Algorithm design and analysis, including SAT problem, Information Retrieval, and Bioinformatics.

Dongbo recieved his Ph. D. degree from Institute of Computing Technology, Chinese Academy of Sciences in 2001.

 Visiting Scholar, Post-doctoral Fellow, Department of Computer Science, University of Waterloo, (Advisor: Ming Li) Apr. 2006 --- July 2008

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.

   

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.

   

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.

Book Chapter

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

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

CSB 06, CPM 07, RECOMB 07, RECOMB 08, ISMB 08

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）