[Selected]
1. Shiying Sheng, Chunyuan Wu，Xiaoju Dong(通讯作者)，Shengtao Chen. An Analysis on Online Dynamic Graph Layout using Parallel Computing. In: 17th IEEE International Symposium on Parallel and Distributed Processing with Applications (ISPA2019), to appear.(EI国际会议)
2. Shiying Sheng, Xiaoju Dong and Chunyuan Wu. Online dynamic graph drawing with inverse Markov analysis. In: the 12th International Symposium on Visual Information Communication and Interaction (VINCI2019), 28:1-28:2.（ACM国际会议）
3. Chenlu Li, Xiaoju Dong, Wei Liu, Shiying Sheng, Aijuan Qian. SSRDVis: Interactive visualization for event sequences summarization and rare detection. Journal of Visualization, to appear.
4. Xin Fan, Chenlu Li, Xiaoru Yuan, Xiaoju Dong, Jie Liang. An interactive visual analytics approach for network anomaly detection through smart labeling. Journal of Visualization, 22(5): 955-971.
5. Xiaoju Dong, Yuxi Fu, Daniele Varacca. Extensional Petri net. Formal Aspects of Computing. 2019, 31(1): 47-58. (期刊, SCI， CCF B类)
6. Xin Fan, Chenlu Li, Xiaoju Dong(通讯作者). A real-time network security visualization system based on incremental learning. Journal of Visualization, 2019, 22(1): 215-229.（期刊, SCI）
7. 张浩城, 吴晓洁, 唐翔, 舒润萱, 丁天琛, 董笑菊(通讯作者). 基于可视分析的网络异常检测系统. 网络与信息安全学报，2018, 4(2): 40-54.（期刊）
8. Chunyuan Wu,Shiying Sheng, Xiaoju Dong(通讯作者).Research on visualization systems for ddos attack detection.The 2018 IEEE International Conference on Systems, Man, and Cybernetics (SMC2018)，2018：2986-2991. (会议, EI)
9. Wei Liu, Xinying Han, Xiaoju Dong(通讯作者), Zhiwen Qiang, Xuwei Chen. Visual Analysis of Scientific Life of Scholars Based on Digital Humanities. In: Xu Z., Gao X., Miao Q., Zhang Y., Bu J. (eds) Big Data. Big Data 2018. Communications in Computer and Information Science, 2018, 945, 461-473. Springer, Singapore.（会议，EI）
10. Haocheng Zhang, Xiang Tang, Chenlu Li, Yiming Bian, Xiaoju Dong(通讯作者), Xin Fan. PBSVis: A Visual System for Studying Behavior Patterns of Pseudo Base Stations. ICPCSEE (1) 2018: 599-610. (会议, EI)
11. Haocheng Zhang, Wei Liu, Hao Xiong, Xiaoju Dong(通讯作者): Analyzing data flow diagrams by combination of formal methods and visualization techniques. Journal of Visual Languages and Computing. 2018，48: 41-51.（期刊, SCI）
12. Chenlu Li, Xiaoju Dong(通讯作者), Xiaoru Yuan: Metro-Wordle: An Interactive Visualization for Urban Text Distributions Based on Wordle. Visual Informatics，2018, 2(1): 50-59（期刊）
13. Xin Fan, Wenjie Luo, Xiaoju Dong(通讯作者), Rui Su: A Network Visualization System for Anomaly Detection and Attack Tracing. ICPCSEE (1), 2018: 560-574 (会议, EI)
14. Mengxuan Sun, Xiaoju Dong, Fan Wu, Guihai Chen. An Efficient Privacy-Preserving Fingerprint-Based Localization Scheme Employing Oblivious Transfer. MSN 2017: 110-132.（会议，EI）
15. Xiang Tang, Xiaoju Dong(通讯作者), Hengjia Zhang. CWordle: A Visual Analytics System for Extracting the Topics of Speech. In: IC4S 2017, Advances in Computer Communication and Computational Sciences. vol 760. Springer, Singapore, 2018: 85-95.(会议，EI)
16. Hao Xiong, Haocheng Zhang, Xiaoju Dong(通讯作者),?Lingxi Meng,?Wenyang Zhao: DFDVis: A Visual Analytics System for Understanding the Semantics of Data Flow Diagram. ICPCSEE(1), 2017:?660-673.（会议, EI）
17. 张毅凡, 董笑菊(通讯作者). 分布式拒绝服务的可视分析. 网络与信息安全学报, 2017, 3(2): 53-65. (期刊)
18. Xiang Wang, Zhenzhe Zheng, Fan Wu, Xiaoju Dong, Shaojie Tang, Guihai Chen: Strategy-Proof Data Auctions with Negative Externalities: (Extended Abstract). AAMAS 2016: 1269-1270. (会议)
19. Licong Deng, Xiaoju Dong(通讯作者). A survey of Dynamic Graph Visualization. ChinaVis2016.
20. Xiaoju Dong, Yuxi Fu, Daniele Varacca. Place Bisimulation and Liveness for Open Petri Nets. In: SETTA2016, LNCS 9984, Springer, 2016:1-17.（会议，EI）
21. 李彦龙,李国强,董笑菊(通讯作者). 树比较可视化方法综述. 软件学报, 2016, 27(5):1074-1090（期刊，一级）
22. Jianxin Xue, Xiaoju Dong. New Approach to Proving Local Cause Bisimulation Axiomatically. The Proceedings of 2012 IEEE International Conference on Computer Science and Automation Engineering (CSAE2012), 2012: 199-203. (会议，EI)
23. Jianxin Xue, Xiaoju Dong. A Fully Abstract View for Local Cause Semantics. The 7th International Conference on Grid and Pervasive Computing (GPC 2012), LNCS 7296, 2012: 198-209.（会议，EI）
24. Zhenhua Dong, Xiaoju Dong. Representing Bounded Petri Nets by Process Calculi. Journal of Shanghai Jiao Tong University, 2011, 45(7): 980-984. (in Chinese with English abstract)
25. Chunyi Huang, Xiaoju Dong. Maximally parallel attribute on P systems: properties and applications. Pre-proceedings of the International Conference Bio-Inspired Computing--Theory and Applications, 2007. Also in Progress in Natural Science. 2008, 18(5): 629-632.
