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。

生物信息学（AI辅助的蛋白质结构预测、蛋白质设计），计算机算法（AI辅助的算法设计）

081202-计算机软件与理论

生物信息学, 算法设计与分析

1994-07--2000-07   中科院计算所   硕士，博士
1990-07--1994-07   山东大学计算机系   本科

 

• 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)

   

2006-07~2008-07,加拿大滑铁卢大学计算机系, 博士后，访问学者
2000-07~现在, 中科院计算所, 助研，副研，研究员

算法设计与分析
计算机算法设计与分析
科学前沿进展名家系列讲座IV
生物信息学中的统计模型
生物信息学中的算法设计

   

[1] Nature Machine Intelligence. 2024,   通讯作者  
[2] 卜东波. Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. NeurIPS. 2023, 第 1 作者
[3] Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, WeiMou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu, Lenore Cowen. Accurate and efficient protein sequence design through learning concise local environment of residues. BIOINFORMATICS[J]. 2023, 39(3): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027430/.
[4] 卜东波. Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement. NeurIPS. 2023, 第 1 作者
[5] Kong, Lupeng, Ju, Fusong, Zheng, Weimou, Zhu, Jianwei, Sun, Shiwei, Xu, Jinbo, Bu, Dongbo. ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2022, http://dx.doi.org/10.1089/cmb.2021.0430.
[6] Ju, Fusong, Zhu, Jianwei, Zhang, Qi, Wei, Guozheng, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. BIOINFORMATICS[J]. 2022, 38(4): 990-996, http://dx.doi.org/10.1093/bioinformatics/btab777.
[7] 卜东波. Mainstream encoding-decoding methods of DNA data storage. CCF Trans. High Perform. Comput.[J]. 2022, 第 1 作者  通讯作者  4(1): 23-33, 
[8] 卜东波. FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. NAR Genomics and Bioinformatics. 2021, 第 1 作者  通讯作者  
[9] Ju, Fusong, Zhu, Jianwei, Shao, Bin, Kong, Lupeng, Liu, TieYan, Zheng, WeiMou, Bu, Dongbo. 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.
[10] 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.
[11] 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.
[12] 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/.
[13] 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. GUT. 2019, 68(12): 2254-+, 
[14] 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.
[15] 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, http://dx.doi.org/10.1093/bioinformatics/btz367.
[16] 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.
[17] Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, WeiMou Zheng, Dongbo Bu. 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.
[18] 卜东波. Toward Automated Identification of Glycan Branching Patterns 2 Using Multistage Mass Spectrometry with Intelligent Precursor 3 Selection. Analytical Chemistry. 2018, 第 1 作者  通讯作者  
[19] 刘翟, 卜东波, 石铁流, 权建校, 汪德鹏, 师咏勇, 伯晓晨, 韩文报. 生物芯概念计算——生物信息计算的新概念. 中国科学：生命科学[J]. 2018, 第 2 作者48(3): 341-342, http://lib.cqvip.com/Qikan/Article/Detail?id=674863033.
[20] 黄春林, 刘兴武, 邓明华, 周杨, 卜东波. 复杂网络上疾病传播溯源算法综述. 计算机学报[J]. 2018, 第 5 作者41(6): 1376-1399, http://lib.cqvip.com/Qikan/Article/Detail?id=675687009.
[21] 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.
[22] 王超, 朱建伟, 张海仓, 巩海娥, 郑伟谋, 卜东波. 蛋白质三级结构预测算法综述. 计算机学报[J]. 2018, 第 6 作者41(4): 760-779, http://lib.cqvip.com/Qikan/Article/Detail?id=7000514037.
[23] 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.
[24] 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.
[25] 张海仓, 高玉娟, 邓明华, 郑伟谋, 卜东波. 蛋白质中残基远程相互作用预测算法研究综述. 计算机研究与发展[J]. 2017, 第 5 作者54(1): 1-19, http://lib.cqvip.com/Qikan/Article/Detail?id=671129858.
[26] 卜东波. 串联质谱寡糖结构鉴定方法综述. PIBB. 2017, 第 1 作者  通讯作者  
[27] 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.
[28] 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.
