Jun Hu Ph.D
Correspondence Suzhou Institute Of Systems Medicine, Suzhou, China, 215123
Email junh_cs@126.com or hujunum@zjut.edu.cn
OCRID https://orcid.org/0000-0001-9202-7515
ResearchGate https://www.researchgate.net/profile/Jun_Hu14
Brief Biography 

Mr. Jun Hu received his B.S. degree in computer science from AnHui Normal University in 2011. From 2011 to 2018, he acted as a Ph.D Student of School of Computer Science and Engineering in NanJing University of Science and Technology and a member of Pattern Recognition and Bioinformatics Group, led by professor Dong-Jun Yu. From 2016 to 2017, he acted as a visiting student at the University of Michigan (Ann Arbor) in U.S.A, led by professor Yang Zhang. He is currently a research associate professor in Chinese Academy of Medical Sciences Suzhou Institute of Systems Medicine. His current interests include bioinformatics and deep learning.

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Published Papers ( >>Google Scholar Citation Profile)(x+y)(>> Web Servers)


Journal Papers

  • Jun Hu*, Yu Zhou, Wen-Yi Zhou*, Xiaogen Zhou*. RLEAAI: Improving Antibody-Antigen Interaction Prediction Using Protein Language Model and Sequence Order Information [J]. Briefings in Bioinformatics, 2025, xx(xx): bbaf238. IN PRESS. [DOI:https://doi.org/10.1093/bib/bbaf238]

  • Jing Zou, Wenyi Zhang, Jun Hu*, Xiaogen Zhou*, Biao Zhang*. DockEM: an enhanced method for atomic-scale protein–ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps [J]. Briefings in Bioinformatics, 2025, 26(2): bbaf091. [DOI:https://doi.org/10.1093/bib/bbaf091]

  • Jun Hu*, Yuxuan Tang, Yu Zhou, Zhe Li, Bing Rao, Guijun Zhang*. Improving DNA 6mA site prediction via integrating bidirectional long short-term memory, convolutional neural network, and self-attention mechanism [J]. Journal of Chemical Information and Modeling, 2023, 63(17): 5689-5700. [DOI:https://doi.org/10.1021/acs.jcim.3c00698]

  • [2] Xue-Qiang Fan, Bing Lin, Jun Hu*, Zhong-Yi Guo. I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning [J]. Journal of Chemical Information and Modeling, 2023, 63: 1076-1086. [DOI:10.1021/acs.jcim.2c01465] [code]

  • 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 [J]. Journal of Chemical Information and Modeling, 2023, 63(3): 1044-1057. [DOI:10.1021/acs.jcim.2c00943] [Web Server]

  • Jun Hu, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang. Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-based Cube-Format Feature [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022, 19(6): 3635-3645. [DOI:10.1109/TCBB.2021.3123828] [Web Server]

  • Liang Rao, Ning-Xin Jia, Jun Hu#, Dong-Jun Yu#, and Gui-Jun Zhang#. ATPdock: a template-based method for ATP-specific protein–ligand docking [J]. Bioinformatics, 2021, 631: 114358. [DOI:10.1093/bioinformatics/btab667] [Web Server]

  • Xue-Qiang Fan, Jun Hu#, Ning-Xin Jia, Dong-Jun Yu#, and Gui-Jun Zhang#. Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework [J]. Analytical Biochemistry, 2021, 631: 114358. [DOI:10.1016/j.ab.2021.114358] [Web Server]

  • Jun Hu, Lin-Lin Zheng, Yan-Song Bai, Ke-Wen Zhang, Dong-Jun Yu, and Gui-Jun Zhang. Accurate prediction of protein-ATP binding residues using position-specific frequency matrix [J]. Analytical Biochemistry, 2021, 626: 114241. [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.ab.2021.114241] [Web Server] (WOS: 000663454300003)

  • Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, and Dong-Jun Yu. TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features [J]. Journal of Chemical Information and Modeling, 2021, 61(1): 505-515. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.0c00735] [Web Server] (WOS: 000613719400044)

