TREC-10 Experiments at CAS-ICT: Filtering, Web and QA. - Bin Wang 004; Hongbo Xu; Zhifeng Yang; Yue Liu; Xueqi Cheng; Dongbo Bu; Shuo Bai (TREC, 2001)

A Note on the Single Genotype Resolution Problem. - Hao Lin; Zefeng Zhang; Qiang-Feng Zhang; Dongbo Bu; Ming Li 001 (J. Comput. Sci. Technol., 2004)

An Optimized Algorithm of High Spatial-temporal Efficiency for MegaBlast. - Guangming Tan; Lin Xu; Yishan Jiao; Shengzhong Feng; Dongbo Bu; Ninghui Sun (ICPADS (2), 2005)

NONCODE: an integrated knowledge database of non-coding RNAs. - Changning Liu; Baoyan Bai; Geir Skogerbø; Lun Cai; Wei Deng; Yong Zhang 006; Dongbo Bu; Yi Zhao 013; Runsheng Chen (Nucleic Acids Res., 2005)

Improving locality of nonserial polyadic dynamic programming. - Guangming Tan; Ninghui Sun; Dongbo Bu (IPDPS, 2006)

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. - Zhuo Zhang; Shiwei Sun; Xiaopeng Zhu; Suhua Chang; Xiaofei Liu; Chungong Yu; Dongbo Bu; Runsheng Chen (BMC Bioinform., 2006)

Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment. - Guangming Tan; Lin Xu; Dongbo Bu; Shengzhong Feng; Ninghui Sun (J. Comput. Sci. Technol., 2006)

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. - Xiang Chen; Simin He 001; Dongbo Bu; Runsheng Chen; Wen Gao 001 (BIBE, 2007)

Finding Compact Structural Motifs. - Jianbo Qian; Shuai Cheng Li 001; Dongbo Bu; Ming Li 001; Jinbo Xu (CPM, 2007)

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. - Chungong Yu; Yu Lin 001; Shiwei Sun; Jinjin Cai; Jingfen Zhang; Dongbo Bu; Zhuo Zhang; Runsheng Chen (J. Bioinform. Comput. Biol., 2007)

Finding Largest Well-Predicted Subset of Protein Structure Models. - Shuai Cheng Li 001; Dongbo Bu; Jinbo Xu; Ming Li 001 (CPM, 2008)

Designing succinct structural alphabets. - Shuai Cheng Li 001; Dongbo Bu; Xin Gao 001; Jinbo Xu; Ming Li 001 (ISMB, 2008)

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. - Yu Lin 001; Yantao Qiao; Shiwei Sun; Chungong Yu; Gongjin Dong; Dongbo Bu (RECOMB, 2008)

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. - Xiang Chen; Simin He 001; Dongbo Bu; Fa Zhang; Zhiyong Wang; Runsheng Chen; Wen Gao 001 (Bioinform., 2008)

PEARL: Probing Entity Aggregation in Real Life. - Xingwu Liu; Yunfei Bai; Chunlin Huang; Xiaoyan Wang; Dongbo Bu (GreenCom, 2011)

PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum. - Yantao Qiao; Hong Zhang; Dongbo Bu; Shiwei Sun (BMC Bioinform., 2011)

Incorporating Ab Initio energy into threading approaches for protein structure prediction. - Mingfu Shao; Sheng Wang 001; Chao Wang; Xiongying Yuan; Shuai Li; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2011)

ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. - Shenghui Zhang; Yaojun Wang; Dongbo Bu; Hong Zhang; Shiwei Sun (BMC Bioinform., 2011)

Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification. - Xiongying Yuan; Yi Zhao; Changning Liu; Dongbo Bu (J. Bioinform. Comput. Biol., 2011)

Finding Nearly Optimal GDT Scores. - Shuai Cheng Li 001; Dongbo Bu; Jinbo Xu; Ming Li 001 (J. Comput. Biol., 2011)

Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture. - Guangming Tan; Ping Liu 001; Dongbo Bu; Yanbing Liu 007 (J. Comput. Sci. Technol., 2011)

How Accurately Can We Model Protein Structures with Dihedral Angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi Ramandi; Ming Li 001 (WABI, 2012)

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations. - Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Clustering 100, 000 Protein Structure Decoys in Minutes. - Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Towards Reliable Automatic Protein Structure Alignment. - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (WABI, 2013)

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi; Ming Li 001 (Algorithms Mol. Biol., 2013)

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction. - Yaojun Wang; Fei Yang; Peng Wu; Dongbo Bu; Shiwei Sun (BMC Bioinform., 2015)

