All Publications

文章

GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data.

Tianjiao Zhang, Ziheng Zhang, Liangyu Li, Benzhi Dong, Guohua Wang, Dandan Zhang.

Briefings in Bioinformatics, 2024.

SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution.

Fang Wang, Chunpu Liu, Jiawei Li, Fan Yang, Jiangning Song, Tianyi Zang, Jianhua Yao, Guohua Wang.

Nucleic Acids Research, 2024.

GSL-DTI: Graph structure learning network for Drug-Target interaction prediction.

Zixuan E, Guanyu Qiao, Guohua Wang*, Yang Li*.

Methods, 2024.

SERT-StructNet: Protein secondary structure prediction method based on multi-factor hybrid deep model .

Benzhi Dong, Zheng Liu, Dali Xu, Chang Hou, Guanghui Dong, Tianjiao Zhang Guohua Wang *.

Computational and Structural Biotechnology Journal , 2024.

Boosting knowledge diversity, accuracy, and stability via tri-enhanced distillation for domain continual medical image segmentation.

Zhanshi Zhu, Xinghua Ma, Wei Wang, Suyu Dong, Kuanquan Wang, Lianming Wu, Gongning Luo, Guohua Wang, Shuo Li.

Medical Image Analysis, 2024.

VirGrapher: a graph-based viral identifier for long sequences from metagenomes.

Yan Miao, Zhenyuan Sun, Chenjing Ma, Chen Lin, Guohua Wang, Chunxue Yang.

Briefings in Bioinformatics, 2024.

Prediction of protein N-terminal acetylation modification sites based on CNN-BiLSTM-attention model.

Jinsong Ke, Jianmei Zhao, Hongfei Li, Lei Yuan, Guanghui Dong, Guohua Wang*.

Computers in Biology and Medicine, 2024.

GTADC: A Graph-Based Method for Inferring Cell Spatial Distribution in Cancer Tissues.

Tianjiao Zhang, Ziheng Zhang, Liangyu Li, Jixiang Ren, Zhenao Wu, Bo Gao, Guohua Wang*.

Biomolecules, 2024.

CPPLS-MLP: a method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.

Tianjiao Zhang, Zhenao Wu, Liangyu Li, Jixiang Ren, Ziheng Zhang, Guohua Wang*.

Briefings in Bioinformatics, 2024.

scZAG: Integrating ZINB-Based Autoencoder with Adaptive Data Augmentation Graph Contrastive Learning for scRNA-seq Clustering.

Tianjiao Zhang, Jixiang Ren, Liangyu Li, Zhenao Wu, Ziheng Zhang, Guanghui Dong and Guohua Wang *.

International Journal of Molecular Sciences, 2024.

Hierarchical multimodal self-attention-based graph neural network for DTI prediction.

Jilong Bian, Hao Lu, Guanghui Dong, Guohua Wang.

Briefings in Bioinformatics, 2024.

HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses.

Qiang Yang, Long Xu, Weihe Dong Xiaokun Li, Kuanquan Wang, Suyu Dong, Xianyu Zhang, Tiansong Yang, Feng Jiang, Bin Zhang, Gongning Luo, Xin Gao, Guohua Wang.

Briefings in Bioinformatics, 2024.

SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies.

Heng Hu, Runtian Gao, Wentao Gao, Bo Gao, Zhongjun Jiang, Murong Zhou, Guohua Wang, Tao Jiang.

Briefings in Bioinformatics, 2024.

TransGINmer: Identifying viral sequences from metagenomes with self-attention and Graph Isomorphism Network.

Jianan Wang, Zhenyuan Sun, Guohua Wang, Yan Miao.

Future Generation Computer Systems, 2024.

scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data .

Zhenze Liu, Yingjian Liang, Guohua Wang, Tianjiao Zhang.

Briefings in Bioinformatics, 2024.

DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information .

Yan Miao, Zhenyuan Sun, Chen Lin, Haoran Gu, Chenjing Ma, Yingjian Liang, Guohua Wang.

Briefings in Bioinformatics, 2024.

Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer.

Lingyu Cui; Hongfei Li; Jilong Bian; Guohua Wang; Yingjian Liang.

Briefings in Bioinformatics, 2023.

End-to-end interpretable disease–gene association prediction.

Yang Li; Zihou Guo; Keqi Wang; Xin Gao; Guohua Wang.

Briefings in Bioinformatics, 2023.

MCANet: shared-weight-based MultiheadCrossAttention network for drug–target interaction prediction.

Jilong Bian; Xi Zhang; Xiying Zhang; Dali Xu; Guohua Wang.

Briefings in Bioinformatics, 2023.

