; Quan Zou 001; Chen Lin 001 (Briefings Bioinform., 2022)

MDICC: novel method for multi-omics data integration and cancer subtype identification. - Ying Yang; Sha Tian; Yushan Qiu; Pu Zhao; Quan Zou 001 (Briefings Bioinform., 2022)

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. - Meng Zhang 046; Cangzhi Jia; Fuyi Li; Chen Li 021; Yan Zhu 006; Tatsuya Akutsu; Geoffrey I. Webb; Quan Zou 001; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2022)

A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape. - Yongqing Zhang; Zixuan Wang; Yuanqi Zeng; Yuhang Liu; Shuwen Xiong; Maocheng Wang; Jiliu Zhou; Quan Zou 001 (Briefings Bioinform., 2022)

A survey on the algorithm and development of multiple sequence alignment. - Yongqing Zhang; Qiang Zhang; Jiliu Zhou; Quan Zou 001 (Briefings Bioinform., 2022)

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data. - Mengyuan Zhao; Wenying He; Jijun Tang; Quan Zou 001; Fei Guo 001 (Briefings Bioinform., 2022)

GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks. - Mengting Niu; Quan Zou 001; Chunyu Wang 002 (Bioinform., 2022)

i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites. - Mobeen Ur Rehman; Hilal Tayara; Quan Zou 001; Kil To Chong 001 (Bioinform., 2022)

NerLTR-DTA: drug-target binding affinity prediction based on neighbor relationship and learning to rank. - Xiaoqing Ru; Xiucai Ye; Tetsuya Sakurai; Quan Zou 001 (Bioinform., 2022)

Predicting protein-peptide binding residues via interpretable deep learning. - Ruheng Wang; Junru Jin; Quan Zou 001; Kenta Nakai; Leyi Wei (Bioinform., 2022)

Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks. - Yansu Wang; Ximei Luo; Quan Zou 001 (Bioinform., 2022)

webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. - Zilong Zhang; Feifei Cui; Wei Su; Lijun Dou; Anqi Xu; Chen Cao 002; Quan Zou 001 (Bioinform., 2022)

DeepMPM: a mortality risk prediction model using longitudinal EHR data. - Fan Yang 010; Jian Zhang; Wanyi Chen; Yongxuan Lai; Ying Wang; Quan Zou 001 (BMC Bioinform., 2022)

AMPpred-EL: An effective antimicrobial peptide prediction model based on ensemble learning. - Hongwu Lv; Ke Yan 003; Yichen Guo; Quan Zou 001; Abd El-Latif Hesham; Bin Liu 014 (Comput. Biol. Medicine, 2022)

A road map for happiness: The psychological factors related cell types in various parts of human body from single cell RNA-seq data analysis. - Ziwei Wang; Ying Zhang 060; Qun Li; Quan Zou 001; Qing Liu (Comput. Biol. Medicine, 2022)

iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank. - Hao Wu 066; Qi Liang; Wenxiang Zhang; Quan Zou 001; Abd El-Latif Hesham; Bin Liu 014 (Comput. Biol. Medicine, 2022)

Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. - Zilong Zhang; Feifei Cui; Chen Cao 002; Qingsuo Wang; Quan Zou 001 (Comput. Biol. Medicine, 2022)

MechRetro is a chemical-mechanism-driven graph learning framework for interpretable retrosynthesis prediction and pathway planning. - Yu Wang; Chao Pang; Yuzhe Wang; Yi Jiang; Junru Jin; Sirui Liang; Quan Zou 001; Leyi Wei (CoRR, 2022)

DeepM6ASeq-EL: prediction of human N6-methyladenosine (m6A) sites with LSTM and ensemble learning. - Juntao Chen; Quan Zou 001; Jing Li (Frontiers Comput. Sci., 2022)

Identification and classification of promoters using the attention mechanism based on long short-term memory. - Qingwen Li; Lichao Zhang; Lei Xu 047; Quan Zou 001; Jin Wu; Qingyuan Li (Frontiers Comput. Sci., 2022)

String kernels construction and fusion: a survey with bioinformatics application. - Ren Qi; Fei Guo 001; Quan Zou 001 (Frontiers Comput. Sci., 2022)

