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Dongbo Bu
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2020 – today
- 2024
- [j44]Fan Liu, Han Zhou, Xiaonong Li, Liangliang Zhou, Chungong Yu, Haicang Zhang, Dongbo Bu, Xinmiao Liang:
GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states. BMC Bioinform. 25(1): 343 (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
NIERT: Accurate Numerical Interpolation Through Unifying Scattered Data Representations Using Transformer Encoder. IEEE Trans. Knowl. Data Eng. 36(11): 6731-6744 (2024) - [c20]Xingquan Li
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 - [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
- [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
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. Genom. Proteom. Bioinform. 21(5): 913-925 (2023) - [j37]Tiansu Gong
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) - [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 - [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
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
- [j36]Fusong Ju
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. Bioinform. 38(4): 990-996 (2022) - [j35]Chenyang Wang, Guannan Ma
Mainstream encoding-decoding methods of DNA data storage. CCF Trans. High Perform. Comput. 4(1): 23-33 (2022) - [j34]Lupeng Kong
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. J. Comput. Biol. 29(2): 92-105 (2022) - [i3]Shizhe Ding, Dongbo Bu:
NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder. CoRR abs/2209.09078 (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
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. BMC Bioinform. 22(3): 533 (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
Glycan immunogenicity prediction based on Graph neural network. BIBM 2021: 348-353 - 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) - [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
2010 – 2019
- 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) - [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
- [j23]Jianwei Zhu, Sheng Wang
Protein threading using residue co-variation and deep learning. Bioinform. 34(13): i263-i273 (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) - 2017
- [j22]Jianwei Zhu, Haicang Zhang, Shuai Cheng Li
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
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
Condensing Raman spectrum for single-cell phenotype analysis. BMC Bioinform. 16(S18): S15 (2015) - [j17]Dandan Song, Jiaxing Chen
Parameterized BLOSUM Matrices for Protein Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 686-694 (2015) - 2013
- [j16]Xuefeng Cui, Shuai Cheng Li
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? Algorithms Mol. Biol. 8: 5 (2013) - [c11]Xuefeng Cui, Shuai Cheng Li
Towards Reliable Automatic Protein Structure Alignment. WABI 2013: 18-32 - 2012
- [j15]Shuai Cheng 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
Clustering 100, 000 Protein Structure Decoys in Minutes. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 765-773 (2012) - [c10]Xuefeng Cui, Shuai Cheng Li
How Accurately Can We Model Protein Structures with Dihedral Angles? WABI 2012: 274-287 - 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
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
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) - [c9]Xingwu Liu, Yunfei Bai, Chunlin Huang, Xiaoyan Wang, Dongbo Bu:
PEARL: Probing Entity Aggregation in Real Life. GreenCom 2011: 238-241
2000 – 2009
- 2009
- [j7]Dongbo Bu, Ming Li, Shuai Cheng Li
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
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinform. 24(18): 1994-2001 (2008) - [c8]Shuai Cheng Li
Finding Largest Well-Predicted Subset of Protein Structure Models. CPM 2008: 44-55 - [c7]Shuai Cheng Li
Designing succinct structural alphabets. ISMB 2008: 182-189 - [c6]Yu Lin
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB 2008: 154-166 - 2007
- [j5]Chungong Yu, Yu Lin
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinform. Comput. Biol. 5(2a): 297-311 (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
Finding Compact Structural Motifs. CPM 2007: 142-149 - 2006
- [j4]Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu
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) - [c3]Guangming Tan, Ninghui Sun, Dongbo Bu:
Improving locality of nonserial polyadic dynamic programming. IPDPS 2006 - 2005
- [j2]Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 33(Database-Issue): 112-115 (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 - 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) - 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
Coauthor Index
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last updated on 2024-11-19 21:42 CET by the dblp team
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