CanMethdb: a database for genome-wide DNA methylation annotation in cancers.

Jianmei Zhao; Fengcui Qian; Xuecang Li; Zhengmin Yu; Jiang Zhu; Rui Yu; Yue Zhao; Ke Ding; Yanyu Li; Yongsan Yang; Qi Pan; Jiaxin Chen; Chao Song; Qiuyu Wang; Jian Zhang; Guohua Wang; Chunquan Li.

Bioinformatics, 2023.

miProBERT: identification of microRNA promoters based on the pre-trained model BERT.

Xin Wang; Xin Gao; Guohua Wang; Dan Li.

Briefings in Bioinformatics, 2023.

scWECTA: A weighted ensemble classification framework for cell type assignment based on single cell transcriptome.

Tongtong Ren; Shan Huang; Qiaoming Liu; Guohua Wang.

Computers in Biology and Medicine, 2023.

DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.

Tianjiao Zhang; Liangyu Li; Hailong Sun; Guohua Wang.

Bioinformatics, 2023.

Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI.

Chonghui Liu; Yan Zhang; Xin Gao; Guohua Wang.

BMC biology, 2023.

Chromosome‐level genome assembly of a triploid poplar Populus alba 'Berolinensis'.

Song Chen; Yue Yu; Xinyu Wang; Sui Wang; Tianjiao Zhang; Yan Zhou; Ruihan He; Nan Meng; Yiran Wang; Wenxuan Liu; Zhijie Liu; Jinwen Liu; Qiwen Guo; Haijiao Huang; Ronald R Sederoff; Guohua Wang; Guanzheng Qu; Su Chen.

Molecular Ecology Resources, 2023.

DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome.

Tianjiao Zhang; Liangyu Li; Hailong Sun; Dali Xu; Guohua Wang.

Briefings in Bioinformatics, 2023.

MTGDC: a multi-scale tensor graph diffusion clustering for single-cell RNA sequencing data.

Qiaoming Liu; Dong Wang; Li Zhou; Jie Li; Guohua Wang.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023.

MicroRNA Promoter Identification in Human with a Three-level Prediction Method.

Xin Wang; Jie Li; Guohua Wang.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023.

Identification of adaptor proteins by incorporating deep learning and PSSM profiles.

Wentao Gao, Dali Xu, Hongfei Li, Junping Du, Guohua Wang, Dan Li.

Methods, 2023.

Feature selection combined with top-down and bottom-up strategies for survival analysis: A case of prognostic prediction in glioblastoma.

Yanan Liu, Xudong Zhao, Jilong Bian, Guohua Wang.

Computers in Biology and Medicine, 2023.

MMCL-CDR: Enhancing Cancer Drug Response Prediction with Multi-Omics and Morphology Images Contrastive Representation Learning.

Yang Li, Zihou Guo, Xin Gao, Guohua Wang.

Bioinformatics, 2023.

DAEMDA: A Method with Dual-Channel Attention Encoding for miRNA-Disease Association Prediction.

Benzhi Dong, Weidong Sun, Dali Xu, Guohua Wang, Tianjiao Zhang.

Biomolecules, 2023.

MDformer: A transformer-based method for predicting miRNA-Disease associations using multi-source feature fusion and maximal meta-path instances encoding.

Benzhi Dong, Weidong Sun, Dali Xu, Guohua Wang, Tianjiao Zhang.

Computers in Biology and Medicine, 2023.

ASAS-EGB: A statistical framework for estimating allele-specific alternative splicing events using transcriptome data.

Lili Dong, Jianan Wang, Guohua Wang.

Computers in Biology and Medicine, 2023.

Identifying cancer driver genes using a two-stage random walk with restart on a gene interaction network.

Ping Meng, Guohua Wang, Hongzhe Guo, Tao Jiang.

Computers in Biology and Medicine, 2023.

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling.

Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang & Jianhua Yao.

Nature Machine Intelligence, 2023.

Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Hongfei Li; Yue Gong; Yifeng Liu; Hao Lin; Guohua Wang.

Briefings in Bioinformatics, 2022.

A survey on computational methods in discovering protein inhibitors of SARS-CoV-2.

Qiaoming Liu; Jun Wan; Guohua Wang.

Briefings in Bioinformatics, 2022.

Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms.

Xudong Zhao; Tong Liu; Guohua Wang.

Briefings in Bioinformatics, 2022.

Drug–target interaction predication via multi-channel graph neural networks.

Yang Li; Guanyu Qiao; Keqi Wang; Guohua Wang.

Briefings in Bioinformatics, 2022.

Complex genome assembly based on long-read sequencing.

Tianjiao Zhang; Jie Zhou; Wentao Gao; Yuran Jia; Yanan Wei; Guohua Wang.

