My publications
* Authors are equally contributed
My publications
* Authors are equally contributed
Yang, Yiyan; Jiang, Xiaofang (2023). Evolink: A Phylogenetic Approach for Rapid Identification of Genotype-Phenotype Associations in Large-scale Microbial Multispecies Data. Bioinformatics, 39(5), btad215.
Yang, Yiyan; Dufault-Thompson, Keith; Yan, Wei; Cai, Tian; Xie, Lei; Jiang, Xiaofang (2023). Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning. bioRxiv, 2023-06. (in review at GigaScience)
Yang, Yiyan*; Zhang, Chuanlun*; Lenton, Timothy M; Yan, Xinmiao; Zhu, Maoyan; Zhou, Mengdi; Tao, Jianchang; Phelps, Tommy J; Cao, Zhiwei (2021). The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Molecular Biology and Evolution, 38(9), 3637-3648.
Mou, Zhongyu*; Yang, Yiyan*; Hall, A Brantley; Jiang, Xiaofang (2021). The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. BMC genomics, 22, 1-11.
Hall, Brantley; Levy, Sophia; Default-Tompson, Keith; Minabou, Glory; Weiss, Ashley; Braccia, Domenick; Jenkins, Conor; Yang, Yiyan; Arp, Gabi; Abeysinghe, Stephenie; et al. (2023). Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen. bioRxiv, 2023.02.07.527579. (Accepted by Nature Microbiology)
Yang, Yiyan; Yan, Wei; Hall, A Brantley; Jiang, Xiaofang (2021). Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination. Molecular Biology and Evolution, 38(4), 1241-1248.
Yang, Yiyan; Dufault-Thompson, Keith; Salgado Fontenele, Rafaela; Jiang, Xiaofang (2022). Putative host-derived insertions in the genomes of circulating SARS-CoV-2 variants. mSystems, 7(3), e00179-22.
Qiu, Tianyi*; Yang, Yiyan*; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan (2018). CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens. Nature Communications, 9(1), 1772.
Xu, Hongyang*; Yang, Yiyan*; Wang, Shuning; Zhu, Ruixin; Qiu, Tianyi; Qiu, Jingxuan; Zhang, Qingchen; Jin, Li; He, Yungang; Tang, Kailin (2016). Predicting the mutating distribution at antigenic sites of the influenza virus. Scientific Reports, 6(1), 20239.
Salgado Fontenele, Rafaela; Yang, Yiyan; Driver, Erin M; Magge, Arjun; Kraberger, Simona; Custer, Joy M; Dufault-Thompson, Keith; Cox, Erin; Newell, Melanie Engstrom; Varsani, Arvind; et al. (2023). Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Science of The Total Environment, 877, 162862.
Qiu, Jingxuan; Qiu, Tianyi; Yang, Yiyan; Wu, Dingfeng; Cao, Zhiwei (2016). Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2. Scientific reports, 6(1), 1-9.
Yan, Xinmiao; Yang, Yiyan; Chen, Zikun; Yin, Zuojing; Deng, Zeliang; Qiu, Tianyi; Tang, Kailin; Cao, Zhiwei (2020). H-RACS: a handy tool to rank anti-cancer synergistic drugs. Aging (Albany NY), 12(21), 21504.
Qiu, Tianyi; Qiu, Jingxuan; Yang, Yiyan; Zhang, Lu; Mao, Tiantian; Zhang, Xiaoyan; Xu, Jianqing; Cao, Zhiwei (2020). A benchmark dataset of protein antigens for antigenicity measurement. Scientific Data, 7(1), 212.
Tan, Chen; Yang, Yiyan; Song, Maomao; Cao, Zhiwei; Sun, Xinghuai; Lei, Yuan; Chen, Junyi (2020). Cell senescence altered the miRNA expression profile in porcine angular aqueous plexus cells. Molecular Vision, 26, 76.
Zhang, Qingchen; Zhang, Lu; Zhou, Chen; Yang, Yiyan; Yin, Zuojing; