基本信息
卜东波 男 汉族 博导 中国科学院计算技术研究所
电子邮件:dbu@ict.ac.cn
联系电话:86-10-62601019
手机号码:
通信地址:中科院计算所 北京中关村科学院南路6号
邮政编码:100190

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。

教育背景

   
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)

工作经历

   
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.
  • 教授课程

       

    出版信息

       
    发表论文

    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.
    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

      

    科研活动

       
    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

    指导学生

    黄春林  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2009 from 中科大电子系)

    张海仓  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2009 from 中国矿业大学计算机系)

    邵明富  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2008 from 北理工)  

    袁雄鹰  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2007 from 北大生物系)

    乔彦涛  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2006 from 天津大学)

    韦 祎    硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2006 from 南京邮电大学)

    杨继爽  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2006 rom 河北科技大学)

    董恭谨  硕士研究生  081202-计算机软件与理论  80132-计算技术研究所(2005 from 山东大学)

    林宇     硕士研究生  081202-计算机软件与理论  80132-计算技术研究所 (2004 from 中科大)