MLapSVM-LBS: Predicting DNA-binding proteins via a multiple Laplacian regularized support vector machine with local behavior similarity. - Mengwei Sun; Prayag Tiwari; Yuqing Qian; Yijie Ding; Quan Zou 001 (Knowl. Based Syst., 2022)

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. - Chen Cao 002; Jianhua Wang; Devin Kwok; Feifei Cui; Zilong Zhang; Da Zhao; Mulin Jun Li; Quan Zou 001 (Nucleic Acids Res., 2022)

Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization. - Yijie Ding; Prayag Tiwari; Fei Guo 001; Quan Zou 001 (Neural Networks, 2022)

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach. - Mengting Niu; Quan Zou 001; Chen Lin 001 (PLoS Comput. Biol., 2022)

CRCF: A Method of Identifying Secretory Proteins of Malaria Parasites. - Changli Feng; Jin Wu; Haiyan Wei; Lei Xu 047; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Significance-Based Essential Protein Discovery. - Yan Liu 085; Hao Liang; Quan Zou 001; Zengyou He (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

SgRNA-RF: Identification of SgRNA On-Target Activity With Imbalanced Datasets. - Mengting Niu; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

C-Loss Based Higher Order Fuzzy Inference Systems for Identifying DNA N4-Methylcytosine Sites. - Yijie Ding; Prayag Tiwari; Quan Zou 001; Fei Guo 001; Hari Mohan Pandey (IEEE Trans. Fuzzy Syst., 2022)

MDADP: A Webserver Integrating Database and Prediction Tools for Microbe-Disease Associations. - Lei Wang 069; Hao Li; Yuqi Wang 006; Yihong Tan; Zhiping Chen; Tingrui Pei; Quan Zou 001 (IEEE J. Biomed. Health Informatics, 2022)

A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data. - Ran Su; Haitang Yang; Leyi Wei; Siqi Chen 001; Quan Zou 001 (PLoS Comput. Biol., 2022)

Deep learning models for disease-associated circRNA prediction: a review. - Yaojia Chen; Jiacheng Wang 009; Chuyu Wang; Mingxin Liu; Quan Zou 001 (Briefings Bioinform., 2022)

WMSA: a novel method for multiple sequence alignment of DNA sequences. - Yanming Wei; Quan Zou 001; Furong Tang; Liang Yu 002 (Bioinform., 2022)

Exploring Parameter-Efficient Fine-Tuning of a Large-Scale Pre-Trained Model for scRNA-seq Cell Type Annotation. - Yuhang Liu; Tianhao Li; Zixuan Wang; Guiquan Zhu; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems. - Yunyun Su; Feifei Cui; Shiyu Yan; Quan Zou 001; Chen Cao 002; Zilong Zhang (BIBM, 2023)

KDProg: A Knowledge distillation graph neural network for cancer prognosis prediction and analysis. - Shuwen Xiong; Zixuan Wang; Junming Zhang; Hong Luo; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

HGTDG: An Interpretable Heterogeneous Graph Transformer Framework for Cancer Driver Gene Prediction. - Shuwen Xiong; Zixuan Wang; Junming Zhang; Guiquan Zhu; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

Virtual Screening of Traditional Chinese Medicine for Discovery of Potential Anti-SARS-CoV-2 Lead Molecules. - Xin Zhang 103; Quan Zou 001 (ICBBT, 2023)

Recall DNA methylation levels at low coverage sites using a CNN model in WGBS. - Ximei Luo; Yansu Wang; Quan Zou 001; Lei Xu 047 (PLoS Comput. Biol., 2023)

Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via $L_{2,1/2}$L2,1/2-Matrix Norm. - Yijie Ding; Wenying He; Jijun Tang; Quan Zou 001; Fei Guo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Protein-DNA Binding Residues Prediction Using a Deep Learning Model With Hierarchical Feature Extraction. - Shixuan Guan; Quan Zou 001; Hongjie Wu; Yijie Ding (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Multi-View Kernel Sparse Representation for Identification of Membrane Protein Types. - Yuqing Qian; Yijie Ding; Quan Zou 001; Fei Guo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Enhancer-FRL: Improved and Robust Identification of Enhancers and Their Activities Using Feature Representation Learning. - Chao Wang 043; Quan Zou 001; Ying Ju; Hua Shi (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Decision Tree for Sequences. - Zengyou He; Ziyao Wu; Guangyao Xu; Yan Liu 085; Quan Zou 001 (IEEE Trans. Knowl. Data Eng., 2023)

