Dong-Jun Yu

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 58

Top Topics

Binding Protein

Top Venues

Journal of chemical information and modeling

Briefings in bioinformatics

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings in bioinformatics 25 (2) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings in bioinformatics 25 (2) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. Journal of chemical information and modeling (2024)
Muhammad Arif, Ge Fang, Huma Fida, Saleh Musleh, Dong-Jun Yu, Tanvir Alam
iMRSAPred: Improved Prediction of Anti-MRSA Peptides Using Physicochemical and Pairwise Contact-Energy Properties of Amino Acids. ACS omega 9 (2) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. Journal of chemical information and modeling 64 (4) (2024)
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. Journal of chemical information and modeling 64 (4) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings in bioinformatics 25 (2) (2024)
Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. Journal of chemical information and modeling 64 (15) (2024)
Muhammad Arif, Ge Fang, Huma Fida, Saleh Musleh, Dong-Jun Yu, Tanvir Alam
iMRSAPred: Improved Prediction of Anti-MRSA Peptides Using Physicochemical and Pairwise Contact-Energy Properties of Amino Acids. ACS omega 9 (2) (2024)
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. Journal of chemical information and modeling (2024)
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings in bioinformatics 25 (2) (2024)
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm. Bioinformatics (Oxford, England) 40 (4) (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings in bioinformatics 25 (2) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. Journal of chemical information and modeling 64 (4) (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings in bioinformatics 25 (2) (2024)
Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. Journal of chemical information and modeling (2023)
Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. Journal of chemical information and modeling 63 (3) (2023)
Fang Ge, Muhammad Arif, Zihao Yan, Hanin Alahmadi, Apilak Worachartcheewan, Dong-Jun Yu, Watshara Shoombuatong
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction. Journal of chemical information and modeling (2023)
Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. Journal of chemical information and modeling 63 (3) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics 24 (1) (2023)
Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. Journal of chemical information and modeling 63 (3) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics 24 (1) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics (2022)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Fang Ge, Ying Zhang, Jian Xu, Arif Muhammad, Jiangning Song, Dong-Jun Yu
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings in bioinformatics 23 (1) (2022)
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. Journal of chemical information and modeling 63 (1) (2022)
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. Briefings in bioinformatics 23 (5) (2022)
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. Journal of chemical information and modeling (2022)
Guan-Yu Zhu, Yan Liu, Peng-Hao Wang, Xibei Yang, Dong-Jun Yu
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning. Journal of chemical information and modeling 62 (17) (2022)
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. Journal of chemical information and modeling 63 (1) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. Journal of chemical information and modeling 62 (7) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. Bioinformatics (Oxford, England) 38 (16) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS computational biology 18 (12) (2022)
Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. Briefings in bioinformatics 22 (6) (2022)
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B Gasser, Dong-Jun Yu, Geoffrey I Webb, Jiangning Song
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. Journal of chemical information and modeling 62 (17) (2022)
Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Briefings in bioinformatics 22 (5) (2021)
Yang Li, Chengxin Zhang, Eric W Bell, Wei Zheng, Xiao-Gen Zhou, Dong-Jun Yu, Yang Zhang
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS computational biology 17 (3) (2021)
Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. Journal of chemical information and modeling 61 (1) (2021)
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Briefings in bioinformatics (2021)
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in bioinformatics 22 (3) (2021)
Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T Marquez Lago, Jian Li, Dong-Jun Yu, Jiangning Song
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings in bioinformatics 22 (5) (2021)
Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. Journal of chemical information and modeling 60 (6) (2020)
Yi-Heng Zhu, Jun Hu, Xiao-Ning Song, Dong-Jun Yu
DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines. Journal of chemical information and modeling 59 (6) (2019)
Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. Journal of chemical information and modeling 58 (2) (2018)