  • Fang Ge, Jun Hu, Yiheng Zhu, Arif M, and Dongjun Yu. TargetMM: accurate missense mutation prediction by utilizing local and global sequence information with classifier ensemble. Combinatorial Chemistry & High Throughput Screening. 2020 [Download Citation with Endnote or BibTex Format] [DOI:10.2174/1386207323666201204140438] (PMID:33280588)

  • Jun Hu, Liang Rao, Xueqiang Fan, and Guijun Zhang. Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model. Analytical Biochemistry. 2020, 604:113799 [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.ab.2020.113799] [Standalone Program] (WOS:000556551500012)

  • Yiheng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, and Dongjun Yu. Accurate Multi-Stage Prediction of Protein Crystallization Propensity Using Deep-Cascade Forest with Sequence-Based Features. Briefings in Bioinformatics. 2021, 22(3):bbaa076. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbaa076] [No Web Server]

  • Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, and Jianzhong Su. scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures. Bioinformatics. 2020, 36(4): 4217-4219. [Download Citation with Endnote or BibTex Format] [DOI:10.1101/2020.01.15.907592] [No Web Server](WOS:000583886000021)

  • Yiheng Zhu, Jun Hu, Yong Qi, XiaoNing Song, and Dongjun Yu. Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites. Combinatorial Chemistry & High Throughput Screening. 2019, 22, 455-469 [DOI:10.2174/1386207322666190925125524] [No Web Server]

  • Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang. Assembling multi-domain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America. 2019, 116: 15930-15938 [Download Citation with Endnote or BibTex Format] [DOI:10.1073/pnas.1905068116] [Web Server](WOS:xxx)

  • Zhangwei Li, Ke Sun, Xiaohu Hao, Jun Hu, Laifa Ma, Xiaogen Zhou, Guijun Zhang. Loop enhanced conformational resampling method for protein structure prediction. IEEE Transactions on NanoBioscience. 2019, 18(4):567-577. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TNB.2019.2922101] [No Web Server](WOS:000498049700008)

  • Guijun Zhang, Tengyu Xie, Xiaogen Zhou, Liujing Wang, Jun Hu. Protein structure prediction using population-based algorithm guided by information entropy. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2021, 18(2):697-707. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2921958] [No Web Server](WOS:000638400100015)

  • Guijun Zhang, Xiaoqi Wang, Laifa Ma, Liujing Wang, Jun Hu, Xiaogen Zhou. Two-stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2020, 17(6):2119-2130. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2917452] [No Web Server](WOS:000597841800026)

  • Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, and Yang Zhang. ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics. 2019, 35(2):4647-4655. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bioinformatics/btz291] [Web Server](WOS:000501728500014)

  • 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. 2019, 59(6):3057-3071. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.8b00749] [Web Server](WOS:000473116500050)

  • Jun Hu, Xiao-Gen Zhou, Yi-Heng Zhu, Dong-Jun Yu, Guijun Zhang. TargetDBP: Accurate DNA-Binding Protein Prediction via Sequence-based Multi-View Feature Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2020, 17(4):1419-1429. [In Press] [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2893634] [Web Server](WOS:000556777900029)

  • Jun Hu, Zi Liu, Dong-Jun Yu, and Yang Zhang. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening [J]. Bioinformatics, 2018, 34(13): 2209-2218. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bioinformatics/bty081] [Web Server] (WOS:000438247800073) (PubMed ID: 29462237)

  • Jun Hu, Yang Li, Yang Zhang, and Dong-Jun Yu. ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons [J]. Journal of Chemical Information and Modeling, 2018, 58(2): 501-510. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.7b00397] [Web Server] (WOS: 000426613800029)

  • Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, and Dong-Jun Yu. Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-based Features and Boosting Multiple SVMs [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(6): 1389-1398. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2016.2616469] [Web Server] [Dataset] (WOS: 000418112400017)