Matrix reconstruction with reliable neighbors for predicting potential MiRNA-disease associations. - Hailin Feng; Dongdong Jin; Jian Li 032; Yane Li; Quan Zou 001; Tongcun Liu (Briefings Bioinform., 2023)

Subspace projection-based weighted echo state networks for predicting therapeutic peptides. - Xiaoyi Guo; Prayag Tiwari; Quan Zou 001; Yijie Ding (Knowl. Based Syst., 2023)

PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression. - Liangjie Sun; Yushan Qiu; Wai-Ki Ching; Pu Zhao; Quan Zou 001 (PLoS Comput. Biol., 2023)

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder. - Jing Jiang; Junlin Xu; Yuansheng Liu; Bosheng Song; Xiulan Guo; Xiangxiang Zeng; Quan Zou 001 (Briefings Bioinform., 2023)

SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data. - Yushan Qiu; Chang Yan; Pu Zhao; Quan Zou 001 (Briefings Bioinform., 2023)

WMSA 2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies. - Juntao Chen; Jiannan Chao; Huan Liu 024; Fenglong Yang; Quan Zou 001; Furong Tang (Briefings Bioinform., 2023)

CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. - Zhongshen Li; Junru Jin; Wenjia He; Wentao Long; Haoqing Yu; Xin Gao 001; Kenta Nakai; Quan Zou 001; Leyi Wei (Briefings Bioinform., 2023)

MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactions. - Haoran Sun; Zhaoqi Song; Qiuming Chen; Meiling Wang; Furong Tang; Lijun Dou; Quan Zou 001; Fenglong Yang (Briefings Bioinform., 2023)

Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites. - Shihu Jiao; Xiucai Ye; Chunyan Ao; Tetsuya Sakurai; Quan Zou 001; Lei Xu 047 (Bioinform., 2023)

Optimization of drug-target affinity prediction methods through feature processing schemes. - Xiaoqing Ru; Quan Zou 001; Chen Lin 001 (Bioinform., 2023)

AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional Networks. - Ali Raza; Jamal Uddin; Abdullah Almuhaimeed; Shahid Akbar; Quan Zou 001; Ashfaq Ahmad (J. Chem. Inf. Model., 2023)

FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultralong datasets. - Pinglu Zhang; Huan Liu 024; Yanming Wei; Yixiao Zhai; Qinzhong Tian; Quan Zou 001 (Zenodo, 2023)

GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in Genomics. - Zijie Shen; Enhui Shen; Qian-Hao Zhu; Longjiang Fan; Quan Zou 001; Chu-Yu Ye (Adv. Intell. Syst., 2023)

Predicting active enhancers with DNA methylation and histone modification. - Ximei Luo; Qun Li; Yifan Tang; Yan Liu 085; Quan Zou 001; Jie Zheng; Ying Zhang 060; Lei Xu 047 (BMC Bioinform., 2023)

Multi-correntropy fusion based fuzzy system for predicting DNA N4-methylcytosine sites. - Yijie Ding; Prayag Tiwari; Fei Guo 001; Quan Zou 001 (Inf. Fusion, 2023)

Cell-Specific Highly Correlated Network for Self-Supervised Distillation in Cell Type Annotation. - Tianhao Li; Yugui Xu; Sihan He; Yuhang Liu; Zixuan Wang; Zhigan Zhou; Yongqing Zhang; Quan Zou 001 (BIBM, 2024)

RNASite: A one-stop tool website that integrates multiple RNA modification site databases and servers. - Jiahao Yuan; Xingfeng Li 001; Zilong Zhang; Qingchen Zhang 001; Quan Zou 001; Feifei Cui (BIBM, 2024)

AAHLDMA: Predicting Drug-Microbe Associations Based on Bridge Graph Learning. - Yaojia Chen; Mengting Niu; Yi Liu 112; Jiacheng Wang 009; Yijie Ding; Quan Zou 001 (ICIC (LNBI 2), 2024)

