Jiaoyun Yang, Yun Xu, Yi Shang. "A new progressive algorithm for multiple longest common subsequences problem and its efficient parallelization". IEEE Trans. on Parallel and Distributed Systems, 2012. DOI: 10.1109/TPDS.2012.202. Preprint
Yun Xu, Da Teng, Yiming Lei. "MinePhos: a literature mining system for protein phoshphorylation information extraction". IEEE Trans. on Comput. Biology & Bioinformatics, 2012, 9(1): 311-315
Yan Li, Jianping Wang, Chunming Qiao, Ashwin Gumaste, Yun Xu, Yinlong Xu. "Integrated Fiber-Wireless (FiWi) Access Networks Supporting Inter-ONU Communications". IEEE/OSA Journal of Lightwave Technology, 2010, 28(5): 714-724
Yun Xu, ZhiHao Wang, YiMing Lei, YuZhong Zhao and Yu Xue. "MBA: A Literature Mining System for Extracting Biomedical Abbreviations". BMC Bioinformatics, 2009, 10:14
Zhi-Hui Hu, Yun Xu, Liu-Sheng Huang and Howard Leung. "A Chinese Handwriting Education System with Automatic Error Detection". The Journal of Software (JSW), 2009, 4(2): 101-106
Guoliang Chen, Guangzhong Sun, Yun Xu and Bai Long. "Integrated research of parallel computing: Status and Future", Chinese Sci Bull, 2009, 54: 1845-1853
Yuzhong Zhao, Yun Xu, Zhihao Wang, Hong Zhang and Guoliang Chen. "A Better Block Partition and Ligation Strategy for Individual Haplotyping". Bioinformatics, 2008, 24(23): 2720-2725
Yun Xu, Bingfeng Yan, Guoliang Chen. "Core Management and Algorithms in all-to-all Multicast". Chinese Journal of Computer Research and Development, 2008, 45(6): 923-929 (In Chinese)
Kunpeng Zhang, Yun Xu, Guoliang Chen. "PECB: Prediction of Enzyme Catalytic Residues Based on Naïve Bayes Classification". Int. J. of Bioinformatics Research and Application, 2008, 4(3):295-305
Yuzhong Zhao, Yun Xu, Qiangfeng Zhang, Guoliang Chen. "An Overview of the Haplotype Problems and Algorithms". Frontiers of Computer Science in China, 2007, Vol.1, No3 : 272-282
Zhang, Qiangfeng, Xu, Yun, Chen, Guoliang, Che, Haoyang. "Haplotyping and Haplotype Frequency Estimates on Trio Genotype Data". Chinese Journal of Software, 2007, Vol.18, No.9:2090-2099
Qiangfeng Zhang, Yuzhong Zhao, Guoliang Chen, Yun Xu. "Estimate haplotype frequencies in pedigrees". BMC Bioinformatics, 2006, 7 (S4):S5
Yun Xu, Guoliang Chen, Qiangfeng Zhang, Jun Gu. "Efficiency Analysis of Asynchronic Parallelization of Randomized Algorithms". Chinese Journal of Software, 2003, Vol.14, No.5:871-876. (In Chinese)
Yun Xu, Guoliang Chen, Guoyi Zhang. "A Modified DP Algorithm for Solving Hard SAT Problems". Journal of University of Science and Technology of China, 2002, Vol.32, No.3:358-362. (In Chinese)
Yun Xu, Guoliang Chen, Yinlong Xu, Jun Gu. "O(m^2) Time Randomized Algorithms for SAT Problem". Chinese Journal of Computers, 2001, Vol.24, No.11:1136-1141. (In Chinese)
Haitao Jiang, Yun Xu, Yin Liao, Guojie Jin, Guoliang Chen. UKCF A New Graphics Driver Cross-platform Translation Framework for Virtual Machines. NPC2012, Accepted.
Yun Xu, Yan Li. “ONU Patching for Efficient VoD Service over Integrated Fiber-Wireless (FiWi) Access Networks”. The 6th International ICST Conference on Communications and Networking in China (CHINACOM 2011), August 17-19, 2011, Harbin, China. (Invited Paper)
Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang. "A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform". The 10th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP2010), Busan, Korea on May 21 ~ 23, 2010, Page(s): 79-90
Jiaoyun Yang, Yun Xu, Yi Shang. "An Efficient Parallel Algorithm for Longest Common Subsequence Problem on GPUs". Proceedings of the World Congress on Engineering (WCE 2010),2010, June 30 - July 2, 2010, London, U.K., Page(s): 499-504
Yun Xu, Mingzhi Shao, Da Teng. "Optimization of Triangular Matrix Functions in BLAS Library on Looson2F". IFIP International Conference on Network and Parallel Computing (NPC 2010), Zhengzhou, China, 13-15, Sept. 2010. Page(s): 35-45
Yu, Linbin, Xu, Yun. "A parallel gibbs sampling algorithm for motif finding on GPU". IEEE International Symposium on Parallel and Distributed Processing with Applications(ISPA 2009), Chengdu, Sichuan, China, 2009, pp555-558
Zhang, Hong; Xu, Yun; Zhao, Yuzhong. "Discovery of motif pairs from protein-protein interaction networks". Proceedings. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing(IJCBS 2009), Shanghai, China, August, 2009, pp293-296
Z. H. Hu, H. Leung and Yun Xu. Stroke Correspondence Based on Graph Matching for Detecting Stroke Production Errors in Chinese Character Handwriting. 8th Pacific-Rim Conference on Multimedia (PCM), 2007, p734-743