Yun Xu (徐云)

My Students

• Current Master&Ph.D. Students:

  2021：Citing Wu（吴慈霆），Jia Gao（高佳），Yang Yi（伊洋），Jifan Shi（石济帆），Huamin Wen（温华铭），Yuting Li（李玉婷，博士生）

  2020：Zihan Den（邓子含），Tianyu Wang（王天宇），Biao Wang（王彪），Min Xiong（熊敏）

  2019 and before：Zelin Yu（余泽霖），Wenjie Wang（王文杰），Dong Sun（孙栋），Bihuan Ban（班必奂），Xie Wu（吴邪），Huan Liu（刘欢，博士生）

  　

• Gone but not forgotten:

  2021：Menya Liu(刘梦雅，北京)，Xuyang Zhong（钟旭阳，杭州），Dehao Zhang(张德浩，西安)，Genyuan Xin（邢耕源 ，北京），Ming Wu（吴鸣，北京，博士毕业）

  2020：Gen Huang(黄根，杭州)，Yue Zhou（邹悦，杭州），Wei Chen(陈伟，上海)，Peijia Tang（唐佩佳，无锡）

  2019：Siyi Song（宋思怡，杭州），Kangqi Ying（殷康麒，南京），Ruifeng Zhang（张睿峰，杭州），Haoyu Chen（程昊宇，美国，博士毕业），Pengcheng Wang（王鹏程，南京，博士毕业）

  2018：Min Wang（汪敏，上海），Hongwei Liu(刘宏伟，北京)， Ruidong Guo（郭睿东，上海）

  2017: Zhongxiao He（何忠峭，深圳），Guangyu Long（龙光宇，合肥）

  2016：Xiaoxin Chen (陈晓欣，南京)，Peiran Zhang（张沛然，上海），Xiangbing Liu（刘向彬，上海），Yong Zhang(张勇，香港读博)

  2015：Yanan Zhao（赵雅男，上海），Bo Chen - Little（陈波-小，上海）,Ji wu（吴极，合肥）

  2014: Jaoyun Yang（杨矫云， 合肥，博士毕业），Weihua Pang（潘玮华，美国读博），Xinxin Zhang（张鑫鑫，杭州），Ting Li（李婷，北京）

  2013: Haitao Jiang（姜海涛，上海，博士毕业），Wenhua Cheng（程文华，苏州），Pengyu Nie（聂鹏宇，北京），Jiabing Liu（刘家兵，上海），Tao Yan（晏涛，无锡，博士毕业） 

  2012：Xiaohui Yao（姚晓辉，美国读博），Da Teng（縢达，读博），Wenjun Li（李文军，合肥）

  2011：Yan Li（李燕，南京，博士毕业），Pengfei Qiu(邱鹏飞，北京)，Ying Wang(王颖,上海)，Bo Chen（陈波，苏州）

  2010：Zhihui Hu（胡智慧，上海，博士毕业），Yuzhong Zhao（赵裕众，杭州，博士毕业），Mingzhi Shao（邵明芝，杭州），Yiming Lei（雷一鸣，上海）

  2009：Hong Zhang（张弘，美国读博），Linbing Yu（余林彬，美国读博），Wei Bao（鲍微，北京）

  2008：Zhihao Wang（王志浩，石家庄），Yan Luo（罗兖，上海），He Huang（黄河，转博）

  2007: Kunpeng Zhang(张坤鹏，美国读博)，Haiyang Wang(王海洋，深圳)

  2006: Binfeng Yan(鄢冰峰，合肥)，Zhili Chen(陈至立，转博)

  2005: Tao Mao(毛涛，北京)，Zilin Hu(胡自林 ，上海)

Selected Papers Publications

   Journal Papers

• Haoyu Cheng, Yong Zhang and Yun Xu*. "BitMapper2: a GPU-accelerated all-mapper based on the sparse q-gram index". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019, 16(3): 886-897.

• Haoyu Cheng, Ming Wu, Yun Xu*; “FMtree: a fast locating algorithm of FM-indexes for genomic data”. Bioinformatics, 2018, 34(3): 416–424.

• Haoyu Cheng, Huaipan Jiang, Jiaoyun Yang, Yun Xu*, Yi Shang*. BitMapper: an efficient all-mapper based on bit-vector computing. BMC Bioinformatics, 2015, 16: 192

• Weihua Pan, Yanan Zhao, Yun Xu*, Fengfeng Zhou*. WinHAP2: an extremely fast haplotype phasing program for long genotype sequences. BMC Bioinformatics, 2014, 15:164

• Jiaoyun Yang, Yun Xu*, Yi Shang* and Guoliang Chen. "A Space-Bounded Anytime Algorithm for the Multiple Longest Common Subsequence Problem." IEEE Trans. on Knowledge and Data Engineering, 2014, 26(11): 2599-2609.

• Jiaoyun Yang, Yun Xu*, Xiaohui Yao and Guoliang Chen. "FNphasing: A novel fast heuristic algorithm for haplotype phasing based on flow network model." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10(2): 372-382.