Spatial Domain Identifying: Graph Attention Network with Two Different Decoders. - Yi Liu 112; Quan Zou 001 (ICIC (LNBI 1), 2024)

iAFPs-Mv-BiTCN: Predicting antifungal peptides using self-attention transformer embedding and transform evolutionary based multi-view features with bidirectional temporal convolutional networks. - Shahid Akbar; Quan Zou 001; Ali Raza; Fawaz Khaled Alarfaj (Artif. Intell. Medicine, 2024)

ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction. - Lijun Cai; Guanyu Yue; Yifan Chen; Li Wang 145; Xiaojun Yao; Quan Zou 001; Xiangzheng Fu; Dong-Sheng Cao 001 (Briefings Bioinform., 2024)

GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering. - Lu-Bin Cui; Guiliang Guo; Michael K. Ng 001; Quan Zou 001; Yushan Qiu (Briefings Bioinform., 2024)

Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction. - Limuxuan He; Quan Zou 001; Qi Dai; Shuang Cheng; Yansu Wang (Briefings Bioinform., 2024)

scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks. - Tianxiang Liu; Cangzhi Jia; Yue Bi; Xudong Guo; Quan Zou 001; Fuyi Li (Briefings Bioinform., 2024)

scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization. - Yushan Qiu; Dong Guo; Pu Zhao; Quan Zou 001 (Briefings Bioinform., 2024)

TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach. - Matee Ullah; Shahid Akbar; Ali Raza; Kashif Ahmad Khan; Quan Zou 001 (Briefings Bioinform., 2024)

stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization. - Runqing Wang; Qiguo Dai; Xiaodong Duan; Quan Zou 001 (Briefings Bioinform., 2024)

MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning. - Tao Wang; Zhen Li 015; Linlin Zhuo; Yifan Chen; Xiangzheng Fu; Quan Zou 001 (Briefings Bioinform., 2024)

Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization. - Rui Wang; Tao Wang; Linlin Zhuo; Jinhang Wei; Xiangzheng Fu; Quan Zou 001; Xiaojun Yao (Briefings Bioinform., 2024)

FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Briefings Bioinform., 2024)

A two-task predictor for discovering phase separation proteins and their undergoing mechanism. - Yetong Zhou; Shengming Zhou; Yue Bi; Quan Zou 001; Cangzhi Jia (Briefings Bioinform., 2024)

Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs. - Zhecheng Zhou; Linlin Zhuo; Xiangzheng Fu; Quan Zou 001 (Briefings Bioinform., 2024)

SBSM-Pro: support bio-sequence machine for proteins. - Yizheng Wang; Yixiao Zhai; Yijie Ding; Quan Zou 001 (Sci. China Inf. Sci., 2024)

Multi-source data integration for explainable miRNA-driven drug discovery. - Zhen Li 015; Qingquan Liao; Wenbin Liu; Peng Xu 004; Linlin Zhuo; Xiangzheng Fu; Quan Zou 001 (Future Gener. Comput. Syst., 2024)

Drug repositioning by multi-aspect heterogeneous graph contrastive learning and positive-fusion negative sampling strategy. - Junkai Liu; Fuyuan Hu; Quan Zou 001; Prayag Tiwari; Hongjie Wu; Yijie Ding (Inf. Fusion, 2024)

Random subsequence forests. - Zengyou He; Jiaqi Wang; Mudi Jiang; Lianyu Hu 001; Quan Zou 001 (Inf. Sci., 2024)

DeepAIPs-Pred: Predicting Anti-Inflammatory Peptides Using Local Evolutionary Transformation Images and Structural Embedding-Based Optimal Descriptors with Self-Normalized BiTCNs. - Shahid Akbar; Matee Ullah; Ali Raza; Quan Zou 001; Wajdi Alghamdi (J. Chem. Inf. Model., 2024)

AMPpred-MFA: An Interpretable Antimicrobial Peptide Predictor with a Stacking Architecture, Multiple Features, and Multihead Attention. - Changjiang Li; Quan Zou 001; Cangzhi Jia; Jia Zheng (J. Chem. Inf. Model., 2024)

