Dongbo Bu

77 papers A* 3A 2B 5C 4Misc 1Journal 56Unranked 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
Designing faster mixed integer linear programming algorithm via learning the optimal path.
CoRR
Ruizhi Liu, Liming Xu, Xulin Huang, Jingyan Sui, Shizhe Ding, Boyang Xia, Chungong Yu, Dongbo Bu
2026 J jnl
GGFlow: A Graph Flow Matching Method with Efficient Optimal Transport.
Trans. Mach. Learn. Res.
Xiaoyang Hou, Tian Zhu, Milong Ren, Dongbo Bu, Xin Gao, Chunming Zhang, Shiwei Sun
2025 J jnl
A survey on deep learning-based algorithms for the traveling salesman problem.
Frontiers Comput. Sci.
Jingyan Sui, Shizhe Ding, Xulin Huang, Yue Yu, Ruizhi Liu, Boyang Xia, Zhenxin Ding, Liming Xu, Haicang Zhang, Chungong Yu, Dongbo Bu
2024 Misc conf
Accurate Interpolation of Scattered Data Via Learning Relation Graph.
ICASSP
Shizhe Ding, Boyang Xia, Jingyan Sui, Dongbo Bu
2024 J jnl
Accurate and robust protein sequence design with CarbonDesign.
Nat. Mac. Intell.
Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
2024 J jnl
DMSS: An Attention-Based Deep Learning Model for High-Quality Mass Spectrometry Prediction.
Big Data Min. Anal.
Yihui Ren, Yu Wang, Wenkai Han, Yikang Huang, Xiaoyang Hou, Chunming Zhang, Dongbo Bu, Xin Gao, Shiwei Sun
2024 J jnl
GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states.
BMC Bioinform.
Fan Liu, Han Zhou, Xiaonong Li, Liangliang Zhou, Chungong Yu, Haicang Zhang, Dongbo Bu, Xinmiao Liang
2024 J jnl
Improving Molecular Graph Generation with Flow Matching and Optimal Transport.
CoRR
Xiaoyang Hou, Tian Zhu, Milong Ren, Dongbo Bu, Xin Gao, Chunming Zhang, Shiwei Sun
2024 B conf
Multilevel Temporal-Spectral Fusion Network for Multivariate Time Series Classification.
IJCNN
Xulin Huang, Shizhe Ding, Xinru Zhang, Jingyan Sui, Yue Yu, Dongbo Bu
2024 J jnl
NIERT: Accurate Numerical Interpolation Through Unifying Scattered Data Representations Using Transformer Encoder.
IEEE Trans. Knowl. Data Eng.
Shizhe Ding, Boyang Xia, Milong Ren, Dongbo Bu
2024 J jnl
NeuralGLS: learning to guide local search with graph convolutional network for the traveling salesman problem.
Neural Comput. Appl.
Jingyan Sui, Shizhe Ding, Boyang Xia, Ruizhi Liu, Dongbo Bu
2024 A* conf
NeuralSteiner: Learning Steiner Tree for Overflow-avoiding Global Routing in Chip Design.
NeurIPS
Ruizhi Liu, Zhisheng Zeng, Shizhe Ding, Jingyan Sui, Xingquan Li, Dongbo Bu
2024 J jnl
Understanding is Compression.
CoRR
Ziguang Li, Chao Huang, Xuliang Wang, Haibo Hu, Cole Wyeth, Dongbo Bu, Quan Yu, Wen Gao, Xingwu Liu, Ming Li
2024 B conf
iEDA: An Open-source infrastructure of EDA.
ASPDAC
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
2023 J jnl
A Theory of Human-Like Few-Shot Learning.
CoRR
Zhiying Jiang, Rui Wang, Dongbo Bu, Ming Li
2023 A* conf
Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement.
NeurIPS
Shizhe Ding, Boyang Xia, Dongbo Bu
2023 J jnl
Accurate and efficient protein sequence design through learning concise local environment of residues.
Bioinform.
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
2023 J jnl
EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction.
Bioinform.
Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun
2023 A* conf
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model.
NeurIPS
Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
2023 J jnl
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model.