Briefings in Bioinformatics, 2022.

CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins.

Tianjiao Zhang; Yuran Jia; Hongfei Li; Dali Xu; Jie Zhou; Guohua Wang.

Briefings in Bioinformatics, 2022.

Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in Arabidopsis thaliana.

Ralf Müller-Xing; Rhomi Ardiansyah; Qian Xing; Léa Faivre; Jingjing Tian; Guohua Wang; Yucai Zheng; Xue Wang; Tingting Jing; Erica De Leau.

Journal of Experimental Botany, 2022.

Supervised graph co-contrastive learning for drug–target interaction prediction.

Yang Li; Guanyu Qiao; Xin Gao; Guohua Wang.

Bioinformatics, 2022.

SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

Yu Chen; DongLiang You; TianJiao Zhang; GuoHua Wang.

Frontiers in Plant Science, 2022.

Identification of Prognostic Biomarkers for Bladder Cancer Based on DNA Methylation Profile.

Shumei Zhang; Jingyu Zhang; Qichao Zhang; Yingjian Liang; Youwen Du; Guohua Wang.

Frontiers in Cell and Developmental Biology, 2022.

scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells.

Qiaoming Liu; Ximei Luo; Jie Li; Guohua Wang.

Briefings in Bioinformatics, 2022.

Identification of Diagnostic Markers for Breast Cancer Based on Differential Gene Expression and Pathway Network.

Shumei Zhang; Haoran Jiang; Bo Gao; Wen Yang; Guohua Wang.

Frontiers in Cell and Developmental Biology, 2022.

Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins .

Xudong Zhao; Jingwen Zhai; Tong Liu; Guohua Wang.

Briefings in Bioinformatics, 2022.

An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.

Longxi Zhou; Xianglin Meng; Yuxin Huang; Kai Kang; Juexiao Zhou; Yuetan Chu; Haoyang Li; Dexuan Xie; Jiannan Zhang; Weizhen Yang; Na Bai; Yi Zhao; Mingyan Zhao; Guohua Wang; Lawrence Carin; Xigang Xiao; Kaijiang Yu; Zhaowen Qiu; Xin Gao.

Nature Machine Intelligence, 2022.

PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.

Ke Ding; Shanwen Sun; Yang Luo; Chaoyue Long; Jingwen Zhai; Yixiao Zhai; Guohua Wang.

Genomics, Proteomics & Bioinformatics, 2022.

DeepST: identifying spatial domains in spatial transcriptomics by deep learning.

Chang Xu; Xiyun Jin; Songren Wei; Pingping Wang; Meng Luo; Zhaochun Xu; Wenyi Yang; Yideng Cai; Lixing Xiao; Xiaoyu Lin; Hongxin Liu; Rui Cheng; Fenglan Pang; Rui Chen; Xi Su; Ying Hu; Guohua Wang; Qinghua Jiang.

Nucleic Acids Research, 2022.

Regenotyping structural variants through an accurate force-calling method.

Tao Jiang; Shuqi Cao; Yadong Liu; Shiqi Liu; Bo Liu; GuoHua Wang; Yadong Wang.

bioRxiv, 2022.

Genome sequence assembly evaluation using long-range sequencing data.

Dengfeng Guan; Shane A McCarthy; Jonathan MD Wood; Ying Sims; William Chow; Zemin Ning; Kerstin Howe; Guohua Wang; Yadong Wang; Richard Durbin.

bioRxiv, 2022.

StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy.

Xin Wang; Yadong Liu; Jie Li; Guohua Wang.

BMC Bioinformatics, 2022.

i6mA-Vote: cross-species identification of DNA N6-methyladenine sites in plant genomes based on ensemble learning with voting.

Zhixia Teng; Zhengnan Zhao; Yanjuan Li; Zhen Tian; Maozu Guo; Qianzi Lu; Guohua Wang.

Frontiers in plant science, 2022.

IOFS-SA: An interactive online feature selection tool for survival analysis.

Xudong Zhao; Yuanyuan He; Youlin Wu; Tong Liu; Guohua Wang.

Computers in Biology and Medicine, 2022.

dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost.

Hongfei Li; Lei Shi; Wentao Gao; Zixiao Zhang; Lichao Zhang; Yuming Zhao; Guohua Wang.

Methods, 2022.

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; Quan Zou; Guohua Wang.

Bioinformatics, 2021.

The stacking strategy-based hybrid framework for identifying non-coding RNAs.

Xin Wang; Yang Yang; Jian Liu; Guohua Wang.

Briefings in Bioinformatics, 2021.

