卜东波

卜东波

 

院计算技术研究所 研究员

 

承担科研项目情况:

863课题“功能基因组” NSFC课题“基于随机场的蛋白质结构预测新算法” NSFC重大课题“非规范知识处理”子课题 973生物信息学课题等

 

简历:

19909月—19947月 山东大学计算机科学系软件专业,获工学学士学位

19949月—19977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

19979月—200011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》

20014月至今 于中科院计算所生物信息学研究组工作

20064-20087月,于加拿大滑铁卢大学李明教授实验室访问学者、博士后

研究方向:

算法设计与分析,包括SAT问题,信息检索以及生物信息学

获奖及荣誉:

获得中国科学院院长奖学金

代表论著:

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-博导计算机系统结构

* 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. Book Chapter

* Consensus Approaches to Protein Structure Prediction. Chapter 5 in the book Machine Learning in Bioinformatics, John Wiley & Sons, 2008