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| 1 | Antigenic variation of the human influenza A(H3N2) virus during the 2014–2015 winter season显示文摘The human influenza A(H3N2) virus dominated the 2014–2015 winter season in many countries and caused massive morbidity and mortality because of its antigenic variation. So far, very little is known about the antigenic patterns of the recent H3N2 virus. By systematically mapping the antigenic relationships of H3N2 strains isolat ed since 2010, we discov ered that two groups with obvious antigenic divergence, named SW13(A/Switzerland/9715293/2013-like strains) and HK14(A/Hong Kong/5738/2014-like strains), co-circulated during the 2014–2015 winter season. HK14 group co-circulated with SW13 in Europe and the United States during this season, while there were few strains of HK14 in China's Mainland, where SW13 has dominated since 2012. Furthermore, we found that substitutions near the receptor-binding site on hemagglutinin played an important role in the antigenic variation of both the groups. These findings provide a comprehensive understanding of the recent antigenic evolution of H3N2 virus and will aid in the selection of vaccine strains. | HUA Sha LI XiYan LIU Mi CHENG YanHui PENG YouSong HUANG WeiJuan TAN MinJu WEI HeJiang GUO JunFeng WANG DaYan WU AiPing SHU YueLong JIANG TaiJiao | 2015 | Science China(Life Sciences)2015，58，9： | 17 |
| 2 | Computational analysis of antigenic epitopes of avian influenza A (H7N9) viruses显示文摘Influenza virus can rapidly change its antigenicity, via mutation in the hemagglutinin(HA) protein, to evade host immunity. The emergence of the novel human-infecting avian H7N9 virus in China has caused widespread concern. However, evolution of the antigenicity of this virus is not well understood. Here, we inferred the antigenic epitopes of the HA protein from all H7 viruses, based on the five well-characterized HA epitopes of the human H3N2 virus. By comparing the two major H7 phylogenetic lineages, i.e., the Eurasian lineage and the North American lineage, we found that epitopes A and B are more frequently mutated in the Eurasian lineage, while epitopes B and C are more frequently mutated in the North American lineage. Furthermore, we found that the novel H7N9 virus(derived from the Eurasian lineage) isolated in China in the year 2013, contains six frequently mutated sites on epitopes that include site 135, which is located in the receptor binding domain. This indicates that the novel H7N9 virus that infects human may already have been subjected to gradual immune pressure and receptor-binding variation. Our results not only provide insights into the antigenic evolution of the H7 virus but may also help in the selection of suitable vaccine strains. | LIU Mi SONG TingRui HUA Sha WU AiPing JIANG TaiJiao | 2015 | Science China(Life Sciences)2015，58，7： | 6 |
| 3 | Human BDCA2^+CD123^+CD56^+ dendritic cells (DCs) related to blastic plasmacytoid dendritic cell neoplasm represent a unique myeloid DC subset显示文摘树枝状的房间(DC ) 包括二个机能上地不同的子集:plasmacytoid DC (pDCs ) 和 myeloid DC (mDCs ) 。pDCs 被专攻类型的快速、巨大的分泌物我响应通过使用费的 nucleic 酸的干扰素(IFN-I ) 相似受体(TLR )-7 或 TLR-9。在这份报告,我们描绘了 CD56 < 啜 class= “ a-plus-plus ” >+ DC 人口包括 CD123 和 BDCA2 表示典型 pDC 标记,但是生产与 pDCs 作比较的少得多 IFN-I。另外, CD56 < 啜 class= “ a-plus-plus ” > 和由介绍的染色体宽的 transcriptional 的 mDCs 然而并非 pDCs 的 + DC 簇。因此, CD56 < 啜 class= “ a-plus-plus ” >+ DC 机能上地由在 TLR4 刺激和 priming na 之上生产 IL-12 类似于 mDCs ? 没有优先的激活的 ve T 房间。这些数据建议 CD56 < 啜 class= “ a-plus-plus ” >+ DC 代表与一些 pDC 特征混合的一个新奇 mDC 子集。CD4 < 啜 class= “ a-plus-plus ” >+ CD56 < 啜 class= “ a-plus-plus ” >+ hematological 恶意作为 blastic plasmacytoid 被分类树枝状的房间瘤(BPDCN ) 由于它 pDCs 的典型分子的表示。然而,我们证明 BPDCN 接近 CD56 < 啜 class= “ a-plus-plus ” >+ DC 比由介绍的全球基因表示的 pDCs。因此,我们建议 CD4 < 啜 class= “ a-plus-plus ” >+ CD56 < 啜 class= “ a-plus-plus ” >+ 瘤可以是 CD56 的一个肿瘤对应物 < 啜 class= “ a-plus-plus ” >+ mDCs 然而并非 pDCs。 | Haisheng Yu Peng Zhang Xiangyun Yin Zhao Yin QuanxinG Shi Ya Cui Guanyuan Liu Shouli Wang Pier Paolo Piccaluga Taijiao Jiang Liguo Zhang | 2015 | Protein & Cell2015，6，4： | 6 |