26. Chunyi Huang, Xiaoju Dong, Huan Long. Solving the sort problem using a P system. Journal of Shanghai Jiao Tong University, 2008, 42(2): 206-208. (in Chinese with English abstract)
27. Xian Xu, Xiaoju Dong. Study on a new variant of tissue P systems. Science of Computer, 2008. (in Chinese with English abstract)
28. Min Zhang, Zhengwei Qi, Xiaoju Dong. Executable Specification of P Systems with Active Membranes and Its Implementation. Journal of Shanghai Jiao Tong University, 2008. (in Chinese with English abstract)
29. Qing Zhuang, Xiaojuan Cai, Xiaoju Dong, Zhengwei Qi. A Verification Tool for Security Protocol on GSPM. Computer Engineering. 2008. (in Chinese with English abstract)
30. Xiaoju Dong, Yuxi Fu. Barbed Congruence of Asymmetry and Mismatch. Journal of Computer Science and Technology, 22(4), 2007: 575-579.
31. Xian Xu, Xiaoju Dong and Yuxi Fu. A Model in kappa for DNA Addition. Proceedings of Workshop on Membrane Computing and Biologically Inspired Process Calculi, July 9, 2006 (MeCBIC2006). Also in Electronic Notes in Theoretical Computer Science, 171(2), 2007: 209-222.
32. Yang Pu, Xiaoju Dong. Continuous simulation of biomolecular systems based on process calculus. In Proc. of International Symposium on Artificial Life and Robotics, Oita, Japan, January 25-27, 2007.
33. Dan Li, Min Zhang, Xiaoju Dong. κ-Calculus Model for the Life-Cycle of Lambda Phage. Journal of Shanghai Jiao Tong University. 2007: 42-22. (in Chinese with English abstract)
34. Xiaoju Dong and Yuxi Fu. Barbed Congruence of the Asymmetric Chi Calculus. Journal of Harbin Institute of Technology, 13(4), 2006: 444-451.
35. Xiaoju Dong, Jiahua Ni, Yuxi Fu. Modeling the biological and chemical reactive processes using process calculi. The Annual Conference of Theoretical Computer Science of China, 2006. (in Chinese)
36. Yang Pu, Xiaoju Dong. The simulation and analysis of the tile self-assemble. The Annual Conference of Theoretical Computer Science of China, 2006. (in Chinese).
37. Yang Pu, Yanbin Yu, Xiaoju Dong. Simulation of biomolecular processes by using stochastic P systems. In Proc. of International Workshop on High Performance Computing in the Life Sciences (HPCLife), Ouro Preto, Brazil, 2006.
38. Farong Zhong, Yuxi Fu, Xiaoju Dong. Bisimulation Congruence for Asymmetric χ≠-Calculus. Proceedings-Fifth International Symposium on Parallel and Distributed Computing，2006: 173-184.
39. Yonggen Gu, Yuxi Fu, Yang Li, Xiaoju Dong. A Generic Model for Symbolic Analyzing Security Protocols. CIT 2005, IEEE, 2005: 680-684.
40. Xiaoju Dong, Yuxi Fu, Xu Xian. A Survey of Systems Biology Formal Models. The Annual Conference of Theoretical Computer Science of China. 2005. (in Chinese)
41. Zhupeng Dong, Xiaoju Dong, Xian Xu, Yuxi Fu, Zhizhou Zhang, Lin He. An Implementation for Mapping SBML to BioSPI. FSKD(2), Lecture Notes in Computer Science, LNAI 3614, 2005: 1128-1131.
42. Zhupeng Dong, Xiaoju Dong，Jiahua Ni. Research on Systems Biology Models Conversion. Journal of Shanghai Jiao Tong University, 39(8), 2005: 1280–1283. (in Chinese with English Abstract)
43. Yuxi Fu, Xiaoju Dong. Formalizing the Environment View of Process Equivalence. The International Symposium on Computational and Information Sciences (CIS’04), Shanghai, December 16-18, Lecture Notes in Computer Science 3314, 2004: 336-345.
44. Xiaoju Dong, Farong Zhong and Yuxi Fu. Bisimulation Lattice of Asymmetric Chi Calculus with Mismatch. High Technology Letters, 9(4), 2003: 50-55.
45. Xiaoju Dong and Yuxi Fu. Observing Asymmetry and Mismatch. In A Ohori, APLAS 2003, Lecture Notes in Computer Science 2895, Springer-Verlag, Nov. 27-29, Beijing, China, 2003: 2-19.
46. Xiaoju Dong and Guochang Gu. AUV Global Path Planning Allowing for Ocean Current. In Proceedings of the 3rd World Congress on Intelligent Control and Automation, IEEE Press, June28---July 2, Hefei, China, 2000: 1230-1234.
47. Xiaoju Dong, Jingyu Liu, Guochang Gu. Implementation of Motion-viewing Simulation Based on OpenGL. Computer Engineering, 25(12), 1999: 25-26.