Parameterized BLOSUM Matrices for Protein Alignment. - Dandan Song; Jiaxing Chen; Guang Chen; Ning Li; Jin Li; Jun Fan; Dongbo Bu; Shuai Cheng Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Condensing Raman spectrum for single-cell phenotype analysis. - Shiwei Sun; Xuetao Wang; Xin Gao 001; Lihui Ren; Xiaoquan Su; Dongbo Bu; Kang Ning 001 (BMC Bioinform., 2015)

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. - Chao Wang; Haicang Zhang; Wei-Mou Zheng; Dong Xu 002; Jianwei Zhu; Bing Wang; Kang Ning 001; Shiwei Sun; Shuai Cheng Li 001; Dongbo Bu (Bioinform., 2016)

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. - Jianwei Zhu; Haicang Zhang; Shuai Cheng Li 001; Chao Wang; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2017)

Improving prediction of burial state of residues by exploiting correlation among residues. - Hai'e Gong; Haicang Zhang; Jianwei Zhu; Chao Wang; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2017)

Protein threading using residue co-variation and deep learning. - Jianwei Zhu; Sheng Wang 001; Dongbo Bu; Jinbo Xu (Bioinform., 2018)

DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. - Hao Chen 097; Dipan Shaw; Jianyang Zeng 001; Dongbo Bu; Tao Jiang 001 (Bioinform., 2019)

Best-first search guided multistage mass spectrometry-based glycan identification. - Yaojun Wang; Dongbo Bu; Chuncui Huang; Hui Wang; Jinyu Zhou; Junchuan Dong; Weiyi Pan; Jingwei Zhang; Qi Zhang; Yan Li; Shiwei Sun (Bioinform., 2019)

Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. - Chao Wang; Yi Wei; Haicang Zhang; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

De novo glycan structural identification from mass spectra using tree merging strategy. - Fusong Ju; Jingwei Zhang; Dongbo Bu; Yan Li; Jinyu Zhou; Hui Wang; Yaojun Wang; Chuncui Huang; Shiwei Sun (Comput. Biol. Chem., 2019)

Constrained maximum weighted bipartite matching: a novel approach to radio broadcast scheduling. - Shaojiang Wang; Tianyong Wu; Yuan Yao; Dongbo Bu; Shaowei Cai 001 (Sci. China Inf. Sci., 2019)

Seq-SetNet: Exploring Sequence Sets for Inferring Structures. - Fusong Ju; Jianwei Zhu; Guozheng Wei; Qi Zhang; Shiwei Sun; Dongbo Bu (CoRR, 2019)

Mut-Detecter: An EGFR activating mutation type classification method with a deep convolutional neural network. - Yaojun Wang; Xinyu Hua; Yu Wang; Chunming Zhang; Dongbo Bu; Shiwei Sun; Xingce Wang (BIBM, 2020)

ISSEC: inferring contacts among protein secondary structure elements using deep object detection. - Qi Zhang; Jianwei Zhu; Fusong Ju; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2020)

Learning 3-opt heuristics for traveling salesman problem via deep reinforcement learning. - Jingyan Sui; Shizhe Ding; Ruizhi Liu; Liming Xu; Dongbo Bu (ACML, 2021)

SASA-Net: A spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances. - Tiansu Gong; Fusong Ju; Shiwei Sun; Dongbo Bu (BIBM, 2021)

Glycan immunogenicity prediction based on Graph neural network. - Yu Wang 225; Hui Wang; Meijie Hou; Yaojun Wang; Dongbo Bu; Chunming Zhang; Chuncui Huang; Shiwei Sun (BIBM, 2021)

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. - Bin Huang; Guozheng Wei; Bing Wang; Fusong Ju; Yi Zhong; Zhuozheng Shi; Shiwei Sun; Dongbo Bu (BMC Bioinform., 2021)

FALCON2: a web server for high-quality prediction of protein tertiary structures. - Lupeng Kong; Fusong Ju; Haicang Zhang; Shiwei Sun; Dongbo Bu (BMC Bioinform., 2021)

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. - Fusong Ju; Jianwei Zhu; Qi Zhang; Guozheng Wei; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2022)

Mainstream encoding-decoding methods of DNA data storage. - Chenyang Wang; Guannan Ma; Di Wei; Xinru Zhang; Peihan Wang; Cuidan Li; Jing Xing; Zheng Wei; Bo Duan; Dongxin Yang; Pei Wang; Dongbo Bu; et al. (CCF Trans. High Perform. Comput., 2022)

NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder. - Shizhe Ding; Dongbo Bu (CoRR, 2022)

ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. - Lupeng Kong; Fusong Ju; Wei-Mou Zheng; Jianwei Zhu; Shiwei Sun; Jinbo Xu; Dongbo Bu (J. Comput. Biol., 2022)

Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement. - Shizhe Ding; Boyang Xia; Dongbo Bu (NeurIPS, 2023)

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. - Shiwei Liu; Tian Zhu; Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (NeurIPS, 2023)

A Theory of Human-Like Few-Shot Learning. - Zhiying Jiang; Rui Wang; Dongbo Bu; Ming Li (CoRR, 2023)

iEDA: An Open-Source Intelligent Physical Implementation Toolkit and Library. - Xingquan Li; Simin Tao; Zengrong Huang; Shijian Chen; Zhisheng Zeng; Liwei Ni; Zhipeng Huang 009; Chunan Zhuang; Hongxi Wu; Weiguo Li; Xueyan Zhao; He Liu; et al. (CoRR, 2023)

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. - Bin Huang; Lupeng Kong; Chao Wang; Fusong Ju; Qi Zhang; Jianwei Zhu; Tiansu Gong; Haicang Zhang; Chungong Yu; Wei-Mou Zheng; Dongbo Bu (Genom. Proteom. Bioinform., 2023)

Accurate and efficient protein sequence design through learning concise local environment of residues. - 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; et al. (Bioinform., 2023)

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction. - Xiaoyang Hou; Yu Wang; Dongbo Bu; Yaojun Wang; Shiwei Sun (Bioinform., 2023)

iEDA: An Open-source infrastructure of EDA. - Xingquan Li; Zengrong Huang; Simin Tao; Zhipeng Huang 009; Chunan Zhuang; Hao Wang; Yifan Li; Yihang Qiu; Guojie Luo; Huawei Li 001; Haihua Shen; Mingyu Chen 001; et al. (ASPDAC, 2024)

Accurate Interpolation of Scattered Data Via Learning Relation Graph. - Shizhe Ding; Boyang Xia; Jingyan Sui; Dongbo Bu (ICASSP, 2024)

Multilevel Temporal-Spectral Fusion Network for Multivariate Time Series Classification. - Xulin Huang; Shizhe Ding; Xinru Zhang; Jingyan Sui; Yue Yu; Dongbo Bu (IJCNN, 2024)

NeuralSteiner: Learning Steiner Tree for Overflow-avoiding Global Routing in Chip Design. - Ruizhi Liu; Zhisheng Zeng; Shizhe Ding; Jingyan Sui; Xingquan Li; Dongbo Bu (NeurIPS, 2024)

DMSS: An Attention-Based Deep Learning Model for High-Quality Mass Spectrometry Prediction. - Yihui Ren 004; Yu Wang 225; Wenkai Han; Yikang Huang; Xiaoyang Hou; Chunming Zhang; Dongbo Bu; Xin Gao 001; Shiwei Sun (Big Data Min. Anal., 2024)

Understanding is Compression. - Ziguang Li; Chao Huang; Xuliang Wang; Haibo Hu; Cole Wyeth; Dongbo Bu; Quan Yu; Wen Gao 001; Xingwu Liu; Ming Li 001 (CoRR, 2024)

Improving Molecular Graph Generation with Flow Matching and Optimal Transport. - Xiaoyang Hou; Tian Zhu; Milong Ren; Dongbo Bu; Xin Gao 001; Chunming Zhang; Shiwei Sun (CoRR, 2024)

Accurate and robust protein sequence design with CarbonDesign. - Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (Nat. Mac. Intell., 2024)

NeuralGLS: learning to guide local search with graph convolutional network for the traveling salesman problem. - Jingyan Sui; Shizhe Ding; Boyang Xia; Ruizhi Liu; Dongbo Bu (Neural Comput. Appl., 2024)

NIERT: Accurate Numerical Interpolation Through Unifying Scattered Data Representations Using Transformer Encoder. - Shizhe Ding; Boyang Xia; Milong Ren; Dongbo Bu (IEEE Trans. Knowl. Data Eng., 2024)

GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states. - Fan Liu; Han Zhou; Xiaonong Li; Liangliang Zhou; Chungong Yu; Haicang Zhang; Dongbo Bu; Xinmiao Liang (BMC Bioinform., 2024)

A survey on deep learning-based algorithms for the traveling salesman problem. - Jingyan Sui; Shizhe Ding; Xulin Huang; Yue Yu; Ruizhi Liu; Boyang Xia; Zhenxin Ding; Liming Xu; Haicang Zhang; Chungong Yu; Dongbo Bu (Frontiers Comput. Sci., 2025)