| 4 | Influenza activity during the outbreak of coronavirus disease 2019 in Chinese mainland显示文摘Since coronavirus disease 2019(COVID-19)might circulate in the following seasons,it is essential to understand how COVID-19 influences other respiratory diseases,especially influenza.In this study,we analyzed the influenza activity from mid-November 2019 to March 2020 in Chinese mainland and found that the influenza season endedmuch earlier than previous seasons for all subtypes and lineages,which may have resulted from the circulation of COVID-19 and measures such as travel control and personal protection.These findings provide rudimentary knowledge of the cocirculation patterns of the two types of viruses. | Mi Liu Lizong Deng Dayan Wang Taijiao Jiang | 2020 | Biosafety and Health2020，2，4： | 3 |
| 5 | Pseudovirus-based neuraminidase inhibition assays reveal potential H5N1 drug-resistant mutations显示文摘The use of antiviral drugs such as influenza neuraminidase (NA) inhibitors is a critical strategy to prevent and control flu pandemic, but this strategy faces the challenge of emerging drug-resistant strains. For a highly pathogenic avian influenza (HPAI) H5N1 virus, biosafety restrictions have significantly limited the efforts to monitor its drug responses and mechanisms involved. In this study, a rapid and biosafe assay based on NA pseudovirus was developed to study the resistance of HPAI H5N1 virus to NA inhibitor drugs. The H5N1 NA pseudovirus was comprehensively tested using oseltamivir-sensitive strains and their resistant mutants. Results were consistent with those in previous studies, in which live H5N1 viruses were used. Several oseltamivir-resistant mutations reported in human H1N1 were also identified to cause decreased oseltamivir sensitivity in H5N1 NA by using the H5N1 NA pseudovirus. Thus, H5N1 NA pseudoviruses could be used to monitor HPAI H5N1 drug resistance rapidly and safely. | Yi Lu Taijiao Jiang | 2013 | Protein & Cell2013，4，5： | 3 |
| 6 | Network of co-mutations in Ebola virus genome predicts the disease lethality显示文摘 | Lizong Deng Mi Liu Sha Hua Yousong Peng Aiping Wu F Xiao-Feng Qin Genhong Cheng Taijiao Jiang | 2015 | Cell Research2015，25，6： | 1 |
| 7 | Trap1a is an X-linked and cell-intrinsic regulator of thymocyte development显示文摘The X-linked Trap1a gene encodes the tumor rejection antigen P1A,which is expressed in fetal tissues and multiple lineages of tumor cells.The function of this gene remains unknown.Using chimeric mice with wild-type(WT)and Trap1a^(−/y)bone marrow,we show that Trap1a^(−/y)donor cells are capable of generating most lineages of hematopoietic cells,with the notable exception of T cells.Deletion of Trap1a selectively arrests T-cell development at double-negative stage 1(DN1,with a CD4^(−)CD8^(−)CD25^(−)CD44^(+)phenotype).Because Trap1a is expressed in Lin^(−)Sca-1^(+)c-Kit^(+)and common lymphoid progenitors but not in immature thymocytes(DN1-DN4),Trap1a mutations affect the differentiation potential of progenitor cells without directly acting on T cells.Despite a similarity in the blockade of DN1 to DN2 transition,the Trap1a^(−/y)DN1 cells have normal expression of c-Kit,in contrast to what was reported in the Notch1^(−/−)DN1.Complementary DNA profiling of Trap1a^(−/y)and WT embryonic stem cells shows that Trap1a does not regulate the Notch pathway.Our data reveal that Trap1a is an X-linked regulator that affects the differentiation potential of progenitor cells into T cells through a Notch-independent mechanism and identify an important function for the Trap1a gene. | Chi-Shan Li Fei Tang Peng Zhang Taijiao Jiang Thomas L Saunders Pan Zheng Yang Liu | 2017 | Cellular & Molecular Immunology2017，14，8： | 1 |