Deep Generative Models in De Novo Drug Molecule Generation. - Chao Pang; Jianbo Qiao; Xiangxiang Zeng; Quan Zou 001; Leyi Wei (J. Chem. Inf. Model., 2024)

AMDGT: Attention aware multi-modal fusion using a dual graph transformer for drug-disease associations prediction. - Junkai Liu; Shixuan Guan; Quan Zou 001; Hongjie Wu; Prayag Tiwari; Yijie Ding (Knowl. Based Syst., 2024)

Sequence homology score-based deep fuzzy network for identifying therapeutic peptides. - Xiaoyi Guo; Ziyu Zheng; Kang Hao Cheong; Quan Zou 001; Prayag Tiwari; Yijie Ding (Neural Networks, 2024)

MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. - Hao Duan; Qingchen Zhang 001; Feifei Cui; Quan Zou 001; Zilong Zhang (PLoS Comput. Biol., 2024)

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization. - Yuqing Qian; Quan Zou 001; Mengyuan Zhao; Yi Liu 112; Fei Guo 001; Yijie Ding (PLoS Comput. Biol., 2024)

MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm. - Chao Wang 043; Quan Zou 001 (PLoS Comput. Biol., 2024)

ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification. - Tao Wang; Linlin Zhuo; Yifan Chen; Xiangzheng Fu; Xiangxiang Zeng; Quan Zou 001 (PLoS Comput. Biol., 2024)

Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model. - Yanpeng Yang; Yanyi Zheng; Quan Zou 001; Jian Li 032; Hailin Feng (PLoS Comput. Biol., 2024)

TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. - Yixiao Zhai; Jiannan Chao; Yizheng Wang; Pinglu Zhang; Furong Tang; Quan Zou 001 (PLoS Comput. Biol., 2024)

PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites. - Mingshuai Chen; Quan Zou 001; Ren Qi; Yijie Ding (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Prediction of Potential miRNA-Disease Associations Based on a Masked Graph Autoencoder. - Hailin Feng; Chenchen Ke; Quan Zou 001; Zhechen Zhu; Tongcun Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Hyb_SEnc: An Antituberculosis Peptide Predictor Based on a Hybrid Feature Vector and Stacked Ensemble Learning. - Xiuhao Fu; Hao Duan; Xiaofeng Zang; Chunling Liu; Xingfeng Li 001; Qingchen Zhang 001; Zilong Zhang; Quan Zou 001; Feifei Cui (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

AGML: Adaptive Graph-Based Multi-Label Learning for Prediction of RBP and as Event Associations During EMT. - Yushan Qiu; Wensheng Chen; Wai-Ki Ching; Hongmin Cai; Hao Jiang 009; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Multiple Kronecker RLS fusion-based link propagation for drug-side effect prediction. - Yuqing Qian; Ziyu Zheng; Prayag Tiwari; Yijie Ding; Quan Zou 001 (Trans. Mach. Learn. Res., 2024)

FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization. - Jici Jiang; Hongdi Pei; Jiayu Li; Mingxin Li; Quan Zou 001; Zhibin Lv (Briefings Bioinform., 2024)

Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2. - Mengting Niu; Chunyu Wang 002; Yaojia Chen; Quan Zou 001; Lei Xu 047 (Briefings Bioinform., 2024)

FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. - Pinglu Zhang; Huan Liu 024; Yanming Wei; Yixiao Zhai; Qinzhong Tian; Quan Zou 001 (Bioinform., 2024)

AttentionMGT-DTA: A multi-modal drug-target affinity prediction using graph transformer and attention mechanism. - Hongjie Wu; Junkai Liu; Tengsheng Jiang; Quan Zou 001; Shujie Qi; Zhiming Cui; Prayag Tiwari; Yijie Ding (Neural Networks, 2024)

AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding. - Yaojia Chen; Jiacheng Wang 009; Chunyu Wang 002; Quan Zou 001 (PLoS Comput. Biol., 2024)

FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using t-blocks based on FOur Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Zenodo, 2024)

Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning. - Yizheng Wang; Xin Zhang 103; Ying Ju; Qing Liu; Quan Zou 001; Yazhou Zhang; Yijie Ding; Ying Zhang 060 (Frontiers Comput. Sci., 2024)

