卜东波 - 中国科学院大学 - 计算机科学与技术学院

个人简介

学历 Education Institute of Computing Technology, Chinese Academy of Sciences, Ph.D., 2001 (Advisors: Guojie Li, Thesis title: Theory of Clustering/Classification and Their Applications in Text Mining. ) Institute of Computing Technology, Chinese Academy of Sciences, Master, 1997 (Advisors: Shuo Bai, Thesis title: SAT Problem: Theory and Algorithms.) Shandong University, Department of Computer Science, B.Sc., 1994. 学位计算所 19970901--20010701 博士出国学习工作 2006-2008 Visiting Scholar, Post-doctoral fellow, University of Waterloo, Canada (Advisor: Ming Li) 工作简历 Associate Professor, Institute of Computing Technology, Chinese Academy of Sciences, May 2004 --- present Visiting Scholar, Post-doctoral Fellow, Department of Computer Science, University of Waterloo, (Advisor: Ming Li) Apr. 2006 --- July 2008. Assistant Professor, Institute of Computing Technology, Chinese Academy of Sciences, Apr. 2001 --- Apr. 2004. 发表著作 Book Chapter Consensus Approaches to Protein Structure Prediction. Chapter 5 in the book Machine Learning in Bioinformatics, John Wiley & Sons, 2008 科研项目 863: Functional Genmics Research 2003-2005 973: Algorithms in Bioinformatics 2003-2008 NSFC: Protein Structure Prediction Based on Markov Random Field 2009-2012 NSFC: Non-canonical Knowledge Processing 2005-2009 CAS: Special Machine for Bioinformatics. 2003-2005 参与会议 CSB 06, CPM 07, RECOMB 07, RECOMB 08, ISMB 08

研究领域

算法设计与分析。包括SAT问题理论和算法，信息检索，生物信息学。

近期论文

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Articles Published or Accepted in Refereed Journals and Conferences Improving consensus contact prediction via server correlation reduction, BMC structural biology. 06/2009; 9(1):28. FragQA: predicting local fragment quality of a sequence-structure alignment. In The 18th International Conference on Genome Informatics (GIW 2007), pp. 27-39, Singapore, 2007. Best paper award. Fragment-HMM: A new approach to protein structure prediction, Protein Sci. 2008 17: 1925-1934 Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra, J. Proteome Res., 7 (01), 202–208, 2008. 10.1021 Finding Largest Well-Predicted Subset of Protein Structure Models. CPM 2008: 44-55 Designing succinct structural alphabets. ISMB 2008: 182-189 A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB 2008: 154-166 FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics 24(18): 1994-2001 (2008) 2007 Finding Compact Structural Motifs. CPM 2007: 142-149 An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinformatics and Computational Biology 5(2a): 297-311 (2007) 2006 Improving locality of nonserial polyadic dynamic programming. IPDPS 2006 Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm, FEBS Letters, 580(7) 2006; 1891-1896 A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinformatics 7: 222 (2006) Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment. J. Comput. Sci. Technol. 21(6): 973-978 (2006) 2005 An Iterative Algorithm to Quantify the Factors Influencing Peptide Fragmentation for MS/MS Spectrum, CSB 2006 An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast. ICPADS (2) 2005: 704-708 NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Research 33(Database-Issue): 2005; 112-115 The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast. Nucleic Acids Res., September 8, 2004; 32(16): 4804 – 4811 A Note on the Single Genotype Resolution Problem. JCST, Vol.19, No.2, March 2004 254-258 LSA: More Accurate DNA Fragment Assembly. RECOMB 2003 Satellite meeting at Stanford Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Research, 2003.Vol.31, No.9 2443-2450 TREC-10 Experiments at CAS-ICT: Filtering, Web and QA. TREC 2001 Implementation of Text Categorization System Based on VSM. Application Research of Computers, 2001. Modeling the Phase Transition Phenomena of Satisfiability Problem, Proceeding of International Conference for Young Computer Scientist 99. Recent Software Developments: FALCON, an Ab Initio method for protein structure prediction. Ranked 3rd in the FR-H category in CASP8 PI, a database-searching package for tandem mass spectra.