  • Jun Hu, Ke Han, Yang Li, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM [J]. Amino Acids, 2016, 48(11): 2533-2547. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000386691700005)

  • Jun Hu, Yang Li, Wu-Xia Yan, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. KNN-based Dynamic Query-Driven Sample Rescaling Strategy for Class Imbalance Learning [J]. Neurocomputing, 2016, 191: 363-373. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000375165900031)

  • Jun Hu, Yang Li, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. GPCR-drug Interactions Prediction Using Random Forest with Drug-Association-Matrix-Based Post-Processing Procedure [J]. Computational Biology and Chemistry, 2016, 60: 59-71. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000369678300007)

  • Wuxia Yan, Sheng Wang, Jun Hu, and Chuancai Liu. Fronto-parallel building facades stitching. Electronics Letters, 2016, 52(18): 1524-1526. (WOS: 000383378500010)

  • Xue He, Ke Han, Jun Hu, Hui Yan, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition. Journal of Membrane Biology, 2015, 248(6): 1005-1014. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000363265100007)

  • Dong-Jun Yu, Jun Hu, Qian-Mu Li, Zhen-Min Tang, Jing-Yu Yang, and Hong-Bin Shen. Constructing Query-Driven Dynamic Machine Learning Model with Application to Protein-Ligand Binding Sites Prediction. IEEE Transactions on NanoBioscience, 2015, 14(1): 45-58. [Web Server] (WOS: 000350884300006)

  • Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, and Hong-Bin Shen. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(3): 611-621. [Web Server] (WOS: 000356608100013)

  • Dong-Jun Yu, Jun Hu, Hui Yan, Xi-Bei Yang, Jing-Yu Yang, and Hong-Bin Shen. Enhancing Protein-Vitamin Binding Residues Prediction by Multiple Heterogeneous Subspace SVMs Ensemble. BMC Bioinformatics, 2014, 15:297. [PDF] [Web Server] (WOS: 000344891200001)

  • Dong-Jun Yu, Jun Hu, Jing Yang, Hong-Bin Shen, Jinhui Tang, and Jing-Yu Yang. Designing template-free predictor for targeting protein-ligand binding sites with classifier ensemble and spatial clustering. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10(4): 994-1008. [Web Server] (WOS: 000328640700016)

  • Dong-Jun Yu, Jun Hu, Xiaowei Wu, Hong-Bin Shen, Jun Chen, Zhenmin Tang, Jian Yang, and Jingyu Yang. Learning Protein Multi-View Features in Complex Space,  Amino Acids. 2013, 44(5): 1365-1379. [Web Server] (WOS: 000317682100012)

  • Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhen-Min Tang and Jing-Yu Yang. TargetATPsite: A Template-free Method for ATP Binding Sites Prediction with Residue Evolution Image Sparse Representation and Classifier Ensemble. Journal of Computational Chemistry, 2013, 34(11): 974-985.  ( Inside Cover Story) [Web Server] (WOS: 000316627400009)

  • Dong-Jun Yu, Jun Hu, Zhen-Min Tang, Hong-Bin Shen, Jian Yang, and Jing-Yu Yang. Improving Protein-ATP Binding Residues Prediction by Boosting SVMs with Random Under-Sampling. Neurocomputing, 2013, 104: 180-190. [Web Server] (WOS: 000316163500017)

Conference Papers

  • Jun Hu, Zi Liu, and Dong-Jun Yu*. Enhancing Protein-ATP and Protein-ADP Binding Sites Prediction Using Supervised Instance-Transfer Learning. The 4th Asian Conference on Pattern Recognition (ACPR 2017). 2017: 759-763

  • Dong-Jun Yu, Jun Hu, Jian-Hua Xie, Yong Qi, and Zhen-Min Tang. Supervised Kernel Self-Organizing Map. 2012 Sino-foreign-interchange Workshop on Intelligence Science and Intelligent Data Engineering (IScIDE 2012). Springer, Nanjing, LNCS 7751, pp. 246--253. Springer, Heidelberg (2013). (Accession number: 13373489)

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