Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. - Yong Zhang 006; Shaojuan Li; Geir Skogerbø; Zhihua Zhang; Xiaopeng Zhu; Zefeng Zhang; Shiwei Sun; Hongchao Lu; Baochen Shi; Runsheng Chen (BMC Bioinform., 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)

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)

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)

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)

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)

The Effect of Technology Usage Habits on Consumers' Intention to Continue Use Mobile Payments. - Lin Jia; Dianne J. Hall; Shiwei Sun (AMCIS, 2014)

Job Applicants' Information Privacy-Protective Response: Exploring the Roles of Technology Readiness and Trust. - John R. Drake; Dianne J. Hall; Shiwei Sun; Yichuan Wang (AMCIS, 2015)

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)

User ratings analysis in social networks through a hypernetwork method. - Qi Suo; Shiwei Sun; Nick Hajli; Peter E. D. Love (Expert Syst. Appl., 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)

Recovery Satisfaction, attitudinal Loyalty and Behavioural Loyalty: the Moderating Role of Perceived Risk. - Gaoshan Wang; Shiwei Sun; Liang Ma; Huixia Han (PACIS, 2016)

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)

The applications of social commerce constructs. - Mohana Shanmugam; Shiwei Sun; Asra Amidi; Farzad Khani; Fariborz Khani (Int. J. Inf. Manag., 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)

DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks. - Xiuquan Du; Shiwei Sun; Changlin Hu; Yu Yao 008; Yuan-Ting Yan; Yanping Zhang 001 (J. Chem. Inf. Model., 2017)

Fiducial marker detection via deep learning approach for electron tomography. - Yu Hao; Renmin Han; Xiaohua Wan; Fa Zhang 001; Shiwei Sun (BIBM, 2018)

Understanding the Factors Affecting the Organizational Adoption of Big Data. - Shiwei Sun; Casey G. Cegielski; Lin Jia; Dianne J. Hall (J. Comput. Inf. Syst., 2018)

Cerebrovascular Segmentation Algorithm Based on Focused Multi-Gaussians Model and Weighted 3D Markov Random Field. - Zhilong Lv; Rui Yan 009; Xinyu Liu 008; Zhongke Wu; Yicheng Zhu; Shiwei Sun; Fa Zhang 001; Xingce Wang; Xiaohua Wan (BIBM, 2019)

Optimizing the Electronic Health Records Through Big Data Analytics: A Knowledge-Based View. - Caifeng Zhang; Rui Ma; Shiwei Sun; Yujie Li 001; Yichuan Wang 001; Zhijun Yan (IEEE Access, 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)

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)

SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data. - Wenyan Gu; Aizhong Zhou; Lusheng Wang 001; Shiwei Sun; Xuefeng Cui; Daming Zhu (ISBRA, 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)

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)

SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data. - Wenyan Gu; Aizhong Zhou; Lusheng Wang 001; Shiwei Sun; Xuefeng Cui; Daming Zhu (J. Comput. Biol., 2021)

Automated Patching for Unreproducible Builds. - Zhilei Ren; Shiwei Sun; Jifeng Xuan; Xiaochen Li; Zhide Zhou; He Jiang 001 (ICSE, 2022)

More User Engagement in Online Community: Effects of Posting and Replying Behaviors on Detection of Depression. - Junwei Kuang; Zhijun Yan; Shiwei Sun (PACIS, 2022)

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)

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)

When Job Candidates Experience Social Media Privacy Violations: A Cross-Culture Study. - Shiwei Sun; John R. Drake; Dianne J. Hall (J. Glob. Inf. Manag., 2022)

Integrative Drug Discovery Platform: A Modular Approach for Efficient and Automated Virtual Screening. - Tianci Li; Lulu Xie; Zhonghai Zhang; Xu Li; Bo Duan; Gang Niu 008; Shiwei Sun; Fa Zhang 001; Runting Zhang; Guangming Tan; Chunming Zhang (BIBM, 2023)

Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval. - Yongshuai Wang; Xiaojun Cai; Defeng Li; Shiwei Sun; Cheng Chen; Xuefeng Cui (BIBM, 2023)

Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries. - Yaojun Wang; Shiwei Sun (Genom. Proteom. Bioinform., 2023)

Numerical studies of domain sampling methods for inverse boundary value problems by one measurement. - Shiwei Sun; Gen Nakamura; Haibing Wang (J. Comput. Phys., 2023)

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 (IEEE ACM Trans. Comput. Biol. 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)

Deep Representation Learning for Electron Ionization Mass Spectra Retrieval. - Shibo Liu; Xuan Zhang; Anlei Jiao; Shiwei Sun; Longyang Dian; Xuefeng Cui (BIBM, 2024)

How to Train Your Neural Network for Molecular Structure Generation from Mass Spectra? - Kai Zhao; Yanmin Liu; Longyang Dian; Shiwei Sun; Xuefeng Cui (BIBM, 2024)

Exploring Trial-and-Error in Deep Learning: Initial Application to Isotope Detection in Mass Spectrometry. - Qihong Jiao; Yuxiao Wang; Yongshuai Wang; Shiwei Sun; Xuefeng Cui (Big Data Min. Anal., 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)

The learned range test method for the inverse inclusion problem. - Shiwei Sun; Giovanni S. Alberti (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)

A Multimodal Approach to Depression Detection from Social Media Data. - Mingrui Tang; Dongsong Zhang; Zhu Zhang; Shiwei Sun; Zhijun Yan; Tianmei Wang (PACIS, 2025)