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Viewing Publication 1 - 100 from 124

2024

Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking modelShahid Akbar, Ali Raza, Quan Zou 0001. bmcbi, 25(1):102, December 2024. [doi]

FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimizationJici Jiang, Hongdi Pei, Jiayu Li, Mingxin Li, Quan Zou 0001, Zhibin Lv. bib, 25(2), January 2024. [doi]

Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou 0001, Lei Xu. bib, 25(2), January 2024. [doi]

Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learningYizheng Wang, Xin Zhang, Ying Ju, Qing Liu, Quan Zou 0001, Yazhou Zhang, Yijie Ding, Ying Zhang. fcsc, 18(2):182903, April 2024. [doi]

AttentionMGT-DTA: A multi-modal drug-target affinity prediction using graph transformer and attention mechanismHongjie Wu, Junkai Liu, Tengsheng Jiang, Quan Zou 0001, Shujie Qi, Zhiming Cui, Prayag Tiwari, Yijie Ding. NN, 169:623-636, January 2024. [doi]

FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasetsPinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou 0001. bioinformatics, 40(1), January 2024. [doi]

2023

Enhancer-FRL: Improved and Robust Identification of Enhancers and Their Activities Using Feature Representation LearningChao Wang 0043, Quan Zou 0001, Ying Ju, Hua Shi. tcbb, 20(2):967-975, March - April 2023. [doi]

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 strategiesJuntao Chen, Jiannan Chao, Huan Liu, Fenglong Yang, Quan Zou 0001, Furong Tang. bib, 24(4), July 2023. [doi]

Multi-correntropy fusion based fuzzy system for predicting DNA N4-methylcytosine sitesYijie Ding, Prayag Tiwari, Fei Guo 0001, Quan Zou 0001. inffus, 100:101911, December 2023. [doi]

Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via $L_{2,1/2}$L2,1/2-Matrix NormYijie Ding, Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo 0001. tcbb, 20(1):500-511, January - February 2023. [doi]

Protein-DNA Binding Residues Prediction Using a Deep Learning Model With Hierarchical Feature ExtractionShixuan Guan, Quan Zou 0001, Hongjie Wu, Yijie Ding. tcbb, 20(5):2619-2628, September - October 2023. [doi]

Subspace projection-based weighted echo state networks for predicting therapeutic peptidesXiaoyi Guo, Prayag Tiwari, Quan Zou 0001, Yijie Ding. kbs, 263:110307, March 2023. [doi]

Decision Tree for SequencesZengyou He, Ziyao Wu, Guangyao Xu, Yan Liu, Quan Zou 0001. tkde, 35(1):251-263, 2023. [doi]

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoderJing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou 0001. bib, 24(3), May 2023. [doi]

Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sitesShihu Jiao, Xiucai Ye, Chunyan Ao, Tetsuya Sakurai, Quan Zou 0001, Lei Xu. bioinformatics, 39(10), October 2023. [doi]

Recall DNA methylation levels at low coverage sites using a CNN model in WGBSXimei Luo, Yansu Wang, Quan Zou 0001, Lei Xu. ploscb, 19(6), 2023. [doi]

Predicting active enhancers with DNA methylation and histone modificationXimei Luo, Qun Li, Yifan Tang, Yan Liu, Quan Zou 0001, Jie Zheng, Ying Zhang, Lei Xu. bmcbi, 24(1):414, December 2023. [doi]

Multi-View Kernel Sparse Representation for Identification of Membrane Protein TypesYuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. tcbb, 20(2):1234-1245, March - April 2023. [doi]

SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq dataYushan Qiu, Chang Yan, Pu Zhao, Quan Zou 0001. bib, 24(3), May 2023. [doi]

AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional NetworksAli Raza, Jamal Uddin, Abdullah Almuhaimeed, Shahid Akbar, Quan Zou 0001, Ashfaq Ahmad. jcisd, 63(21):6537-6554, November 2023. [doi]

Optimization of drug-target affinity prediction methods through feature processing schemesXiaoqing Ru, Quan Zou 0001, Chen Lin. bioinformatics, 39(11), November 2023. [doi]

GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in GenomicsZijie Shen, Enhui Shen, Qian-Hao Zhu, Longjiang Fan, Quan Zou 0001, Chu-Yu Ye. aisy, 5(12), December 2023. [doi]

PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progressionLiangjie Sun, Yushan Qiu, Wai-Ki Ching, Pu Zhao, Quan Zou 0001. ploscb, 19(3), March 2023. [doi]

MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactionsHaoran Sun, Zhaoqi Song, Qiuming Chen, Meiling Wang, Furong Tang, Lijun Dou, Quan Zou 0001, Fenglong Yang. bib, 24(6), September 2023. [doi]