Identification of Drug-Side-Effect Association via Multiview Semisupervised Sparse Model. - Yijie Ding; Fei Guo 001; Prayag Tiwari; Quan Zou 001 (IEEE Trans. Artif. Intell., 2024)

MAMLCDA: A Meta-Learning Model for Predicting circRNA-Disease Association Based on MAML Combined With CNN. - Yuanyi Tian; Quan Zou 001; Chunyu Wang 002; Cangzhi Jia (IEEE J. Biomed. Health Informatics, 2024)

Fuzzy Neural Tangent Kernel Model for Identifying DNA N4-Methylcytosine Sites. - Yijie Ding; Prayag Tiwari; Fei Guo 001; Quan Zou 001; Weiping Ding 001 (IEEE Trans. Fuzzy Syst., 2024)

iProps: A Comprehensive Software Tool for Protein Classification and Analysis With Automatic Machine Learning Capabilities and Model Interpretation Capabilities. - Changli Feng; Haiyan Wei; Chugui Xu; Bin Feng 002; Xiaorong Zhu; Jing Liu 068; Quan Zou 001 (IEEE J. Biomed. Health Informatics, 2024)

FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity. - Yanming Wei; Tong Zhou 016; Yixiao Zhai; Liang Yu 002; Quan Zou 001 (Zenodo, 2024)

Dastset and code for Fast sequence alignment for centromere with RaMA. - Pinglu Zhang; Yanming Wei; Qinzhong Tian; Quan Zou 001; Yansu Wang (Zenodo, 2024)

Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking model. - Shahid Akbar; Ali Raza; Quan Zou 001 (BMC Bioinform., 2024)

StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning. - Gul Rukh; Shahid Akbar; Gauhar Rehman; Fawaz Khaled Alarfaj; Quan Zou 001 (BMC Bioinform., 2024)

SeqAlignXGBoost: Sequence Alignment and Feature Selection for m1A Modification Site Identification. - Yizheng Wang; Yijie Ding; Quan Zou 001 (ICIC (28), 2025)

ReAlign-Star: An Optimized Realignment Method for Multiple Sequence Alignment, Targeting Star Algorithm Tools. - Yixiao Zhai; Pinglu Zhang; Yi Liu 112; Quan Zou 001 (ICIC (26), 2025)

Supervised pre-training for feature extraction in cell type annotation of single-cell multi-omics data. - Yongqing Zhang; Tianhao Li; Yuhang Liu; Hong Luo; Yugui Xu; Zixuan Wang; Quan Zou 001 (Appl. Soft Comput., 2025)

An overview of computational methods in single-cell transcriptomic cell type annotation. - Tianhao Li; Zixuan Wang; Yuhang Liu; Sihan He; Quan Zou 001; Yongqing Zhang (Briefings Bioinform., 2025)

AttenRNA: multi-scale deep attentive model with RNA feature variability analysis. - Jing Li; Quan Zou 001; Chao Zhan (Briefings Bioinform., 2025)

PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. - Ruiqi Liu; Shankai Yan; Zilong Zhang; Junlin Xu; Yajie Meng; Qingchen Zhang 001; Leyi Wei; Quan Zou 001; Feifei Cui (Comput. Biol. Chem., 2025)

pACPs-DNN: Predicting anticancer peptides using novel peptide transformation into evolutionary and structure matrix-based images with self-attention deep learning model. - Shahid; Maqsood Hayat; Ali Raza; Shahid Akbar; Wajdi Alghamdi; Nadeem Iqbal 002; Quan Zou 001 (Comput. Biol. Chem., 2025)

SGPS-IMR: Efficiently inferring microbial resistance using self-supervised graph perturbation strategy. - Wentao Wang; Linlin Zhuo; Zhecheng Zhou; Xiangzheng Fu; Quan Zou 001 (Expert Syst. Appl., 2025)

A survey on multi-view fusion for predicting links in biomedical bipartite networks: Methods and applications. - Yuqing Qian; Yizheng Wang; Junkai Liu; Quan Zou 001; Yijie Ding; Xiaoyi Guo; Weiping Ding 001 (Inf. Fusion, 2025)

