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-
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 1997 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, RECOMB08, 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）