2022

MDADP: A Webserver Integrating Database and Prediction Tools for Microbe-Disease AssociationsLei Wang 0069, Hao Li, Yuqi Wang, Yihong Tan, Zhiping Chen, Tingrui Pei, Quan Zou 0001. titb, 26(7):3427-3434, 2022. [doi]

NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequencesChunyan Ao, Quan Zou 0001, Liang Yu. bib, 23(1), 2022. [doi]

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association studyChen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou 0001. nar, 50(D1):1123-1130, 2022. [doi]

6A) sites with LSTM and ensemble learningJuntao Chen, Quan Zou 0001, Jing Li. fcsc, 16(2):162302, 2022. [doi]

C-Loss Based Higher Order Fuzzy Inference Systems for Identifying DNA N4-Methylcytosine SitesYijie Ding, Prayag Tiwari, Quan Zou 0001, Fei Guo 0001, Hari Mohan Pandey. tfs, 30(11):4754-4765, 2022. [doi]

Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localizationYijie Ding, Prayag Tiwari, Fei Guo 0001, Quan Zou 0001. NN, 156:170-178, 2022. [doi]

Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorizationYijie Ding, Jijun Tang, Fei Guo, Quan Zou 0001. bib, 23(2), 2022. [doi]

CRCF: A Method of Identifying Secretory Proteins of Malaria ParasitesChangli Feng, Jin Wu, Haiyan Wei, Lei Xu, Quan Zou 0001. tcbb, 19(4):2149-2157, 2022. [doi]

Kernel Risk Sensitive Loss-based Echo State Networks for Predicting Therapeutic Peptides with Sparse LearningXiaoyi Guo, Yuqing Qian, Prayag Tiwari, Quan Zou 0001, Yijie Ding. bibm 2022: 6-11 [doi]

DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule networkJhabindra Khanal, Hilal Tayara, Quan Zou 0001, Kil To Chong. bib, 23(1), 2022. [doi]

Identification and classification of promoters using the attention mechanism based on long short-term memoryQingwen Li, Lichao Zhang, Lei Xu, Quan Zou 0001, Jin Wu, Qingyuan Li. fcsc, 16(4):164348, 2022. [doi]

Significance-Based Essential Protein DiscoveryYan Liu, Hao Liang, Quan Zou 0001, Zengyou He. tcbb, 19(1):633-642, 2022. [doi]

i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sitesMobeen-ur-Rehman, Hilal Tayara, Quan Zou 0001, Kil To Chong. bioinformatics, 38(16):3885-3891, 2022. [doi]

SgRNA-RF: Identification of SgRNA On-Target Activity With Imbalanced DatasetsMengting Niu, Quan Zou 0001. tcbb, 19(4):2442-2453, 2022. [doi]

GATSDCD: Prediction of circRNA-Disease Associations Based on Singular Value Decomposition and Graph Attention NetworkMengting Niu, Abd El-Latif Hesham, Quan Zou 0001. icic 2022: 14-27 [doi]

Characterizing viral circRNAs and their application in identifying circRNAs in virusesMengting Niu, Ying Ju, Chen Lin, Quan Zou 0001. bib, 23(1), 2022. [doi]

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approachMengting Niu, Quan Zou 0001, Chen Lin. ploscb, 18(1), 2022. [doi]

GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networksMengting Niu, Quan Zou 0001, Chunyu Wang. bioinformatics, 38(8):2246-2253, 2022. [doi]

String kernels construction and fusion: a survey with bioinformatics applicationRen Qi, Fei Guo, Quan Zou 0001. fcsc, 16(6):166904, 2022. [doi]

Identification of drug-side effect association via restricted Boltzmann machines with penalized termYuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. bib, 23(6), 2022. [doi]

NerLTR-DTA: drug-target binding affinity prediction based on neighbor relationship and learning to rankXiaoqing Ru, Xiucai Ye, Tetsuya Sakurai, Quan Zou 0001. bioinformatics, 38(7):1964-1971, 2022. [doi]

Distant metastasis identification based on optimized graph representation of gene interaction patternsRan Su, Yingying Zhu, Quan Zou 0001, Leyi Wei. bib, 23(1), 2022. [doi]

A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics dataRan Su, Haitang Yang, Leyi Wei, Siqi Chen, Quan Zou 0001. ploscb, 18(9):1010402, September 2022. [doi]

MLapSVM-LBS: Predicting DNA-binding proteins via a multiple Laplacian regularized support vector machine with local behavior similarityMengwei Sun, Prayag Tiwari, Yuqing Qian, Yijie Ding, Quan Zou 0001. kbs, 250:109174, 2022. [doi]

Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networksYansu Wang, Ximei Luo, Quan Zou 0001. bioinformatics, 38(14):3541-3548, 2022. [doi]

