Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden. - Aiping Wu 002; Yousong Peng; Xiangjun Du; Yuelong Shu; Taijiao Jiang (PLoS Comput. Biol., 2010)

NCACO-score: An effective main-chain dependent scoring function for structure modeling. - Liqing Tian; Aiping Wu 002; Yang Cao; Xiaoxi Dong; Yun Hu; Taijiao Jiang (BMC Bioinform., 2011)

Exploring protein domain organization by recognition of secondary structure packing interfaces. - Lizong Deng; Aiping Wu 002; Wentao Dai; Tingrui Song; Ya Cui; Taijiao Jiang (Bioinform., 2014)

Uncover protein complexes in E.coli network. - Wei Liu 154; Aiping Wu 002 (BIBM, 2015)

PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences. - Yousong Peng; Lei Yang 002; Honglei Li 002; Yuanqiang Zou; Lizong Deng; Aiping Wu 002; Xiangjun Du; Dayan Wang; Yuelong Shu; Taijiao Jiang (Bioinform., 2016)

A novel index of protein-protein interface propensity improves interface residue recognition. - Wentao Dai; Aiping Wu 002; Liang-Xiao Ma; Yi-Xue Li; Taijiao Jiang; Yuan-Yuan Li (BMC Syst. Biol., 2016)

cooccurNet: an R package for co-occurrence network construction and analysis. - Yuanqiang Zou; Zhiqiang Wu 001; Lizong Deng; Aiping Wu 002; Fan Wu 016; Kenli Li 001; Taijiao Jiang; Yousong Peng (Bioinform., 2017)

Identification of Bridging Centrality in Complex Networks. - Wei Liu 154; Matteo Pellegrini; Aiping Wu 002 (IEEE Access, 2019)

Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors. - Zheng Zhang; Zhaozhong Zhu; Wenjun Chen; Zena Cai; Beibei Xu; Zhiying Tan; Aiping Wu 002; Xingyi Ge; Xinhong Guo; Zhongyang Tan; Zanxian Xia; Haizhen Zhu; et al. (Bioinform., 2019)

FluReassort: a database for the study of genomic reassortments among influenza viruses. - Xiao Ding; Xuye Yuan; Longfei Mao; Aiping Wu 002; Taijiao Jiang (Briefings Bioinform., 2020)

Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes. - Ziyi Chen; Chengyang Ji; Qin Shen; Wei Liu; F. Xiao-Feng Qin; Aiping Wu 002 (Bioinform., 2020)

FluPhenotype - a one-stop platform for early warnings of the influenza A virus. - Congyu Lu; Zena Cai; Yuanqiang Zou; Zheng Zhang; Wenjun Chen; Lizong Deng; Xiangjun Du; Aiping Wu 002; Lei Yang 002; Dayan Wang; Yuelong Shu; Taijiao Jiang; et al. (Bioinform., 2020)

Phage protein receptors have multiple interaction partners and high expressions. - Zheng Zhang; Fen Yu; Yuanqiang Zou; Ye Qiu; Aiping Wu 002; Taijiao Jiang; Yousong Peng (Bioinform., 2020)

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. - Zena Cai; Congyu Lu; Jun He; Li Liu; Yuanqiang Zou; Zheng Zhang; Zhaozhong Zhu; Xingyi Ge; Aiping Wu 002; Taijiao Jiang; Heping Zheng; Yousong Peng (Briefings Bioinform., 2021)

Progress and challenge for computational quantification of tissue immune cells. - Ziyi Chen; Aiping Wu 002 (Briefings Bioinform., 2021)

Compositional diversity and evolutionary pattern of coronavirus accessory proteins. - Jingzhe Shang; Na Han; Ziyi Chen; Yousong Peng; Liang Li; Hangyu Zhou; Chengyang Ji; Jing Meng; Taijiao Jiang; Aiping Wu 002 (Briefings Bioinform., 2021)

Comparative viromes of Culicoides and mosquitoes reveal their consistency and diversity in viral profiles. - Lin Liu; Qin Shen; Nan Li; Yuwen He; Na Han; Xianyue Wang; Jinxin Meng; Yousong Peng; Mei Pan; Yuting Jin; Taijiao Jiang; Wenjie Tan; et al. (Briefings Bioinform., 2021)

Enhancing Cross-lingual Medical Concept Alignment by Leveraging Synonyms and Translations of the Unified Medical Language System. - Luming Chen; Yifan Qi; Aiping Wu 002; Lizong Deng; Taijiao Jiang (HPCC/DSS/SmartCity/DependSys, 2022)

vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data. - Zena Cai; Ping Fu; Ye Qiu; Aiping Wu 002; Gaihua Zhang; Yirong Wang; Taijiao Jiang; Xing-Yi Ge; Haizhen Zhu; Yousong Peng (Briefings Bioinform., 2022)

An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses. - Sifan Ye; Congyu Lu; Ye Qiu; Heping Zheng; Xingyi Ge; Aiping Wu 002; Zanxian Xia; Taijiao Jiang; Haizhen Zhu; Yousong Peng (Bioinform., 2022)

sitePath: a visual tool to identify polymorphism clades and help find fixed and parallel mutations. - Chengyang Ji; Na Han; Yexiao Cheng; Jingzhe Shang; Shenghui Weng; Rong Yang; Hangyu Zhou; Aiping Wu 002 (BMC Bioinform., 2022)

TeaBERT: An Efficient Knowledge Infused Cross-Lingual Language Model for Mapping Chinese Medical Entities to the Unified Medical Language System. - Luming Chen; Yifan Qi; Aiping Wu 002; Lizong Deng; Taijiao Jiang (IEEE J. Biomed. Health Informatics, 2023)

PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network. - Jing Meng; Jingze Liu; Wenkai Song; Honglei Li 002; Jiangyuan Wang; Le Zhang 004; Yousong Peng; Aiping Wu 002; Taijiao Jiang (Briefings Bioinform., 2024)

ARNLE model identifies prevalence potential of SARS-CoV-2 variants. - Yuqi Liu; Jing Li 121; Peihan Li; Yehong Yang; Kaiying Wang; Jinhui Li; Lang Yang; Jiangfeng Liu; Leili Jia; Aiping Wu 002; Juntao Yang; Peng Li 041; et al. (Nat. Mac. Intell., 2025)

Influenza virus reassortment patterns exhibit preference and continuity while uncovering cross-species transmission events. - Xiao Ding; Yun Ma 016; Shicheng Li; Jingze Liu; Luyao Qin; Aiping Wu 002 (Briefings Bioinform., 2025)

TransSSVs: a Transformer-based deep learning model for accurate detection of somatic small variants in paired tumor and normal sequencing data. - Jing Meng; Jiangyuan Wang; Jingze Liu; Wenkai Song; Ming Li; Aiping Wu 002; Taijiao Jiang (Appl. Intell., 2025)