| 8 | Synthetic circuits, devices and modules显示文摘The aim of synthetic biology is to design artificial biological systems for novel applications.From an engineering perspective,construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field.Here,we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements,synthetic circuits and their assemblies into devices and modules.Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells. | Hong Zhang Taijiao Jiang | 2010 | Protein & Cell2010，1，11： | 1 |
| 9 | Large discrepancy between the two-way rNHT distances in hemagglutinin-inhibition assay显示文摘<正>Dear Editor,The influenza viruses cause continual epidemics in human society.As is reported by the World Health Organization(WHO),each year the seasonal influenza viruses,i.e.,human influenza A(H1N1),A(H3N2)and B viruses,infected 5%~15%of the world’s population,leading to about 3 to 5 million cases of severe illness | Yousong Peng Dayan Wang Yuelong Shu Taijiao Jiang | 2016 | Virologica Sinica2016，31，5： | 0 |
| 10 | Reflectin基因起源及其蛋白质逐级组装的性质显示文摘文章简介在自然界中,头足纲动物以动态变色和拟态隐形而著称。这其中涉及两种类型的颜色,分别是色素色彩和结构色彩。Reflectin是一类只存在于头足纲动物体内的特殊蛋白质家族,其构成了它们结构色变化的物质基础,然而其基因来源以及如何介导结构色彩变化的分子机理尚不清楚。 | Zhe Guan Tiantian Cai Zhongmin Liu Yunfeng Dou Xuesong Hu Peng Zhang Xin Sun Hongwei Li Yao Kuang Qiran Zhai Hao Ruan Xuanxuan Li Zeyang Li Qihui Zhu Jingeng Mai Qining Wang Luhua Lai Jianguo Ji Haiguang Liu Bin Xia Taijiao Jiang Shu-Jin Luo Hong-Wei Wang 谢灿 | 2018 | 科学新闻2018，0，4： | 0 |
| 11 | Coevolution signals capture the specific packing of secondary structures in protein architecture显示文摘 | Deng, Lizong Dong, Xiaoxi Wu, Aiping Song, Tingrui Jiang, Taijiao | 2014 | Protein & Cell2014，5，6： | 0 |
| 12 | New targets for controlling Ebola virus disease显示文摘EBOV infects multiple diferent cell types and replicates rapidly in vivo[1].Due to its long ilamentous structure,EBOV is internalized by macropinocytosis ater cell surface receptor binding by the viral glycoprotein(GP).Unlike many other enveloped viruses,EBOV entry process involves multiple steps of traversing of the virion through endosomal vesicle route before its nuclear core is released into cell cytoplasm for replication[2]. | F.Xiao-Feng Qin Cheng-Yu Jiang Taijiao Jiang Genhong Cheng | 2015 | National Science Review2015，2，3： | 0 |
| 13 | Progress and Challenge in Computational Identification of Influenza Virus Reassortment显示文摘Genomic reassortment is an important evolutionary mechanism for influenza viruses.In this process,the novel viruses acquire new characteristics by the exchange of the intact gene segments among multiple influenza virus genomes,which may cause flu endemics and epidemics within or even across hosts.Due to the safety and ethical limitations of the experimental studies on influenza virus reassortment,numerous computational researches on the influenza virus reassortment have been done with the explosion of the influenza virus genomic data.A great amount of computational methods and bioinformatics databases were developed to facilitate the identification of influenza virus reassortments.In this review,we summarized the progress and challenge of the bioinformatics research on influenza virus reassortment,which can guide the researchers to investigate the influenza virus reassortment events reasonably and provide valuable insight to develop the related computational identification tools. | Xiao Ding Luyao Qin Jing Meng Yousong Peng Aiping Wu Taijiao Jiang | 2021 | Virologica Sinica2021，36，6： | 0 |
| 14 | MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets显示文摘 | Xilin Xu Aiping Wu Xinlei Zhang Mingming Su Taijiao Jiang Zhe-Ming Yuan | 2016 | Biophysics Reports2016，2，5： | 0 |
