卜东波 - 中国科学院计算技术研究所 -

个人简介

1990年9月—1994年7月山东大学计算机科学系软件专业，获工学学士学位 1994年9月—1997年7月中国科学院计算技术研究所，国家智能计算机研究开发中心，师从白硕研究员，获工学硕士学位硕士论文题目《SAT问题理论分析及快速求解算法》获得中国科学院院长奖学金 1997年9月—2000年11月中国科学院计算技术研究所，师从李国杰院士和白硕研究员，攻读博士学位博士论文题目《聚类/分类理论研究及其在文本挖掘中的应用》 2001年4月至今于中科院计算所生物信息学研究组工作 2006年4月-2008年7月，于加拿大滑铁卢大学李明教授实验室访问学者、博士后

研究领域

算法设计与分析，包括SAT问题，信息检索以及生物信息学

近期论文

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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 FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics 24(18): 1994-2001 (2008) 2007 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. Book Chapter Consensus Approaches to Protein Structure Prediction. Chapter 5 in the book Machine Learning in Bioinformatics, John Wiley & Sons, 2008