Dongbo Bu

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 38

Top Topics

Bipartite Matching

Attention Mechanism

Top Venues

Publications

Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
Accurate and robust protein sequence design with CarbonDesign. Nat. Mac. Intell. 6 (5) (2024)
Ziguang Li, Chao Huang, Xuliang Wang, Haibo Hu, Cole Wyeth, Dongbo Bu, Quan Yu, Wen Gao, Xingwu Liu, Ming Li
Understanding is Compression. CoRR (2024)
Xingquan Li, Zengrong Huang, Simin Tao, Zhipeng Huang, Chunan Zhuang, Hao Wang, Yifan Li, Yihang Qiu, Guojie Luo, Huawei Li, Haihua Shen, Mingyu Chen, Dongbo Bu, Wenxing Zhu, Ye Cai, Xiaoming Xiong, Ying Jiang, Yi Heng, Peng Zhang, Bei Yu, Biwei Xie, Yungang Bao
iEDA: An Open-source infrastructure of EDA. ASPDAC (2024)
Shizhe Ding, Boyang Xia, Jingyan Sui, Dongbo Bu
Accurate Interpolation of Scattered Data Via Learning Relation Graph. ICASSP (2024)
Jingyan Sui, Shizhe Ding, Boyang Xia, Ruizhi Liu, Dongbo Bu
NeuralGLS: learning to guide local search with graph convolutional network for the traveling salesman problem. Neural Comput. Appl. 36 (17) (2024)
Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. CoRR (2023)
Xingquan Li, Simin Tao, Zengrong Huang, Shijian Chen, Zhisheng Zeng, Liwei Ni, Zhipeng Huang, Chunan Zhuang, Hongxi Wu, Weiguo Li, Xueyan Zhao, He Liu, Shuaiying Long, Wei He, Bojun Liu, Sifeng Gan, Zihao Yu, Tong Liu, Yuchi Miao, Zhiyuan Yan, Hao Wang, Jie Zhao, Yifan Li, Ruizhi Liu, Xiaoze Lin, Bo Yang, Zhen Xue, Fuxing Huang, Zonglin Yang, Zhenggang Wu, Jiangkao Li, Yuezuo Liu, Ming Peng, Yihang Qiu, Wenrui Wu, Zheqing Shao, Kai Mo, Jikang Liu, Yuyao Liang, Mingzhe Zhang, Zhuang Ma, Xiang Cong, Daxiang Huang, Guojie Luo, Huawei Li, Haihua Shen, Mingyu Chen, Dongbo Bu, Wenxing Zhu, Ye Cai, Xiaoming Xiong, Ying Jiang, Yi Heng, Peng Zhang, Biwei Xie, Yungang Bao
iEDA: An Open-Source Intelligent Physical Implementation Toolkit and Library. CoRR (2023)
Zhiying Jiang, Rui Wang, Dongbo Bu, Ming Li
A Theory of Human-Like Few-Shot Learning. CoRR (2023)
Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. NeurIPS (2023)
Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Shizhe Ding, Boyang Xia, Dongbo Bu
Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement. NeurIPS (2023)
Bin Huang, Lupeng Kong, Chao Wang, Fusong Ju, Qi Zhang, Jianwei Zhu, Tiansu Gong, Haicang Zhang, Chungong Yu, Wei-Mou Zheng, Dongbo Bu
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. Genom. Proteom. Bioinform. 21 (5) (2023)
Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu
Accurate and efficient protein sequence design through learning concise local environment of residues. Bioinform. 39 (3) (2023)
Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun
EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction. Bioinform. 39 (10) (2023)
Shizhe Ding, Dongbo Bu
NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder. CoRR (2022)
Chenyang Wang, Guannan Ma, Di Wei, Xinru Zhang, Peihan Wang, Cuidan Li, Jing Xing, Zheng Wei, Bo Duan, Dongxin Yang, Pei Wang, Dongbo Bu, Fei Chen
Mainstream encoding-decoding methods of DNA data storage. CCF Trans. High Perform. Comput. 4 (1) (2022)
Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. J. Comput. Biol. 29 (2) (2022)
Fusong Ju, Jianwei Zhu, Qi Zhang, Guozheng Wei, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. Bioinform. 38 (4) (2022)
Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun, Dongbo Bu
FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC Bioinform. 22 (1) (2021)
Jingyan Sui, Shizhe Ding, Ruizhi Liu, Liming Xu, Dongbo Bu
Learning 3-opt heuristics for traveling salesman problem via deep reinforcement learning. ACML (2021)
Yu Wang, Hui Wang, Meijie Hou, Yaojun Wang, Dongbo Bu, Chunming Zhang, Chuncui Huang, Shiwei Sun
Glycan immunogenicity prediction based on Graph neural network. BIBM (2021)
Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. BMC Bioinform. 22 (3) (2021)
Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu
SASA-Net: A spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances. BIBM (2021)
Yaojun Wang, Xinyu Hua, Yu Wang, Chunming Zhang, Dongbo Bu, Shiwei Sun, Xingce Wang
Mut-Detecter: An EGFR activating mutation type classification method with a deep convolutional neural network. BIBM (2020)
Qi Zhang, Jianwei Zhu, Fusong Ju, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
ISSEC: inferring contacts among protein secondary structure elements using deep object detection. BMC Bioinform. 21 (1) (2020)
Shaojiang Wang, Tianyong Wu, Yuan Yao, Dongbo Bu, Shaowei Cai
Constrained maximum weighted bipartite matching: a novel approach to radio broadcast scheduling. Sci. China Inf. Sci. 62 (7) (2019)
Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. Bioinform. 35 (14) (2019)
Fusong Ju, Jianwei Zhu, Guozheng Wei, Qi Zhang, Shiwei Sun, Dongbo Bu
Seq-SetNet: Exploring Sequence Sets for Inferring Structures. CoRR (2019)
Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. BMC Bioinform. (3) (2019)