| 15 | Prediction of Cell Specific O-GalNAc Glycosylation in Human显示文摘Glycosylation is one of the most extensive post-translation modifications of proteins. Although lots of computational models have been developed to predict the glycosylation sites, none of them considered the tissue and cell specificity of glycosylation. Here, we built a two-step computational method GlycoCell to predict the cell-specific O-GalNAc glycosylation, the most complex type of O-glycosylation reported so far, in 12 human cell types. The first step predicted whether a site had the potential to be O-glycosylated. The model achieved an accuracy of 0.83. The second step predicted whether a potential glycosite would be O-glycosylated in the given cell type. For 12 cell types, a model was built for each cell type. The accuracies for these models ranged from 0.78 to 0.87. To facilitate the usage of GlycoCell for the public, a web server was built which is available at http://gffzzd3a3a31d642d43d8hxvcwcu9bvfp96cuu.ffgz.tsg.suse.edu.cn/GlyoCell/main.htm. It could be useful for investigating the cell-specific O-glycosylation in human. | Yuanqiang Zou Kenli Li Taijiao Jiang Yousong Peng | 2017 | 国际计算机前沿大会会议论文集2017，，2： | 0 |
| 16 | Predicting the Antigenic Variant of Human Influenza A(H3N2) Virus with a Stacked Auto-Encoder Model显示文摘The influenza virus changes its antigenicity frequently due to rapid mutations, leading to immune escape and failure of vaccination. Rapid determination of the influenza antigenicity could help identify the antigenic variants in time. Here, we built a stacked auto-encoder (SAE) model for predicting the antigenic variant of human influenza A(H3N2) viruses based on the hemagglutinin (HA) protein sequences. The model achieved an accuracy of 0.95 in five-fold cross-validations, better than the logistic regression model did. Further analysis of the model shows that most of the active nodes in the hidden layer reflected the combined contribution of multiple residues to antigenic variation. Besides, some features (residues on HA protein) in the input layer were observed to take part in multiple active nodes, such as residue 189, 145 and 156, which were also reported to mostly determine the antigenic variation of influenza A(H3N2) viruses. Overall,this work is not only useful for rapidly identifying antigenic variants in influenza prevention, but also an interesting attempt in inferring the mechanisms of biological process through analysis of SAE model, which may give some insights into interpretation of the deep learning | Zhiying Tan Kenli Li Taijiao Jiang Yousong Peng | 2017 | 国际计算机前沿大会会议论文集2017，，2： | 0 |
| 17 | PREDAV-H1: a user-friendly web server for predicting antigenic variants of influenza H1N1 viruses显示文摘Dear Editor,The influenza H1N1 virus has caused three global pandemics since the beginning of the 20th century(Liu et al.,2015).The first is the notorious Spanish flu in 191&which killed 20-100 million people in the world.It circulated for nearly 40 years and was replaced by influenza H2N2 virus.In 1977,the virus reappeared in Russia and caused global pandemics.It continued to circulate until 2009 when it was replaced by the pandemic H1N1 virus.Influenza H1N1 viruses cause large morbidity and mortality to human society,and will continue to threaten humans.Vaccination is the most effective way to fight against the virus.However,due to rapid mutation of the virus,antigenic drift happens frequently,which leads to inefficiency of influenza vaccines.How to timely identify antigenic variants is an important question in influenza surveillance. | Congyu Lu Mi Liu Aiping Wu Yuelong Shu Yousong Peng Taijiao Jiang | 2019 | Science China(Life Sciences)2019，62，3： | 0 |