SQ-DiffuPep: A multimodal information-guided quantitative latent diffusion model for antimicrobial peptide discovery. - Luoda Tan; Li Wang 145; Xuanbai Ren; Quan Zou 001; Xiaojun Yao; Xiangxiang Zeng; Xiangzheng Fu (Inf. Fusion, 2025)

Improving protein-protein interaction modulator predictions via knowledge-fused language models. - Zitong Zhang; Quan Zou 001; Chunyu Wang 002; Junjie Wang 005; Lingling Zhao (Inf. Fusion, 2025)

Beyond ST-246: Unveiling Potential Inhibitors Targeting VP37 Protein in Silico From Herb and Marine Databases. - Runhua Zhang; Xin Zhang 103; Shulin Zhao 003; Quan Zou 001; Yijie Ding; Xiaoyi Guo; Hongjie Wu (J. Comput. Chem., 2025)

ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. - Aoyun Geng; Zhenjie Luo; Aohan Li; Zilong Zhang; Quan Zou 001; Leyi Wei; Feifei Cui (J. Chem. Inf. Model., 2025)

AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. - Yuanhao Li; Aoyun Geng; Zheyu Zhou; Feifei Cui; Junlin Xu; Yajie Meng; Leyi Wei; Quan Zou 001; Qingchen Zhang 001; Zilong Zhang (J. Chem. Inf. Model., 2025)

m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. - Xinyu Li; Zhenjie Luo; Jingwei Lv; Chao Yang; Shankai Yan; Junlin Xu; Yajie Meng; Leyi Wei; Zilong Zhang; Quan Zou 001; Feifei Cui (J. Chem. Inf. Model., 2025)

Clustering Categorical Data via Multiple Hypothesis Testing. - Lianyu Hu 001; Mudi Jiang; Yan Liu 085; Quan Zou 001; Zengyou He (ACM Trans. Knowl. Discov. Data, 2025)

DSANIB: Drug-Target Interaction Predictions With Dual-View Synergistic Attention Network and Information Bottleneck Strategy. - Zhen Tian; Zhuangzhuang Zhang; Wanning Zhou; Zhixia Teng; Wei Song; Quan Zou 001 (IEEE J. Biomed. Health Informatics, 2025)

deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment. - Yanming Wei; Zhaoyang Huang; Pinglu Zhang; Yizheng Wang; Liang Yu 002; Quan Zou 001 (Zenodo, 2025)

AEGNN-M:A 3D Graph-Spatial Co-Representation Model for Molecular Property Prediction. - Lijun Cai; Yuling He; Xiangzheng Fu; Linlin Zhuo; Quan Zou 001; Xiaojun Yao (IEEE J. Biomed. Health Informatics, 2025)

Computational approaches for circRNA-disease association prediction: a review. - Mengting Niu; Yaojia Chen; Chunyu Wang 002; Quan Zou 001; Lei Xu 047 (Frontiers Comput. Sci., 2025)

GRACE: Unveiling Gene Regulatory Networks With Causal Mechanistic Graph Neural Networks in Single-Cell RNA-Sequencing Data. - Jiacheng Wang 009; Yaojia Chen; Quan Zou 001 (IEEE Trans. Neural Networks Learn. Syst., 2025)

Self-Cumulative Contrastive Graph Clustering. - Xiaoqiang Yan; Kun Deng; Quan Zou 001; Zhen Tian; Hui Yu 001 (IEEE CAA J. Autom. Sinica, 2025)

Multi-Modal Deep Representation Learning Accurately Identifies and Interprets Drug-Target Interactions. - Jiayue Hu; Yuhang Liu; Xiangxiang Zeng; Quan Zou 001; Ran Su; Leyi Wei (IEEE J. Biomed. Health Informatics, 2025)

Multiview Deep Learning-Based Molecule Design and Structural Optimization Accelerates Inhibitor Discover. - Chao Pang; Yu Wang; Yi Jiang; Ruheng Wang; Xiaojun Yao; Quan Zou 001; Xiangxiang Zeng; Ran Su; Leyi Wei (IEEE Trans. Neural Networks Learn. Syst., 2025)