Identifying Plant Pentatricopeptide Repeat Proteins Using a Variable Selection Method.

Xudong Zhao; Hanxu Wang; Hangyu Li; Yiming Wu; Guohua Wang.

Frontiers in Plant Science, 2021.

CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table.

Jianan Wang; Su Chen; Lili Dong; Guohua Wang.

Briefings in Bioinformatics, 2021.

Effects of DNA Methylation on TFs in Human Embryonic Stem Cells.

Ximei Luo; Tianjiao Zhang; Yixiao Zhai; Fang Wang; Shumei Zhang; Guohua Wang.

Frontiers in Genetics, 2021.

A Clustering Ensemble Method for Cell Type Detection by Multiobjective Particle Optimization.

Qiaoming Liu; Xudong Zhao; Guohua Wang.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021.

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads.

Shien Huang; Xinyu He; Guohua Wang; Ergude Bao.

Briefings in Bioinformatics, 2021.

Evaluating disease similarity based on gene network reconstruction and representation.

Yang Li; Wang Keqi; Guohua Wang.

Bioinformatics, 2021.

ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition.

Zhixia Teng; Zitong Zhang; Zhen Tian; Yanjuan Li; Guohua Wang.

BMC Bioinformatics, 2021.

A deep learning approach for filtering structural variants in short read sequencing data.

Yongzhuang Liu; Yalin Huang; Guohua Wang; Yadong Wang.

Briefings in Bioinformatics, 2021.

Efficient iterative Hi-C scaffolder based on N-best neighbors.

Dengfeng Guan; Shane A McCarthy; Zemin Ning; Guohua Wang; Yadong Wang; Richard Durbin.

BMC Bioinformatics, 2021.

Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa.

Liyun Zhang; Conan Chen; Jie Fu; Brendan Lilley; Cynthia Berlinicke; Baranda Hansen; Ding Ding; Guohua Wang; Tao Wang; Daniel Shou.

Elife, 2021.

An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine.

Guang Song; Guohua Wang; Ximei Luo; Ying Cheng; Qifeng Song; Jun Wan; Cedric Moore; Hongjun Song; Peng Jin; Jiang Qian.

Nature Communications, 2021.

A Clustering Ensemble Method for Cell Type Detection by Multiobjective Particle Optimization.

Qiaoming Liu; Xudong Zhao; Guohua Wang.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021.

BYASE: a Python library for estimating gene and isoform level allele-specific expression.

Lili Dong; Jianan Wang; Guohua Wang.

Bioinformatics, 2020.

Evaluating individual genome similarity with a topic model.

Liran Juan; Yongtian Wang; Jingyi Jiang; Qi Yang; Guohua Wang; Yadong Wang.

Bioinformatics, 2020.

Time-resolved expression analysis comparing two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative regulatory networks.

Steven L Walker; Guohua Wang; Kevin B Emmerich; Fang Wang; David T White; Yong Teng; Meera T Saxena; Jiang Qian; Jeff S Mumm.

ADVANCES IN WATER RESOURCES, 2020.

Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses.

Kevin Emmerich, Steven L. Walker, Guohua Wang, David T. White, Anneliese Ceisel, Fang Wang, Yong Teng, Zeeshaan Chunawala, Gianna Graziano, Saumya Nimmagadda, Meera T. Saxena, Jiang Qian, Jeff S. Mumm.

PLoS genetics, 2020.

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles.

Xudong Zhao; Qing Jiao; Hangyu Li; Yiming Wu; Hanxu Wang; Shan Huang; Guohua Wang.

BMC Bioinformatics, 2020.

AFS-DEA: An automatic feature selection platform for differential expression analysis.

Xudong Zhao; Weiqi Su; Hangyu Li; Tong Liu; Denan Kong; Guohua Wang.

2020 IEEE International Conference on Bioinformatics and Biomedicine, 2020.

Identification of methylation states of DNA regions for Illumina methylation BeadChip.

Ximei Luo; Fang Wang; Guohua Wang; Yuming Zhao.

BMC genomics, 2020.

Gene regulatory networks controlling vertebrate retinal regeneration.

Thanh Hoang; Jie Wang; Patrick Boyd; Fang Wang; Clayton Santiago; Lizhi Jiang; Sooyeon Yoo; Manuela Lahne; Levi J Todd; Meng Jia; Cristian Saez; Casey Keuthan; Isabella Palazzo; Natalie Squires; Warren A. Campbell; Fatemeh Rajaii; Trisha Parayil; Vickie Trinh; Dong Won Kim; Guohua Wang; Leah J. Campbell; John Ash; Andy J. Fischer; David R. Hyde; Jiang Qian; Seth Blackshaw.

Science, 2020.