Dong-Jun Yu Ph.D., Associate Professor, Ph.D. Supervisor   [Chinese Version]
Correspondence School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, P. R. China, 210094
Office Phone +86-25-84315751-724

Brief Biography  Publication   Bioinformatics Web Server  Students  Courses 

Brief Biography 

Dr. Dong-Jun Yu received his B.S. degree in computer science and M.S. degree in artificial intelligence from Jiangsu University of Science and Technology in 1997 and 2000, respectively, and the Ph.D. degree in pattern analysis and machine intelligence from Nanjing University of Science and Technology in 2003. In 2008, he acted as an academic visitor at University of York in the UK. He is currently an associate professor in the School of Computer Science and Engineering at Nanjing University of Science and Technology. His current interests include pattern recognition, data mining and bioinformatics.

Dr. Yu is  a member of IEEE and a member of  China Computer Federation (CCF).



        Journal Article

  • 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.  (DOI:10.1109/TCBB.2013.104, In Press)

  • 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.

  • 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 EnsembleJournal of  Computational Chemistry.  2013, 34 (11): 974-985. (Published as Inside Cover Story).

  • 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. 

  • Dong-Jun Yu, Hong-Bin Shen and Jing-Yu Yang.  SOMPNN: An Efficient Non-Parametric Model for Predicting Transmembrane Helices. Amino Acids. 2012, 42 (6): 2195-2205.

  • Dong-Jun Yu,  Xiao-Wei Wu, Hong-Bin Shen, Jian Yang, Zhen-Min Tang, Yong Qi, and Jing-Yu Yang. Enhancing Membrane Protein Subcellular Localization Prediction by Parallel Fusion of Multi-View Features. IEEE Transactions on NanoBioscience. 2012,11 (4): 375-385.

  • Dong-Jun Yu, Hong-Bin Shen and Jing-Yu Yang. SOMRuler: A Novel Interpretable Transmembrane Helices Predictor. IEEE Transactions on NanoBioscience. 2011,10 (2): 121-128.

  • Ya-Nan Zhang^, Dong-Jun Yu^, Shu-Sen Li, Yong-Xian Fan, Yan Huang, and Hong-Bin Shen. Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features. BMC Bioinformatics, 2012, 13 (1): 118.

  • Xi-Bei Yang, Dong-Jun Yu, Jing-Yu Yang, Xiao-Ning Song. Difference Relation-based Rough Set and Negative Rules in Incomplete Information System. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems, 2009, 17 (5): 649-665.

  • Xi-Bei Yang, Dong-Jun Yu, Jing-Yu Yang, Li-Hua Wei. Dominance-based Rough Set Approach to Incomplete Interval-valued Information System. Data & Knowledge Engineering, 2009, 68 (11): 1331-1347.

  • Xi-Bei Yang, Tsau Young Lin, Jing-Yu Yang, Yan Li, Dong-Jun Yu. Combination of interval-valued fuzzy set and soft set. Computers & Mathematics with Applications, 2009, 58 (3): 521-527.

  • Xi-Bei Yang, Jing-Yu Yang, Chen Wu, Dong-Jun Yu. Dominance-based rough set approach and knowledge reductions in incomplete ordered information system. Information Science, 2008, 178 (4): 1219-1234.

  • Yong Xu, Jing-Yu Yang, Jian-Feng Lu, Dong-Jun Yu. An efficient renovation on kernel Fisher discriminant analysis and face recognition experiments. Pattern Recognition, 2004, 37 (10): 2091-2094.

  • Dong-Jun Yu, Xiao-Jun Wu, Edwin R. Hancock, Jing-Yu Yang. Generalized SOM with Applications to Face Gender Determination. Journal of Software. 2011, 34(9): 1719-1725. (In Chinese)

        Conference Paper       

  • 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).  LNCS 7751, pp. 246-253. Springer, Heidelberg (2013).

  • Dong-Jun Yu,  Xiao-Wei Wu, and Wei-Wei Yang. Gender Determination from Single Facial Image by Utilizing Surface Shape Information. Communications in Computer and Information Science, Vol. 288: 696-705. Springer, Heidelberg, 2012.

  • Dong-Jun Yu, Hancock, E.R., Smith, W.A.P.. Learning a Self-organizing Map Model on a Riemannian Manifold. Proceeding of Thirteenth IMA Conference on the Mathematics of Surfaces, Springer Verlag, Lecture Notes in Computer Science, Volume 5654. pages 375-390, 2009.

  • Dong-Jun Yu, Jian-Feng Lu, Jing-Yu Yang. Geodesic Discriminant Analysis on Curved Riemannian Manifold. The Sixth International Conference on Fuzzy Systems and Knowledge Discovery, IEEE Computer Society, vol. 5, pp.379-383, 2009



  • Algorithm Design and Analysis

  • Java Programming


Bioinformatics Web Server

        OSML        Available at:
        A Query-Driven Dynamic Machine Learning Model for Predicting Protein-Ligand Binding Sites.

        TargetATPsite        Available at:
        A Template-free Method for ATP Binding Sites Prediction with Residue Evolution Image Sparse Representation and Classifier Ensemble.

        TargetATP        Available at:
        A Java Web Start Application for Protein-ATP Binding Residue Prediction.

        TargetS        Available at:
        A ligand-specific template-free predictor for targeting protein-ligand binding sites.

        COMSPA        Available at:
        Predicting Protein Structural Classes From Primary Sequence by Learning Multi-View Features in Complex Space.