• Jiaoyun Yang, Yun Xu* and Yi Shang*. "A new progressive algorithm for multiple longest common subsequences problem and its efficient parallelization". IEEE Trans. on Parallel and Distributed Systems, 2013, 24(5): 862-870.

• Tao Yan, Rynson Lau, Yun Xu and Liusheng Huang. "Depth Mapping for Stereoscopic Videos." International Journal of Computer vision, 2013, 102: 293-307.

• Yun Xu*, Jiaoyun Yang, Yuzhong Zhao and Yi Shang. "Improved Voting Algorithms For Planted (l, d) Motif Search." Information Sciences, 2013, 237: 305-312.

• Haitao Jiang, Yun Xu*, Yin Liao, Guojie Jin and  Guoliang Chen. "KBT Operating system kernel level binary translation system," Journal of Software(JSW), 2013, 8(6): 1275-1280.

• Yun Xu*, Da Teng and Yiming Lei. "MinePhos: a literature mining system for protein phoshphorylation information extraction". IEEE Trans. on Comput. Biology & Bioinformatics, 2012, 9(1): 311-315.

• Yun Xu*, Wenhua Cheng, Pengyu Nie, Fengfeng Zhou*. WinHAP: an Efficient haplotype phasing algorithm based on scalable sliding windows. PLOS One, 2012, 7(8): e43163.

• Yan Li, Jianping Wang, Chunming Qiao, Ashwin Gumaste, Yun Xu and 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 and 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 and Guoliang Chen. "An Overview of the Haplotype Problems and Algorithms". Frontiers of Computer Science in China, 2007, 1(3): 272-282.

• Qiangfeng Zhang, Yun Xu, Guoliang Chen and Haoyang Che. "Haplotyping and Haplotype Frequency Estimates on Trio Genotype Data". Chinese Journal of Software, 2007, 18(9): 2090-2009.

• Qiangfeng Zhang, Yuzhong Zhao, Guoliang Chen and Yun Xu. "Estimate haplotype frequencies in pedigrees". BMC Bioinformatics, 2006, 7(S4): S5.

• Yun Xu, Guoliang Chen, Qiangfeng Zhang and Jun Gu. "Efficiency Analysis of Asynchronic Parallelization of Randomized Algorithms". Chinese Journal of Software, 2003, 14(5): 871-876. (In Chinese)

• Yun Xu, Guoliang Chen and Guoyi Zhang. "A Modified DP Algorithm for Solving Hard SAT Problems". Journal of University of Science and Technology of China, 2002, 32(3): 358-362. (In Chinese)

• Yun Xu, Guoliang Chen, Yinlong Xu and Jun Gu. "O(m^2) Time Randomized Algorithms for SAT Problem". Chinese Journal of Computers, 2001, 24(11): 1136-1141. (In Chinese)

   Conference Papers

• Pengcheng Wang, Jeffrey Svajlenko, Yanzhao Wu, Yun Xu and Chanchal K. Roy. CCAligner: a token based large-gap clone detector. The 40th International Conference on Software Engineering (ICSE 2018), May 30 – June 1, 2018, Gothenburg, Sweden.

• Ruidong Guo, Haoyu Cheng, Yun Xu. An efficient filtration method based on variable-length seeds for sequencing sequence alignment. The 8th International Symposium on Parallel Architectures, Algorithms and Programming (PAAP2017). 17-18 June 2017, Haikou, China. Communications in Computer and Information Science, v 729, p 214-223, 2017.

• Hongwei Liu, Yun Xu. A Deep Learning Way for Disease Name Representation and Normalization. The 6th Conference on Natural Language Processing and Chinese Computing (NLPCC 2017). 8-12 November 2017, Dalian, China.

• Min Wang, Pengcheng Wang, Yun Xu. CCSharp: An efficient three-phase code clone detector using modified PDGs. The 24th Asia-Pacific Software Engineering Conference (APSEC 2017), 4-8 December 2017, Nanjing, China.

• Haitao Jiang, Yun Xu, Yin Liao, Guojie Jin and Guoliang Chen. UKCF A New Graphics Driver Cross-platform Translation Framework for Virtual Machines. 9th IFIP International Conference, NPC 2012, Gwangju, Korea, September 6-8, 2012. LNCS 7513, pp.156–163, 2012.

• Yun Xu and 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 and 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 and 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 and 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.

• Linbin Yu and Yun Xu. "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, pp.555-558.

• Hong Zhang, Yun Xu and Yuzhong Zhao. "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, pp.293-296.

• 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.

Grants

Awards

1.“并行计算”课程的创建及其辐射与示范作用，2009，国家教学成果二等奖，排名第2.

2.“并行计算”相关课程教学团队，2009，国家级教学团队，排名第3.

3.“并行计算”课程的创建及其辐射与示范作用，2008，安徽省教学成果特等奖，排名第2.

4. 中国科大王宽诚育才一等奖，2008.

      Since 079046，updated Mar. 23, 2021.