AVID: An integrative framework for discovering functional relationships among proteins. - Taijiao Jiang; Amy E. Keating (BMC Bioinform., 2005)

Paircoil2: improved prediction of coiled coils from sequence. - A. V. McDonnell; Taijiao Jiang; Amy E. Keating; Bonnie Berger (Bioinform., 2006)

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

Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation. - Yang Cao; Lin Song; Zhichao Miao; Yun Hu; Liqing Tian; Taijiao Jiang (Bioinform., 2011)

RASP: rapid modeling of protein side chain conformations. - Zhichao Miao; Yang Cao; Taijiao Jiang (Bioinform., 2011)

NCACO-score: An effective main-chain dependent scoring function for structure modeling. - Liqing Tian; Aiping Wu; 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; Wentao Dai; Tingrui Song; Ya Cui; Taijiao Jiang (Bioinform., 2014)

Prediction of influenza epidemics at the province level in China using search query from "Haosou". - Yuanqiang Zou; Yousong Peng; Li Lu; Taijiao Jiang; Lizong Deng (FSKD, 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; 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; Liang-Xiao Ma; Yi-Xue Li; Taijiao Jiang; Yuan-Yuan Li (BMC Syst. Biol., 2016)

Predicting the Antigenic Variant of Human Influenza A(H3N2) Virus with a Stacked Auto-Encoder Model. - Zhiying Tan; Beibei Xu; Kenli Li 001; Taijiao Jiang; Yousong Peng (ICPCSEE (2), 2017)

Prediction of Cell Specific O-GalNAc Glycosylation in Human. - Yuanqiang Zou; Kenli Li 001; Taijiao Jiang; Yousong Peng (ICPCSEE (2), 2017)

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

Multiple Visual Fields Cascaded Convolutional Neural Network for Breast Cancer Detection. - Haomiao Ni; Hong Liu 007; Zichao Guo; Xiangdong Wang; Taijiao Jiang; Kuansong Wang; Yueliang Qian (PRICAI (1), 2018)

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; 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; Taijiao Jiang (Briefings 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; 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; Taijiao Jiang; Yousong Peng (Bioinform., 2020)

LATTE: A knowledge-based method to normalize various expressions of laboratory test results in free text of Chinese electronic health records. - Kun Jiang; Tao Yang; Chunyan Wu; Luming Chen; Longfei Mao; Yongyou Wu; Lizong Deng; Taijiao Jiang (J. Biomed. Informatics, 2020)

VirusCircBase: a database of virus circular RNAs. - Zena Cai; Yunshi Fan; Zheng Zhang; Congyu Lu; Zhaozhong Zhu; Taijiao Jiang; Tongling Shan; Yousong Peng (Briefings Bioinform., 2021)

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; Taijiao Jiang; Heping Zheng; Yousong Peng (Briefings Bioinform., 2021)

DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network. - Jing Meng; Brandon Victor; Zhen He 002; Hongde Liu; Taijiao Jiang (Briefings Bioinform., 2021)

Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2. - Luyao Qin; Xiao Ding; Yongjie Li; Qingfeng Chen; Jing Meng; Taijiao Jiang (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 (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; 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; 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; Zanxian Xia; Taijiao Jiang; Haizhen Zhu; Yousong Peng (Bioinform., 2022)

PIAT: An Evolutionarily Intelligent System for Deep Phenotyping of Chinese Electronic Health Records. - Lizong Deng; Xu Zhang; Tao Yang; Mi Liu; Luming Chen; Taijiao Jiang (IEEE J. Biomed. Health Informatics, 2022)

Ribocentre: a database of ribozymes. - Jie Deng; Yaohuang Shi; Xuemei Peng; Yuanlin He; Xiaoxue Chen; Mengxiao Li; Xiaowei Lin; Wenjian Liao; Yuanyin Huang; Taijiao Jiang; David M. J. Lilley; Zhichao Miao; et al. (Nucleic Acids Res., 2023)

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; 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; Jiangyuan Wang; Le Zhang 004; Yousong Peng; Aiping Wu; Taijiao Jiang (Briefings Bioinform., 2024)

PREDAC-FluB: predicting antigenic clusters of seasonal influenza B viruses with protein language model embedding based convolutional neural network. - Wenping Xie; Jingze Liu; Chuan Wang; Jiangyuan Wang; Wenjie Han; Yousong Peng; Xiangjun Du; Jing Meng; Kang Ning 001; Taijiao Jiang (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; Taijiao Jiang (Appl. Intell., 2025)