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Journal Articles
- 2024
[j43]Milong Ren, Chungong Yu, Dongbo Bu
, Haicang Zhang:
Accurate and robust protein sequence design with CarbonDesign. Nat. Mac. Intell. 6(5): 536-547 (2024)- [j42]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): 9687-9706 (2024) - [j41]Shizhe Ding, Boyang Xia, Milong Ren, Dongbo Bu:
NIERT: Accurate Numerical Interpolation Through Unifying Scattered Data Representations Using Transformer Encoder. IEEE Trans. Knowl. Data Eng. 36(11): 6731-6744 (2024) - 2023
- [j40]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) - [j39]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) - [j38]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): 913-925 (2023) - [j37]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): 3482-3488 (2023) - 2022
- [j36]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): 990-996 (2022) - [j35]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): 23-33 (2022) - [j34]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): 92-105 (2022) - 2021
- [j33]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): 439 (2021) - [j32]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): 533 (2021) - 2020
- [j31]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): 503 (2020) - 2019
- [j30]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): i284-i294 (2019) - [j29]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): 2991-2997 (2019) - [j28]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): 537:1-537:11 (2019) - [j27]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): 616:1-616:5 (2019) - [j26]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. 20-S(3): 99-108 (2019) - [j25]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: 217-224 (2019) - [j24]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): 72102:1-72102:14 (2019) - 2018
- [j23]Jianwei Zhu, Sheng Wang, Dongbo Bu, Jinbo Xu:
Protein threading using residue co-variation and deep learning. Bioinform. 34(13): i263-i273 (2018) - 2017
- [j22]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): 3749-3757 (2017) - [j21]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): 165-175 (2017) - 2016
- [j20]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): 462-464 (2016) - 2015
- [j19]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: 110:1-110:6 (2015) - [j18]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): S15 (2015) - [j17]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): 686-694 (2015) - 2013
- [j16]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: 5 (2013) - 2012
- [j15]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): 240-248 (2012) - [j14]Shuai Cheng Li, Dongbo Bu, Ming Li:
Clustering 100, 000 Protein Structure Decoys in Minutes. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 765-773 (2012) - 2011
- [j13]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: 234 (2011) - [j12]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: 346 (2011) - [j11]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): S54 (2011) - [j10]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): 299-316 (2011) - [j9]Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li:
Finding Nearly Optimal GDT Scores. J. Comput. Biol. 18(5): 693-704 (2011) - [j8]Guangming Tan, Ping Liu, Dongbo Bu, Yanbing Liu:
Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture. J. Comput. Sci. Technol. 26(5): 866-874 (2011) - 2009
- [j7]Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu:
Finding compact structural motifs. Theor. Comput. Sci. 410(30-32): 2834-2839 (2009) - 2008
- [j6]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): 1994-2001 (2008) - 2007
- [j5]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): 297-311 (2007) - 2006
- [j4]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: 222 (2006) - [j3]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): 973-978 (2006) - 2005
- [j2]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): 112-115 (2005) - 2004
- [j1]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): 254-257 (2004)
Conference and Workshop Papers
- 2024
- [c20]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: 77-82 - [c19]Shizhe Ding, Boyang Xia, Jingyan Sui, Dongbo Bu:
Accurate Interpolation of Scattered Data Via Learning Relation Graph. ICASSP 2024: 7290-7294 - [c18]Xulin Huang, Shizhe Ding, Xinru Zhang, Jingyan Sui, Yue Yu, Dongbo Bu:
Multilevel Temporal-Spectral Fusion Network for Multivariate Time Series Classification. IJCNN 2024: 1-7 - 2023
- [c17]Shizhe Ding, Boyang Xia, Dongbo Bu:
Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement. NeurIPS 2023 - [c16]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 - 2021
- [c15]Jingyan Sui, Shizhe Ding, Ruizhi Liu, Liming Xu, Dongbo Bu:
Learning 3-opt heuristics for traveling salesman problem via deep reinforcement learning. ACML 2021: 1301-1316 - [c14]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: 32-37 - [c13]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: 348-353 - 2020
- [c12]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: 2386-2389 - 2013
- [c11]Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li:
Towards Reliable Automatic Protein Structure Alignment. WABI 2013: 18-32 - 2012
- [c10]Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li:
How Accurately Can We Model Protein Structures with Dihedral Angles? WABI 2012: 274-287 - 2011
- [c9]Xingwu Liu, Yunfei Bai, Chunlin Huang, Xiaoyan Wang, Dongbo Bu:
PEARL: Probing Entity Aggregation in Real Life. GreenCom 2011: 238-241 - 2008
- [c8]Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li:
Finding Largest Well-Predicted Subset of Protein Structure Models. CPM 2008: 44-55 - [c7]Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li:
Designing succinct structural alphabets. ISMB 2008: 182-189 - [c6]Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu:
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB 2008: 154-166 - 2007
- [c5]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: 411-417 - [c4]Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu:
Finding Compact Structural Motifs. CPM 2007: 142-149 - 2006
- [c3]Guangming Tan, Ninghui Sun, Dongbo Bu:
Improving locality of nonserial polyadic dynamic programming. IPDPS 2006 - 2005
- [c2]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: 704-708 - 2001
- [c1]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
Informal and Other Publications
- 2024
- [i7]Ziguang Li, Chao Huang, Xuliang Wang, Haibo Hu, Cole Wyeth, Dongbo Bu, Quan Yu, Wen Gao, Xingwu Liu, Ming Li:
Understanding is Compression. CoRR abs/2407.07723 (2024) - 2023
- [i6]Zhiying Jiang, Rui Wang, Dongbo Bu, Ming Li:
A Theory of Human-Like Few-Shot Learning. CoRR abs/2301.01047 (2023) - [i5]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 abs/2308.01857 (2023) - [i4]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 abs/2310.19849 (2023) - 2022
- [i3]Shizhe Ding, Dongbo Bu:
NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder. CoRR abs/2209.09078 (2022) - 2019
- [i2]Fusong Ju, Jianwei Zhu, Guozheng Wei, Qi Zhang, Shiwei Sun, Dongbo Bu:
Seq-SetNet: Exploring Sequence Sets for Inferring Structures. CoRR abs/1906.11196 (2019) - 2018
- [i1]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 abs/1809.00083 (2018)
Coauthor Index
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