CoRR
Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang
2023 J jnl
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms.
Genom. Proteom. Bioinform.
Bin Huang, Lupeng Kong, Chao Wang, Fusong Ju, Qi Zhang, Jianwei Zhu, Tiansu Gong, Haicang Zhang, Chungong Yu, Wei-Mou Zheng, Dongbo Bu
2023 J jnl
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu
2023 J jnl
iEDA: An Open-Source Intelligent Physical Implementation Toolkit and Library.
CoRR
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
2022 J jnl
Mainstream encoding-decoding methods of DNA data storage.
CCF Trans. High Perform. Comput.
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
2022 J jnl
NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder.
CoRR
Shizhe Ding, Dongbo Bu
2022 J jnl
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs.
J. Comput. Biol.
Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu
2022 J jnl
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction.
Bioinform.
Fusong Ju, Jianwei Zhu, Qi Zhang, Guozheng Wei, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2021 J jnl
FALCON2: a web server for high-quality prediction of protein tertiary structures.
BMC Bioinform.
Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun, Dongbo Bu
2021 J jnl
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.
BMC Bioinform.
Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu
2021 — conf
Glycan immunogenicity prediction based on Graph neural network.
BIBM
Yu Wang, Hui Wang, Meijie Hou, Yaojun Wang, Dongbo Bu, Chunming Zhang, Chuncui Huang, Shiwei Sun
2021 C conf
Learning 3-opt heuristics for traveling salesman problem via deep reinforcement learning.
ACML
Jingyan Sui, Shizhe Ding, Ruizhi Liu, Liming Xu, Dongbo Bu
2021 — conf
SASA-Net: A spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances.
BIBM
Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu
2020 J jnl
ISSEC: inferring contacts among protein secondary structure elements using deep object detection.
BMC Bioinform.
Qi Zhang, Jianwei Zhu, Fusong Ju, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2020 — conf
Mut-Detecter: An EGFR activating mutation type classification method with a deep convolutional neural network.
BIBM
Yaojun Wang, Xinyu Hua, Yu Wang, Chunming Zhang, Dongbo Bu, Shiwei Sun, Xingce Wang
2019 J jnl
Best-first search guided multistage mass spectrometry-based glycan identification.
Bioinform.
Yaojun Wang, Dongbo Bu, Chuncui Huang, Hui Wang, Jinyu Zhou, Junchuan Dong, Weiyi Pan, Jingwei Zhang, Qi Zhang, Yan Li, Shiwei Sun
2019 J jnl
Constrained maximum weighted bipartite matching: a novel approach to radio broadcast scheduling.
Sci. China Inf. Sci.
Shaojiang Wang, Tianyong Wu, Yuan Yao, Dongbo Bu, Shaowei Cai
2019 J jnl
Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling.
BMC Bioinform.
Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2019 J jnl
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
BMC Bioinform.
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2019 J jnl
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning.
Bioinform.
Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang
2019 J jnl
De novo glycan structural identification from mass spectra using tree merging strategy.
Comput. Biol. Chem.
Fusong Ju, Jingwei Zhang, Dongbo Bu, Yan Li, Jinyu Zhou, Hui Wang, Yaojun Wang, Chuncui Huang, Shiwei Sun
2019 J jnl
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
BMC Bioinform.
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2019 J jnl
Seq-SetNet: Exploring Sequence Sets for Inferring Structures.
CoRR
Fusong Ju, Jianwei Zhu, Guozheng Wei, Qi Zhang, Shiwei Sun, Dongbo Bu
2018 J jnl
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
CoRR
Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Shiwei Sun, Yujuan Gao, Ziwei Xie, Minghua Deng, Wei-Mou Zheng, Dongbo Bu
2018 J jnl
Protein threading using residue co-variation and deep learning.
Bioinform.
Jianwei Zhu, Sheng Wang, Dongbo Bu, Jinbo Xu
2017 J jnl
Improving prediction of burial state of residues by exploiting correlation among residues.
BMC Bioinform.
Hai'e Gong, Haicang Zhang, Jianwei Zhu, Chao Wang, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2017 J jnl
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.
Bioinform.