[29] 张佩珩, 卜东波, 熊劲, 谭光明. “面向深度测序大数据量的计算模型与体系结构研究”立项报告. 科技创新导报[J]. 2016, 第 2 作者13(11): 163-163, http://lib.cqvip.com/Qikan/Article/Detail?id=669818304.
[30] 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.
[31] 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.
[32] 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.
[33] 卜东波. 蛋白质结构正则化. Algorithms for Molecular Biology. 2013, 第 1 作者
[34] 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, 
[35] 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.
[36] 柳厅文, 孙永, 卜东波, 郭莉, 方滨兴. 正则表达式分组的1／（1-1／k）-近似算法. 软件学报[J]. 2012, 第 3 作者23(9): 2261-2272, http://lib.cqvip.com/Qikan/Article/Detail?id=43116847.
[37] 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[J]. 2012, 27(9): 1221-1222, http://lib.cqvip.com/Qikan/Article/Detail?id=43282514.
[38] 王耀君, 孙世伟, 卜东波, 刘金刚. 串联质谱谱库搜索鉴定技术综述. 计算机工程[J]. 2012, 第 3 作者38(7): 269-272, http://lib.cqvip.com/Qikan/Article/Detail?id=41609907.
[39] 王耀君, 孙世伟, 卜东波, 刘金刚. 基于特征比对算法的蛋白质质谱鉴定仿真. 计算机仿真[J]. 2012, 第 3 作者29(10): 392-395, http://lib.cqvip.com/Qikan/Article/Detail?id=43536986.
[40] 乔彦涛, 缪佳铮, 孙世伟, 刘金刚, 卜东波. 串联质谱的蛋白质序列鉴定技术综述. 计算机科学与探索[J]. 2010, 第 5 作者97-107, http://lib.cqvip.com/Qikan/Article/Detail?id=32968831.
[41] 徐琳, 李晓民, 谭光明, 刘新春, 卜东波, 冯圣中. 面向FPGA的RNA二级结构预测并行算法研究. 计算机学报[J]. 2006, 第 5 作者29(2): 233-238, http://lib.cqvip.com/Qikan/Article/Detail?id=21182019.
[42] 周昭涛, 卜东波, 程学旗. 文本的图表示初探. 中文信息学报[J]. 2005, 第 2 作者19(2): 36-43, http://lib.cqvip.com/Qikan/Article/Detail?id=15098552.
[43] 张勇, 徐静怡, 邓巍, 张楠, 蔡伦, 赵义, 卜东波, 陈润生. 针对SARS冠状病毒重要蛋白的siRNA设计. 生物化学与生物物理进展[J]. 2003, 第 7 作者30(3): 335-338, http://lib.cqvip.com/Qikan/Article/Detail?id=7995963.
[44] 陈润生. 基于全基因组比较的SARS冠状病毒种系进化分析. 科学通报[J]. 2003, 48(12): 1242-1245, http://lib.cqvip.com/Qikan/Article/Detail?id=9070004.0.
[45] 许洪波, 卜东波, 白硕. 一种针对名义尺度变量的优化聚类算法. 微电子学与计算机[J]. 2003, 第 2 作者20(12): 8-11,15, http://lib.cqvip.com/Qikan/Article/Detail?id=8939008.
[46] 卜东波, 白硕, 李国杰. 文本聚类中权重计算的对偶性策略. 软件学报[J]. 2002, 第 1 作者13(11): 2083-2089, http://lib.cqvip.com/Qikan/Article/Detail?id=7008932.
[47] 卜东波, 许洪波, 白硕. 基于描述复杂性的优化学习算法. 计算机学报[J]. 2002, 第 1 作者25(8): 878-882, http://lib.cqvip.com/Qikan/Article/Detail?id=6603545.
[48] 卜东波, 白硕, 李国杰. 聚类分类中的粒度原理. 计算机学报[J]. 2002, 第 1 作者25(8): 810-816, http://lib.cqvip.com/Qikan/Article/Detail?id=6603536.
[49] 庞剑锋, 卜东波. 基于向量空模型的文本自动分类系统的研究与实现. 计算机应用研究[J]. 2001, 第 2 作者18(9): 23-26, http://lib.cqvip.com/Qikan/Article/Detail?id=5474472.
[50] 卜东波, 庞剑锋, 白硕. 基于向量空间模型的文本自动分类系统的研究与实现. 计算机应用研究[J]. 2001, 第 1 作者18(9): 23, http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=677831&detailType=1.
[51] Bin Huang, Lupeng Kong, Chao Wang, Fusong Ju, Qi Zhang, Jianwei Zhu, Tiansu Gong, Haicang Zhang, Chungong Yu, WeiMou Zheng, Dongbo Bu. Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. GENOMICS, PROTEOMICS & BIOINFORMATICS[J]. 21(5): 913-925, http://dx.doi.org/10.1016/j.gpb.2022.11.014.

Book Chapter

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

  

   

（ 1 ） 蛋白质结构模体识别, 负责人, 国家任务, 2013-01--2016-12
（ 2 ） 中科院交叉团队子课题, 负责人, 国家任务, 2013-01--2014-12
（ 3 ） 面向下一代基因组测序数据的算法研究, 参与, 国家任务, 2012-05--2016-05
（ 4 ） 蛋白质残基间相互作用预测算法研究及其在三级结构预测中的应用, 负责人, 国家任务, 2018-01--2021-12
（ 5 ） DNA活字喷墨与阵列存储技术研究及示范系统, 负责人, 国家任务, 2020-12--2024-01

（1）Improving prediction of burial state of residues by exploiting correlation among residues   2017-01-16
（2）Measuring and optimizing protein sturcture energy function landscape   Dongbo Bu   2013-05-01

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）