| 18 | Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses显示文摘The virulence of influenza viruses is a complex multigenic trait.Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites,ignoring the influence of nucleotide mutations.In this study,we collected>200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis.Fifty of these nucleotide sites only experienced synonymous mutations.Experiments showed that synonymous mutations in three high-scoring nucleotide sites,i.e.,PB1–2031,PB1–633,and PB1–720,enhanced the pathogenicity of the influenza A(H1N1)viruses in mice.Besides,machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built.Overall,this study highlighted the importance of nucleotide mutations,especially synonymous mutations in viral virulence,and provided rapid methods for evaluating the virulence of influenza A viruses.It could be helpful for early warning of newly emerging influenza A viruses. | Peng Yousong Zhu Wenfei Feng Zhaomin Zhu Zhaozhong Zhang Zheng Chen Yongkun Liu Suli Wu Aiping Wang Dayan Shu Yuelong Jiang Taijiao | 2020 | Biosafety and Health2020，2，1： | 0 |
| 19 | Integrated interactome and transcriptome analysis reveals key host factors critical for SARS-CoV-2 infection显示文摘The coronavirus disease 2019(COVID-19)pandemic,caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),has seriously threatened global public health and caused huge economic losses.Omics studies of SARS-CoV-2 can help understand the interaction between the virus and host,thereby providing a new perspective in guiding the intervention and treatment of the SARS-CoV-2 infection.Since large amount of SARS-CoV-2 omics data have been accumulated in public databases,this study aimed to identify key host factors involved in SARSCoV-2 infection through systematic integration of transcriptome and interactome data.By manually curating published studies,we obtained a comprehensive SARS-CoV-2-human protein-protein interactions(PPIs)network,comprising 3591 human proteins interacting with 31 SARS-CoV-2 viral proteins.Using the RobustRankAggregation method,we identified 123 multiple cell line common genes(CLCGs),of which 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signatures.Combined with network analysis,co-expression and functional enrichment analysis,we discovered four key host factors involved in SARS-CoV-2 infection:IFITM1,SERPINE1,DDX60,and TNFAIP2.Furthermore,SERPINE1 was found to facilitate SARSCoV-2 replication,and can alleviate the endoplasmic reticulum(ER)stress induced by ORF8 protein through interaction with ORF8.Our findings highlight the importance of systematic integration analysis in understanding SARS-CoV-2-human interactions and provide valuable insights for future research on potential therapeutic targets against SARS-CoV-2 infection. | Jie Sheng Lili Li Xueying Lv Meiling Gao Ziyi Chen Zhuo Zhou Jingfeng Wang Aiping Wu Taijiao Jiang | 2023 | Virologica Sinica2023，38，4： | 0 |
| 20 | Development of PREDAC-H1pdm to model the antigenic evolution of influenza A/(H1N1)pdm09 viruses显示文摘The Influenza A(H1N1)pdm09 virus caused a global pandemic in 2009 and has circulated seasonally ever since.As the continual genetic evolution of hemagglutinin in this virus leads to antigenic drift,rapid identification of antigenic variants and characterization of the antigenic evolution are needed.In this study,we developed PREDAC-H1pdm,a model to predict antigenic relationships between H1N1pdm viruses and identify antigenic clusters for post-2009 pandemic H1N1 strains.Our model performed well in predicting antigenic variants,which was helpful in influenza surveillance.By mapping the antigenic clusters for H1N1pdm,we found that substitutions on the Sa epitope were common for H1N1pdm,whereas for the former seasonal H1N1,substitutions on the Sb epitope were more common in antigenic evolution.Additionally,the localized epidemic pattern of H1N1pdm was more obvious than that of the former seasonal H1N1,which could make vaccine recommendation more sophisticated.Overall,the antigenic relationship prediction model we developed provides a rapid determination method for identifying antigenic variants,and the further analysis of evolutionary and epidemic characteristics can facilitate vaccine recommendations and influenza surveillance for H1N1pdm. | Mi Liu Jingze Liu Wenjun Song Yousong Peng Xiao Ding Lizong Deng Taijiao Jiang | 2023 | Virologica Sinica2023，38，4： | 0 |
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