Jianwei Zhu, Haicang Zhang, Shuai Cheng Li, Chao Wang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2016 J jnl
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinform.
Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu
2015 J jnl
Condensing Raman spectrum for single-cell phenotype analysis.
BMC Bioinform.
Shiwei Sun, Xuetao Wang, Xin Gao, Lihui Ren, Xiaoquan Su, Dongbo Bu, Kang Ning
2015 J jnl
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction.
BMC Bioinform.
Yaojun Wang, Fei Yang, Peng Wu, Dongbo Bu, Shiwei Sun
2015 J jnl
Parameterized BLOSUM Matrices for Protein Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dandan Song, Jiaxing Chen, Guang Chen, Ning Li, Jin Li, Jun Fan, Dongbo Bu, Shuai Cheng Li
2013 J jnl
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
Algorithms Mol. Biol.
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li
2013 C conf
Towards Reliable Automatic Protein Structure Alignment.
WABI
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li
2012 J jnl
Clustering 100, 000 Protein Structure Decoys in Minutes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuai Cheng Li, Dongbo Bu, Ming Li
2012 C conf
How Accurately Can We Model Protein Structures with Dihedral Angles?
WABI
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li
2012 J jnl
Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuai Cheng Li, Dongbo Bu, Ming Li
2011 J jnl
Finding Nearly Optimal GDT Scores.
J. Comput. Biol.
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
2011 J jnl
Incorporating Ab Initio energy into threading approaches for protein structure prediction.
BMC Bioinform.
Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Li, Wei-Mou Zheng, Dongbo Bu
2011 J jnl
Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification.
J. Bioinform. Comput. Biol.
Xiongying Yuan, Yi Zhao, Changning Liu, Dongbo Bu
2011 — conf
PEARL: Probing Entity Aggregation in Real Life.
GreenCom
Xingwu Liu, Yunfei Bai, Chunlin Huang, Xiaoyan Wang, Dongbo Bu
2011 J jnl
PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum.
BMC Bioinform.
Yantao Qiao, Hong Zhang, Dongbo Bu, Shiwei Sun
2011 J jnl
ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity.
BMC Bioinform.
Shenghui Zhang, Yaojun Wang, Dongbo Bu, Hong Zhang, Shiwei Sun
2011 J jnl
Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture.
J. Comput. Sci. Technol.
Guangming Tan, Ping Liu, Dongbo Bu, Yanbing Liu
2009 J jnl
Finding compact structural motifs.
Theor. Comput. Sci.
Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu
2008 B conf
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry.
RECOMB
Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu
2008 A conf
Designing succinct structural alphabets.
ISMB
Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li
2008 B conf
Finding Largest Well-Predicted Subset of Protein Structure Models.
CPM
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
2008 J jnl
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.
Bioinform.
Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao
2007 C conf
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots.
BIBE
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao
2007 J jnl
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol.
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen
2007 B conf
Finding Compact Structural Motifs.
CPM
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
2006 J jnl
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.
BMC Bioinform.
Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen
2006 J jnl
Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment.
J. Comput. Sci. Technol.
Guangming Tan, Lin Xu, Dongbo Bu, Shengzhong Feng, Ninghui Sun
2006 A conf
Improving locality of nonserial polyadic dynamic programming.
IPDPS
Guangming Tan, Ninghui Sun, Dongbo Bu
2005 — conf
An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast.
ICPADS (2)
Guangming Tan, Lin Xu, Yishan Jiao, Shengzhong Feng, Dongbo Bu, Ninghui Sun
2005 J jnl
NONCODE: an integrated knowledge database of non-coding RNAs.
Nucleic Acids Res.
Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen
2004 J jnl
A Note on the Single Genotype Resolution Problem.
J. Comput. Sci. Technol.
Hao Lin, Zefeng Zhang, Qiang-Feng Zhang, Dongbo Bu, Ming Li
2001 — conf
TREC-10 Experiments at CAS-ICT: Filtering, Web and QA.
TREC
Bin Wang, Hongbo Xu, Zhifeng Yang, Yue Liu, Xueqi Cheng, Dongbo Bu, Shuo Bai