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC Bioinform. 20 (1) (2019)
Fusong Ju, Jingwei Zhang, Dongbo Bu, Yan Li, Jinyu Zhou, Hui Wang, Yaojun Wang, Chuncui Huang, Shiwei Sun
De novo glycan structural identification from mass spectra using tree merging strategy. Comput. Biol. Chem. 80 (2019)
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC Bioinform. 20 (1) (2019)
Yaojun Wang, Dongbo Bu, Chuncui Huang, Hui Wang, Jinyu Zhou, Junchuan Dong, Weiyi Pan, Jingwei Zhang, Qi Zhang, Yan Li, Shiwei Sun
Best-first search guided multistage mass spectrometry-based glycan identification. Bioinform. 35 (17) (2019)
Jianwei Zhu, Sheng Wang, Dongbo Bu, Jinbo Xu
Protein threading using residue co-variation and deep learning. Bioinform. 34 (13) (2018)
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Shiwei Sun, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. CoRR (2018)
Hai'e Gong, Haicang Zhang, Jianwei Zhu, Chao Wang, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Improving prediction of burial state of residues by exploiting correlation among residues. BMC Bioinform. 18 (S-3) (2017)
Jianwei Zhu, Haicang Zhang, Shuai Cheng Li, Chao Wang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. Bioinform. 33 (23) (2017)
Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinform. 32 (3) (2016)
Dandan Song, Jiaxing Chen, Guang Chen, Ning Li, Jin Li, Jun Fan, Dongbo Bu, Shuai Cheng Li
Parameterized BLOSUM Matrices for Protein Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Shiwei Sun, Xuetao Wang, Xin Gao, Lihui Ren, Xiaoquan Su, Dongbo Bu, Kang Ning
Condensing Raman spectrum for single-cell phenotype analysis. BMC Bioinform. 16 (S18) (2015)
Yaojun Wang, Fei Yang, Peng Wu, Dongbo Bu, Shiwei Sun
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction. BMC Bioinform. 16 (2015)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? Algorithms Mol. Biol. 8 (2013)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li
Towards Reliable Automatic Protein Structure Alignment. WABI (2013)
Shuai Cheng Li, Dongbo Bu, Ming Li
Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (1) (2012)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li
How Accurately Can We Model Protein Structures with Dihedral Angles? WABI (2012)
Shuai Cheng Li, Dongbo Bu, Ming Li
Clustering 100, 000 Protein Structure Decoys in Minutes. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Guangming Tan, Ping Liu, Dongbo Bu, Yanbing Liu
Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture. J. Comput. Sci. Technol. 26 (5) (2011)
Xiongying Yuan, Yi Zhao, Changning Liu, Dongbo Bu
Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification. J. Bioinform. Comput. Biol. 9 (2) (2011)
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
Finding Nearly Optimal GDT Scores. J. Comput. Biol. 18 (5) (2011)
Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Li, Wei-Mou Zheng, Dongbo Bu
Incorporating Ab Initio energy into threading approaches for protein structure prediction. BMC Bioinform. 12 (S-1) (2011)
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 Bioinform. 12 (2011)
Xingwu Liu, Yunfei Bai, Chunlin Huang, Xiaoyan Wang, Dongbo Bu
PEARL: Probing Entity Aggregation in Real Life. GreenCom (2011)
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 Bioinform. 12 (2011)
Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu
Finding compact structural motifs. Theor. Comput. Sci. 410 (30-32) (2009)
Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinform. 24 (18) (2008)
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
Finding Largest Well-Predicted Subset of Protein Structure Models. CPM (2008)
Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB (2008)
Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li
Designing succinct structural alphabets. ISMB (2008)
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinform. Comput. Biol. 5 (2a) (2007)
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. BIBE (2007)
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
Finding Compact Structural Motifs. CPM (2007)
Guangming Tan, Lin Xu, Dongbo Bu, Shengzhong Feng, Ninghui Sun
Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment. J. Comput. Sci. Technol. 21 (6) (2006)
Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinform. 7 (2006)
Guangming Tan, Ninghui Sun, Dongbo Bu
Improving locality of nonserial polyadic dynamic programming. IPDPS (2006)
Guangming Tan, Lin Xu, Yishan Jiao, Shengzhong Feng, Dongbo Bu, Ninghui Sun
An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast. ICPADS (2) (2005)
Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 33 (Database-Issue) (2005)
Hao Lin, Zefeng Zhang, Qiang-Feng Zhang, Dongbo Bu, Ming Li
A Note on the Single Genotype Resolution Problem. J. Comput. Sci. Technol. 19 (2) (2004)
Bin Wang, Hongbo Xu, Zhifeng Yang, Yue Liu, Xueqi Cheng, Dongbo Bu, Shuo Bai
TREC-10 Experiments at CAS-ICT: Filtering, Web and QA. TREC (2001)