1）戴东波, 熊赟, 朱扬勇. 基于参考集索引的高效序列查询算(Efficient Algorithm for Sequence Similarity Search Based on Reference Indexing). 软件学报. 2010, 21(4): 718-731.

2）朱扬勇, 戴东波, 熊赟. 序列数据相似性查询技术研究(Sequence Similarity Search Technique Research). 计算机研究与发展. 2010. 47(2): 264-276.

3）Yun Xiong, Yangyong Zhu. Mining Peculiarity Groups in Day-by-Day Behavioral Datasets. In Proceedings of IEEE International Conference on Data Mining (ICDM’09). 2009: 578-587.

4）Yun Xiong, GuangyongZheng, Qing Yang, Yangyong Zhu. A Collaborative Multiagent System for Mining Transcriptional Regulatory Elements.IEEE Intelligent Systems. 2009: 26-37.

5）Gang Zhao, Yun Xiong, Xuchun Su, Longbing Cao, Yangyong Zhu. A Cost-Effective LSH Filter for Fast Pairwise Mining. In Proceedings of IEEE International Conference on Data Mining (ICDM’09). 2009:1088-1093.

6）Yangyong Zhu, Ning Zhong, Yun Xiong. Data Explosion, Data Nature and Dataology.In Proceedings of International Conference on Brain Informatics (BI’09). 2009: 147-158.

7）GuangyongZheng, Kang Tu, Qing Yang, Yun Xiong, Yangyong Zhu, Yixue Li. ITFP: an Integrated Platform of Mammalian Transcription Factors. Bioinformatics. 2008, 24(20): 2416-2417.

8）GuangyongZheng, Qing Yang, Yangyong Zhu. The Combination Approach of SVM and ECOC for Powerful Identification and Classification of Transcription Factor.BMC Bioinformatics. 2008, (9): 282-290.

9）朱扬勇, 熊赟. BioSeg: 一个生物序列数据模型. 计算机科学与探索. 2008, 1: 77-96.

10）朱扬勇, 熊赟. DNA序列数据挖掘技术. 软件学报. 2007, 18(11): 2766-2781.

11）熊赟, 陈越, 朱扬勇. ProFaM：一个蛋白质序列家族挖掘算法. 计算机研究与发展. 2007, 44(7): 1160-1168.

12）Yun Xiong, Yangyong Zhu. A Multi-Supports-Based Sequential Pattern Mining Algorithm. CIT 2005: 170-174.

13）Yun Xiong, Junhua He, Yangyong Zhu. TOPPER: An algorithm for mining top k patterns in biological sequences based on regularity measurement. In Proceedings of IEEE International Conference workshop on Bioinformation and Biomedicine (BIBM'10). 2010: 283-288.

14）戴东波, 汤春蕾, 邱伯仁, 熊赟, 朱扬勇. 一种优化多重过滤的序列查询算法(A Sequence Query Algorithm based on Multiple Filters Optimization). 计算机研究与发展. 2010, 42(10): 1785-1796.

15）Li Xue, Yun Xiong, Yangyong Zhu: A Brain Data Integration Model Based on Multiple Ontology and Semantic Similarity. Brain Informatics 2010: 192-199.

16）Li Xue, Ming Chen, Yun Xiong, Yangyong Zhu: User Navigation Behavior Mining Using Multiple Data Domain Description. Web Intelligence/IAT Workshops 2010: 132-135.

17）Xue Bai, Zezhen Lin, Yun Xiong, Yangyong Zhu. Clustering Based on Yukawa Potential. In Proceedings of 2012 SIAM International Conference on Data Mining (SDM12). 2012: 672-683.

18）Zhicheng Liao, Yun Xiong, Yangyong Zhu. FIND: A Data Cloud Platform for Financial Data Services. In Proceedings of First Internationnal Conference on Data Management Technologies and Applications (DATA2012). 2012: 117-122.

19）Zhijie Lin, Yun Xiong, Yangyong Zhu. Link Prediction Using BenefitRanks in Weighted Networks. The 2012 IEEE/WIC/ACM International Conference on Web Intelligence (WIC’12). 2012.

20）Zhijie Lin, Rui Lu, Yun Xiong, Yangyong Zhu. Learning ontology automatically using Topic Model.In Proceedings of the International Conference on Biomedical Engineering and Biotechnology (iCBEB). 2012, 1(1): 360-363.

21）Zhijie Lin, Yan Chen, Shiwei Wu, Yun Xiong, Yangyong Zhu, GuangyongZheng. Mining hub-based protein complexes in massive biological networks.IEEE BIBM workshop. 2012. (to appear)

22）Li Xue, Yun Xiong, Yangyong Zhu, Jianfeng Wu, Zhiyuan Chen. Stock Trend Prediction By Classifying Aggregative Web Topic-Opinion. PAKDD 2013.

23）Xue Bai, Yun Xiong, Yangyong Zhu, Qi Liu, Zhiyuan Chen. Co-anomaly Event Detection in Multiple Temperature Series. The 2013 International Conference on Knowledge Science, Engineering and Management (KSEM’13), 2013.

24）Xue Bai, Yun Xiong, Yangyong Zhu, Hengshu Zhu. Time Series Representation: A Random Shifting Perspective. Web-Age Information Management (WAIM’13), 2013. (The Best Student Paper Award)

25）Yun Xiong, Yangyong Zhu, Philip S. Yu, Jian Pei. Towards Cohesive Anomaly Mining. The Twenty-Seventh AAAI Conference on Artificial Intelligence (AAAI-13), 2013.

Chapters in Books:

26）Yun Xiong, Ming Chen, Yangyong Zhu. A Domain Driven Mining Algorithm on Gene Sequence Clustering.Chapter in Data Mining for Business Applications. L. B. Cao, Philip S. Yu, et al. (Eds.), 2008: 111-126. Springer.ISBN:9780387794198.