Xue Wu's homepage

I am a graduate student at Computer Science Department, University of Maryland. My advisors are Professor Chau-Wen Tseng and Professor Nathan Edwards. My research focuses on applying high performance computing techniques on bioinformatics. Besides, I also did some projects on computer security and high performance computing . Before I came to here, I was studying at Computer Science Department of Tsinghua University, Beijing, China. Contact Information: Office: 4132 A.V. Williams Building Computer Science Department University of Maryland College Park, MD 20742 Phone: (301) 405-2722 Email: wu at cs.umd.edu [Personal Homepage]
[Research \| Education \| Experience \| My CV]

Papers X. Wu, C.-W. Tseng, P, Rudnick, B. Balgely and N. Edwards, PepArML: An Unsupervised, Model-Free, Combining Peptide Identification Arbiter for Tandem Mass Spectra Via Machine Learning, submitted to Modecular & Cellular Proteomics. [Talk] X. Wu, C.-W. Tseng, and N. Edwards, HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra using Hidden Markov Models, Journal of Computational Biology. 14(8):1025-1043, 2007. [preprint] X. Wu, W.-J. Lee, and C.-W. Tseng, ESTmapper: Efficiently Aligning DNA Sequences to Genomes, Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, CO, April 2005. [pdf] K. Albayraktaroglu, A. Jaleel, X. Wu, B. Jacob, M. Franklin, C.-W. Tseng, and D. Yeung, BioBench: A Benchmark Suite of Bioinformatics Applications, IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Austin, TX, March 2005. Z. Yu, C.-Y. Seng, T. Jiang, X. Wu and W. A. Arbaugh, Robust Routing in Malicious Environment for Ad Hoc Networks, The First Information Security Practice and Experience Conference (ISPEC 2005) , Singapore, April 2005. X. Wang, R. M. M. Chen, X. Wu, and X. An, A Class of Parallel Algorithm for Solving Large Sparse Linear Systems on Multiprocessors, HPC Asia 2000. Book Chapters X. Wu, N. Edwards, and C.-W. Tseng, Peptide Identification via Tandem Mass Spectroscopy, in Computational Biology and Bioinformatics, Advances in Computers, Volume 68 (C.-W. Tseng, ed.), Elsevier, 2006. X. Wu and C.-W. Tseng, Searching Sequence Databases Using High Performance BLASTs , Parallel Computing for Bioinformatics and Computational Biology (A. Zomaya, ed.), John Wiley & Sons, 2005. Posters X. Wu, N.J. Edwards, and C.-W. Tseng. Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. RECOMB Satallite Workshop on Computational Proteomics, 2006. X. Wu, N. Edwards, and C.-W. Tseng, Experimental Comparison of Peptide Identification Algorithms, 9th Annual Conference on Computational Genomics, Baltimore, MD, October 2006. N. Edwards, X. Wu and C.-W. Tseng, Novel Peptide Identification Using ESTs and Genomic Sequence, 2nd Annual Conference of the US Human Proteome Organisation (US HUPO 2006), Boston, MA, March 2006. X. Wu, W.-J. Lee, D. Gupta, and C.-W. Tseng, ESTmapper: Efficiently Clustering EST Sequences Using Genome Maps, RECOMB 2004. X. Wu and C.-W. Tseng, Searching Bioinformatic Sequence Databases using UM-BLAST---A Wrapper for High-Performance BLASTs, RECOMB 2004. Z. Yu, T. Jiang, X. Wu, and W. A. Arbaugh, Risk Based Probabilistic Routing for Ad Hoc Networks, Wireless Security Workshop in conjunction with Mobicom, September 2002. [pdf] Technical Report X. Wu, W.-J. Lee, D. Gupta, and C.-W. Tseng, ESTmapper: Efficiently Clustering EST Sequences Using Genome Maps, University of Maryland Technical Report CS-TR-4575. X. Wu and C.-W. Tseng, Searching Bioinformatic Sequence Databases using UM-BLAST---A Wrapper for High-Performance BLASTs, University of Maryland Technical Report CS-TR-4576. Talks Tandem Mass Peptide Identification with Statisitcal Machine Learning, CBCB, October 2007 Peptide Identification by Spectral Matching of Tandem Mass Spectra using Hidden Markov Models, March 2007 Peptide Identification by Tandem Mass Spectrometry, October 2005 ESTmapper: Efficiently Aligning DNA Sequences to Genomes, Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, CO, April 2005 ESTmapper: Efficiently Clustering EST Sequences Using Genome Maps, CBCB Journal Club, April 2004 Investigation of High Throughput BLASTs, CBCB Journal Club, November 2003. (Please find the related projects at my Bioinformatics page!)

Education August, 2000 - present PhD in Computer Science, University of Maryland at College Park September, 1995 - July 2000 B.E in Computer Science, Tsinghua University

Teaching Experience Fall 2006 Teaching Assistant, CMSC 330 Organization of Programming Languages Fall 2005 Teaching Assistant, CMSC 351 Algorithms Spring 2001 - Spring 2002 Teaching Assistant, CMSC 251 Algorithms Fall 2000 Teaching Assistant, CMSC 330 Programming Languages Working Experience June, 2005 - August, 2005 Calibrant Biosystems June, 2001 - August, 2001 Research Assistant, University of South California - Information Sciences Institute (ISI) October, 1999 - July, 2000 Research Assistant, Chinese Academy of Science

"Success is not final, failure is not fatal: it is the courage to continue that counts." -- Winston Churchill

	Xue Wu