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。

   

 

• 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.

 

计算所 19970901--20010701 博士

2006-2008    Visiting Scholar, Post-doctoral fellow,  University of Waterloo, Canada (Advisor: Ming Li)

   

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.

   

[1] 卜东波. ProALIGN: Directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs. JCB. 2021, [2] 卜东波. FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. NAR Genomics and Bioinformatics. 2021, [3] Fusong Ju, Jianwei Zhu, Bin Shao, Lupeng Kong, TieYan Liu, WeiMou Zheng, Dongbo Bu. CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction. NATURE COMMUNICATIONS[J]. 2021, 12(1): https://doaj.org/article/33cc2239e1a44129b8b0dddfeb060858.
[4] Kong, Lupeng, Ju, Fusong, Zhang, Haicang, Sun, Shiwei, Bu, Dongbo. FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC BIOINFORMATICS[J]. 2021, 22(1): http://dx.doi.org/10.1186/s12859-021-04353-8.
[5] Huang, Bin, Wei, Guozheng, Wang, Bing, Ju, Fusong, Zhong, Yi, Shi, Zhuozheng, Sun, Shiwei, Bu, Dongbo. Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. BMC BIOINFORMATICS[J]. 2021, 22(1): http://dx.doi.org/10.1186/s12859-021-04448-2.
[6] Zhang, Qi, Zhu, Jianwei, Ju, Fusong, Kong, Lupeng, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. ISSEC: inferring contacts among protein secondary structure elements using deep object detection. BMC BIOINFORMATICS[J]. 2020, 21(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643357/.
[7] Liu, Hong, Han, Maozhen, Li, Shuai Cheng, Tan, Guangming, Sun, Shiwei, Hu, Zhiqiang, Yang, Pengshuo, Wang, Rui, Liu, Yawen, Chen, Feng, Peng, Jianjun, Peng, Hong, Song, Hongxing, Xia, Yang, Chu, Liqun, Zhou, Quan, Guan, Feng, Wu, Jing, Bu, Dongbo, Ning, Kang. Resilience of human gut microbial communities for the long stay with multiple dietary shifts. GUTnull. 2019, 68(12): 2254-+, [8] Zhang, Haicang, Zhang, Qi, Ju, Fusong, Zhu, Jianwei, Gao, Yujuan, Xie, Ziwei, Deng, Minghua, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC BIOINFORMATICS[J]. 2019, 20(1): http://dx.doi.org/10.1186/s12859-019-3051-7.
[9] Chen, Hao, Shaw, Dipan, Zeng, Jianyang, Bu, Dongbo, Jiang, Tao. DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. BIOINFORMATICS[J]. 2019, 35(14): I284-I294, [10] Ju, Fusong, Zhang, Jingwei, Bu, Dongbo, Li, Yan, Zhou, Jinyu, Wang, Hui, Wang, Yaojun, Huang, Chuncui, Sun, Shiwei. De novo glycan structural identification from mass spectra using tree merging strategy. COMPUTATIONAL BIOLOGY AND CHEMISTRY[J]. 2019, 80: 217-224, http://dx.doi.org/10.1016/j.compbiolchem.2019.03.015.
[11] Wang, Chao, Wei, Yi, Zhang, Haicang, Kong, Lupeng, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. BMC Bioinformatics[J]. 2019, 20(S3): 99-108, https://doaj.org/article/6ed28e082ad847f19e2703f86cd71abd.
[12] 卜东波. Toward Automated Identification of Glycan Branching Patterns 2 Using Multistage Mass Spectrometry with Intelligent Precursor 3 Selection. Analytical Chemistry. 2018, [13] Zhu, Jianwei, Wang, Sheng, Bu, Dongbo, Xu, Jinbo. Protein threading using residue co-variation and deep learning. BIOINFORMATICS[J]. 2018, 34(13): 263-273, https://www.webofscience.com/wos/woscc/full-record/WOS:000438247800031.
[14] Zhu, Jianwei, Zhang, Haicang, Li, Shuai Cheng, Wang, Chao, Kong, Lupeng, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. BIOINFORMATICS[J]. 2017, 33(23): 3749-3757, http://dx.doi.org/10.1093/bioinformatics/btx514.
[15] Gong, Haie, Zhang, Haicang, Zhu, Jianwei, Wang, Chao, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Improving prediction of burial state of residues by exploiting correlation among residues. BMC BIOINFORMATICS[J]. 2017, 18(Suppl 3): http://dx.doi.org/10.1186/s12859-017-1475-5.
[16] 卜东波. 串联质谱寡糖结构鉴定方法综述. PIBB. 2017, [17] Zhang, Haicang, Gao, Yujuan, Deng, Minghua, Wang, Chao, Zhu, Jianwei, Li, Shuai Cheng, Zheng, WeiMou, Bu, Dongbo. Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS[J]. 2016, 472(1): 217-222, http://ir.itp.ac.cn/handle/311006/23180.
[18] Wang, Chao, Zhang, Haicang, Zheng, WeiMou, Xu, Dong, Zhu, Jianwei, Wang, Bing, Ning, Kang, Sun, Shiwei, Li, Shuai Cheng, Bu, Dongbo. FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. BIOINFORMATICS[J]. 2016, 32(3): 462-464, http://ir.itp.ac.cn/handle/311006/23139.
[19] Wang, Yaojun, Yang, Fei, Wu, Peng, Bu, Dongbo, Sun, Shiwei. OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction. BMC BIOINFORMATICS[J]. 2015, 16(1): http://www.corc.org.cn/handle/1471x/2374290.
[20] Song, Dandan, Chen, Jiaxing, Chen, Guang, Li, Ning, Li, Jin, Fan, Jun, Bu, Dongbo, Li, Shuai Cheng. Parameterized BLOSUM Matrices for Protein Alignment. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2015, 12(3): 686-694, https://www.webofscience.com/wos/woscc/full-record/WOS:000356608100020.
[21] Fu, Xinmiao, Chang, Zengyi, Shi, Xiaodong, Bu, Dongbo, Wang, Chao. Multilevel structural characteristics for the natural substrate proteins of bacterial small heat shock proteins. PROTEIN SCIENCE[J]. 2014, 23(2): 229-237, https://www.webofscience.com/wos/woscc/full-record/WOS:000329939900009.
[22] 卜东波. 蛋白质结构正则化. Algorithms for Molecular Biology. 2013, [23] Li, Shuai Cheng, Bu, Dongbo, Li, Ming. Clustering 100,000 Protein Structure Decoys in Minutes. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2012, 9(3): 765-773, [24] Li, Shuai Cheng, Bu, Dongbo, Li, Ming. Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2012, 9(1): 240-248, https://www.webofscience.com/wos/woscc/full-record/WOS:000296782200020.
[25] 彭拥军, 姚彦, 郭顺, 蒋彩云, 王和生. 针灸血清与蛋白质组学研究. 中医学报. 2012, 27(9): 1221-1222, http://lib.cqvip.com/Qikan/Article/Detail?id=43282514.

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）