Dongbo Bu Professor, Institute of Computing Technology Chinese Academy of Sciences 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China Email: dbu AT ict dot ac dot cn Phone: 86-10-62601019, Fax: 86-10-62601356

Algorithm design and analysis, including SAT problem, and Bioinformatics (especially on genome sequencing/assembly, protein sequencing via mass spectra, protein structure prediction).

• Left Hand, Right Hand, June, 2009, pp. 76-81, ICT Forum 左手论文右手诗 李明

• University of Science and Technology of China, Hefei, China, June, 2009.
• The 2nd Workshop on Intelligent Computing , Fudan University, Shanghai, China, June, 2009.
• The 8th RECOMB conference RECOMB 2008, Singapore, July, 2008.
• Computational System Biology 2006 (CSB) , Standford University, USA, June, 2006.

Please visit our group homepage Bioinformatics group at ICT to see our people, publications, software, and bioinformatics resources. Here are some photos of my group and collaborators. We have a dynamic research group in bioinformatics. We are recruiting brilliant students and post-docs with strong algorithm, programming, and molecular biology backgrounds. If you are strong in at least two of these fields (and have some knowledge in the third) and you are a dedicated worker, please send me an email.

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• Programm Committee of Conferences: BIBM 2007,2008,2009, RECOMB-CP 2009,2010,2011, GIW 2011, ISMB 2011,2012
• Editorial Board of Journals: IJKDB, GPB

• Sony Award 2005.
• Scholarship of Chinese Academy of Sciences, 2001
• Distinguished Researched at ICT, 2010

• CS6012: Algorithm design and analysis, ICT. Fall 2009 , Fall 2010 , Fall 2011
• CS711008Z: Algorithm design and analysis, Graduate School, CAS. Fall 2010 , Fall 2011

• SIGMA Special Interest Group on Mathematics and Algorithms

• Professor, Institute of Computing Technology, Chinese Academy of Sciences, 2010 --- present
• Associate Professor, Institute of Computing Technology, Chinese Academy of Sciences, May 2004 --- 2010
• 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. 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.