Predicting protein-peptide binding residues via interpretable deep learningRuheng Wang, Junru Jin, Quan Zou 0001, Kenta Nakai, Leyi Wei. bioinformatics, 38(13):3351-3360, 2022. [doi]

Single-cell TF-DNA binding prediction and analysis based on transfer learning frameworkZixuan Wang, Yongqing Zhang, Yun Yu, Maocheng Wang, Yuhang Liu, Quan Zou 0001. bibm 2022: 589-594 [doi]

A road map for happiness: The psychological factors related cell types in various parts of human body from single cell RNA-seq data analysisZiwei Wang, Ying Zhang, Qun Li, Quan Zou 0001, Qing Liu. cbm, 143:105286, 2022. [doi]

WMSA: a novel method for multiple sequence alignment of DNA sequencesYanming Wei, Quan Zou 0001, Furong Tang, Liang Yu. bioinformatics, 38(22):5019-5025, November 2022. [doi]

iLncDA-LTR: Identification of lncRNA-disease associations by learning to rankHao Wu, Qi Liang, Wenxiang Zhang, Quan Zou 0001, Abd El-Latif Hesham, Bin Liu 0014. cbm, 146:105605, 2022. [doi]

DeepMPM: a mortality risk prediction model using longitudinal EHR dataFan Yang, Jian Zhang, Wanyi Chen, Yongxuan Lai, Ying Wang, Quan Zou 0001. bmcbi, 23(1):423, 2022. [doi]

MDICC: novel method for multi-omics data integration and cancer subtype identificationYing Yang, Sha Tian, Yushan Qiu, Pu Zhao, Quan Zou 0001. bib, 23(3), 2022. [doi]

A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shapeYongqing Zhang, Zixuan Wang, Yuanqi Zeng, Yuhang Liu, Shuwen Xiong, Maocheng Wang, Jiliu Zhou, Quan Zou 0001. bib, 23(1), 2022. [doi]

Predicting cell type-specific effects of variants on TF-DNA binding by meta-learningYongqing Zhang, Yuhang Liu, Zixuan Wang, Maocheng Wang, Shuwen Xiong, Quan Zou 0001. bibm 2022: 680-685 [doi]

webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integrationZilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou 0001. bioinformatics, 38(13):3488-3489, 2022. [doi]

Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infectionsZilong Zhang, Feifei Cui, Chen Cao, Qingsuo Wang, Quan Zou 0001. cbm, 140:105092, 2022. [doi]

Critical assessment of computational tools for prokaryotic and eukaryotic promoter predictionMeng Zhang, Cangzhi Jia, Fuyi Li, Chen Li 0021, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou 0001, Lachlan J. M. Coin, Jiangning Song. bib, 23(2), 2022. [doi]

A survey on the algorithm and development of multiple sequence alignmentYongqing Zhang, Qiang Zhang, Jiliu Zhou, Quan Zou 0001. bib, 23(3), 2022. [doi]

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic dataMengyuan Zhao, Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo. bib, 23(2), 2022. [doi]

2021

DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNAChao Wang 0043, Ying Ju, Quan Zou 0001, Chen Lin. bioinformatics, 38(1):52-57, 2021. [doi]

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representationLijun Cai, Li Wang, Xiangzheng Fu, Chenxing Xia, Xiangxiang Zeng, Quan Zou 0001. bib, 22(4), July 2021. [doi]

Computational biology and chemistry Special section editorial: Computational analyses for miRNAFeifei Cui, Murong Zhou, Quan Zou 0001. CANDC, 91:107448, 2021. [doi]

IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence AnalysisFeifei Cui, Quan Zou 0001, Qin Ma, Leyi Wei, Jijun Tang, Dariusz Mrozek. access, 9:33110-33119, 2021. [doi]

A comprehensive review of the imbalance classification of protein post-translational modificationsLijun Dou, Fenglong Yang, Lei Xu, Quan Zou 0001. bib, 22(5), 2021. [doi]

Using a low correlation high orthogonality feature set and machine learning methods to identify plant pentatricopeptide repeat coding gene/proteinChangli Feng, Quan Zou 0001, Donghua Wang. ijon, 424:246-254, 2021. [doi]

Instance-Based Classification Through Hypothesis TestingZengyou He, Chaohua Sheng, Yan Liu, Quan Zou 0001. access, 9:17485-17494, 2021. [doi]

MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstructionWenying He, Jijun Tang, Quan Zou 0001, Fei Guo. bib, 22(6), 2021. [doi]

SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learningJing Li, Lichao Zhang, Shida He, Fei Guo, Quan Zou 0001. bib, 22(5), 2021. [doi]

EP3: an ensemble predictor that accurately identifies type III secreted effectorsJing Li, Leyi Wei, Fei Guo, Quan Zou 0001. bib, 22(2):1918-1928, 2021. [doi]

DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequencesJiawei Li, Yuqian Pu, Jijun Tang, Quan Zou 0001, Fei Guo. bib, 22(3), 2021. [doi]

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizersYuansheng Liu, Xiaocai Zhang, Quan Zou 0001, Xiangxiang Zeng. bioinformatics, 37(11):1604-1606, 2021. [doi]

Identification of sub-Golgi protein localization by use of deep representation learning featuresZhibin Lv, Pingping Wang, Quan Zou 0001, Qinghua Jiang. bioinformatics, 36(24):5600-5609, 2021. [doi]

Anticancer peptides prediction with deep representation learning featuresZhibin Lv, Feifei Cui, Quan Zou 0001, Lichao Zhang, Lei Xu. bib, 22(5), 2021. [doi]

A Convolutional Neural Network Using Dinucleotide One-hot Encoder for identifying DNA N6-Methyladenine Sites in the Rice GenomeZhibin Lv, Hui Ding, Lei Wang, Quan Zou 0001. ijon, 422:214-221, 2021. [doi]

iPro2L-PSTKNC: A Two-Layer Predictor for Discovering Various Types of Promoters by Position Specific of Nucleotide CompositionYinuo Lyu, Wenying He, Shuhao Li, Quan Zou 0001, Fei Guo. titb, 25(6):2329-2337, 2021. [doi]

rBPDL: Predicting RNA-Binding Proteins Using Deep LearningMengting Niu, Jin Wu, Quan Zou 0001, Zhendong Liu, Lei Xu. titb, 25(9):3668-3676, 2021. [doi]

A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq dataRen Qi, Jin Wu, Fei Guo, Lei Xu, Quan Zou 0001. bib, 22(4), 2021. [doi]

Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transitionYushan Qiu, Wai-Ki Ching, Quan Zou 0001. bib, 22(6), 2021. [doi]

Prediction of RNA-binding protein and alternative splicing event associations during epithelial-mesenchymal transition based on inductive matrix completionYushan Qiu, Wai-Ki Ching, Quan Zou 0001. bib, 22(5), 2021. [doi]

Application of learning to rank in bioinformatics tasksXiaoqing Ru, Xiucai Ye, Tetsuya Sakurai, Quan Zou 0001. bib, 22(5), 2021. [doi]

Revisiting genome-wide association studies from statistical modelling to machine learningShanwen Sun, BenZhi Dong, Quan Zou 0001. bib, 22(4), 2021. [doi]

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification methodShanwen Sun, Lei Xu, Quan Zou 0001, Guohua Wang. bioinformatics, 37(9):1319-1321, 2021. [doi]

Membrane Protein Identification via Multi-view Graph Regularized k-Local Hyperplane Distance Nearest Neighbor ModelMengwei Sun, Yuqing Qian, Yijie Ding, Jijun Tang, Quan Zou 0001. bibm 2021: 80-85 [doi]

Machine learning for phytopathology: from the molecular scale towards the network scaleYansu Wang, Murong Zhou, Quan Zou 0001, Lei Xu. bib, 22(5), 2021. [doi]

VPTMdb: a viral posttranslational modification databaseYujia Xiang, Quan Zou 0001, Lilin Zhao. bib, 22(4), 2021. [doi]

An in silico approach to identification, categorization and prediction of nucleic acid binding proteinsLei Xu, Shanshan Jiang, Jin Wu, Quan Zou 0001. bib, 22(3), 2021. [doi]

GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressedFenglong Yang, Quan Zou 0001, Bo Gao. bib, 22(5), 2021. [doi]

High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning methodYongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou 0001. bib, 22(6), 2021. [doi]

Critical downstream analysis steps for single-cell RNA sequencing dataZilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou 0001. bib, 22(5), 2021. [doi]

A comprehensive overview and critical evaluation of gene regulatory network inference technologiesMengyuan Zhao, Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo. bib, 22(5), 2021. [doi]

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniquesYun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou 0001, Xiangrong Liu. bmcbi, 22(1):216, 2021. [doi]

2020

Reference-Based Sequence ClassificationZengyou He, Guangyao Xu, Chaohua Sheng, Bo Xu 0008, Quan Zou 0001. access, 8:218199-218214, 2020. [doi]

Protein Complexes Identification with Family-Wise Error Rate ControlZengyou He, Can Zhao, Hao Liang, Bo Xu 0008, Quan Zou 0001. tcbb, 17(6):2062-2073, 2020. [doi]

Transcription factors-DNA interactions in rice: identification and verificationZijie Shen, Yuan Lin, Quan Zou 0001. bib, 21(3):946-956, 2020. [doi]

Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sitesZijie Shen, Quan Zou 0001. bioinformatics, 36(15):4263-4268, 2020. [doi]

PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learningYu P. Zhang, Quan Zou 0001. bioinformatics, 36(13):3982-3987, 2020. [doi]

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