Articles Published or Accepted in Refereed Journals and Conferences

• Shuai Cheng Li, Dongbo Bu, Ming Li, Clustering 100,000 protein structure decoys in minutes, to appear on IEEE Transaction on Computational Biology and Bioinformatics.
• Shuai Cheng Li, Dongbo Bu, Ming Li, Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations, IEEE Transaction on Computational Biology and Bioinformatics, 240-248, 9(1), 2012
• Shuai Cheng Li, Dongbo Bu, Jinbo Xu, and Ming Li. Finding nearly optimal GDT scores, Journal of Computational Biology. May 2011, 18(5): 693-704.
• Shenghui Zhang, Yaojun Wang, Dongbo Bu, Hong Zhang, Shiwei Sun, ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity, BMC bioinformatics. 08/2011; 12(1):346.
• Yantao Qiao, Hong Zhang, Dongbo Bu, Shiwei Sun, PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum, BMC bioinformatics. 01/2011; 12:234.
• Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Weimou Zheng and Dongbo Bu. Incorporating Ab Initio Energy into Threading Approaches for Protein Structure Prediction. BMC Bioinformatics 2010.
• Yi Wei, Mingfu Shao, Jishuang Yang, Chao Wang, Shuai Cheng Li, Dongbo Bu. Approximating Con- served Regions of Protein Structures. CSB 2010.
• Xiongying Yuan, Yi Zhao, Changning Liu, Dongbo Bu, Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification.", J. Bioinformatics and Computational Biology, 299-316, 2011
• D. Bu, M. Li, S. C. Li, J. Qian, J. Xu. Finding compact structural motifs. Theoretical Computer Science. 410 (30-32) 20, 2009
• Gao X, Bu D, Xu J, Li M. Improving consensus contact prediction via server correlation reduction. BMC Struct Biol. 2009; 9: 28.
• S. C. Li, D. Bu, J. Xu, M. Li. Fragment-HMM: A new approach to protein structure prediction, Protein Sci. 2008 17: 1925-1934
• S. Sun, C. Yu, Y. Qiao, Y. Lin, G. Dong, C. Liu, J. Zhang, Z. Zhang, J. Cai, H. Zhang, D. Bu. Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra, J. Proteome Res., 7 (01), 202¿208, 2008.
• S. C. Li, D. Bu, J. Xu, M. Li. Finding Largest Well-Predicted Subset of Protein Structure Models. CPM 2008: 44-55
• S. C. Li, D. Bu, X. Gao, J. Xu, M. Li. Designing succinct structural alphabets. ISMB 2008: 182-189
• Y. Lin, Y. Qiao, S. Sun, C. Yu, G. Dong, D. Bu. A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB 2008: 154-166
• X. Chen, S. He, D. Bu, F. Zhang, Z. Wang, R. Chen, W. Gao 6. FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics 24(18): 1994-2001 (2008)
• X Gao, D Bu, SC Li, J Xu, M Li. FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Informatics, 2008
• J. Qian, S. C. Li, D. Bu, M. Li, J. Xu. Finding Compact Structural Motifs. CPM 2007: 142-149
• C. Yu, Y. Lin, S. Sun, J. Cai, J. Zhang, Z. Zhang, R. Chen, D. Bu. An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinformatics and Computational Biology 5(2a): 297-311 (2007) 2006
• G. Tan, N. Sun, D. Bu. Improving locality of nonserial polyadic dynamic programming. IPDPS 2006
• S. Sun, Y. Zhao, Y. Jiao, Y. Yin, L. Cai, Y. Zhang, H. Lu, R. Chen, D. Bu. Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm, FEBS Letters, 580(7) 2006; 1891-1896
• Z. Zhang, S. Sun, X. Zhu, S. Chang, X. Liu, C. Yu, D. Bu, R. Chen. A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinformatics 7: 222 (2006)
• G. Tan, L. Xu, D. Bu, S. Feng, N. Sun. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment. J. Comput. Sci. Technol. 21(6): 973-978 (2006)
• C. Yu, Y. Lin, S. Sun, J. Cai, J. Zhang, Z. Zhang, R. Chen, D. Bu. An Iterative Algorithm to Quantify the Factors Influencing Peptide Fragmentation for MS/MS Spectrum, CSB 2006
• Z. Zhang. H. Sun, Y. Zhang, Y. Zhao, B. Bai, S. Sun, H. Lu, D. Bu, L. Ling, R. Chen. Genome-wide analysis of mammalian DNA segment fusion/fission. J. Theoretical Bio. 240(2), 2006
• G. Tan, L. Xu, Y. Jiao, S. Feng, D. Bu, N. Sun. An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast. ICPADS (2) 2005: 704-708
• C. Liu, B. Bai, G. Skogerbo, L. Cai, W. Deng, Y. Zhang, D. Bu, Y. Zhao, R. Chen. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Research 33(Database-Issue): 2005; 112-115
• J. Yu, J. Wang, ...,D. Bu,..., J. Wang, G. Wong, H. Yang. The Genomes of Oryza sativa: A History of Duplications. PLoS Biol 3(2): 2005
• H. Lu, Y. Zhao, J. Zhang, Y. Wang, W. Li, X. Zhu, S. Sun, J. Xu, L. Ling, L. Cai, D. Bu, R. Chen. Date of origin of the SARS coronavirus strains. BMC Infectious Diseases 2004, 4:3
• H. Lu, X. Zhu, H. Liu, G. Skogerbø, J. Zhang, Y. Zhang, L. Cai, Y. Zhao, S. Sun, J. Xu, D. Bu, R. Chen. 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
• H. Lin, Z. Zhang, Q. Zhang, D. Bu, M. Li. A Note on the Single Genotype Resolution Problem. J. of Comp. Sci. and Tech., Vol.19, No.2, March 2004 254-258
• J. Zhang, D. Bu, J. Xu, S. He, W. Gao, M. Li. LSA: More Accurate DNA Fragment Assembly. RECOMB 2003 Satellite meeting at Stanford
• D. Bu, Y. Zhao, L. Cai, H. Xue, X. Zhu, H. Lu, J. Zhang, S. Sun, L. Ling, N. Zhang, G. Li, R. Chen. Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Research, 2003.Vol.31, No.9 2443-2450
• D. Bu, S. Bai, G. Li. The Duplex Strategy of Term Weighting in Text Clustering. J. of Software. 13(11), 2002: 2083-2089.
• D. Bu, S. Bai, G. Li. Principle of Granularity in Clustering and Classification. J. Computer. 25(8), 2002: 810-816.
• D. Bu, H. Xu, S. Bai. An optimization algorithm based on description complexity. J. of Computer. 25(8), 2002: 878-882
• B. Wang, H. Xu, Z. Yang, Y. Liu, X. Cheng, D. Bu, S. Bai. TREC-10 Experiments at CAS-ICT: Filtering, Web and QA. TREC 2001
• J. Pang, D. Bu, S. Bai. Implementation of Text Categorization System Based on VSM. Application Research of Computers, 2001.
• D. Bu, S. Bai. Modeling the Phase Transition Phenomena of Satisfiability Problem, Proceeding of International Conference for Young Computer Scientist, 1999.
• D. Bu, S. Bai. Analysis of the phase transition phenomena of 2-3-SAT problem. J. of Software. 9(11), 1998: 828-832.

Book Chapter

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

• FALCON , an Ab Initio method for protein structure prediction. Ranked 3rd in the FR-H category in CASP8
• PI , predicting theoretical spectrum and a database-searching package for tandem mass spectra.
• PEARL, Probing Entity Aggregation in Real Life 珍珠计划 people approximity network 人际近距离接触网络模式对肺结核 流感的传播规律之影响 复杂网络上的疾病传播

Reading, writing, and table tennis.

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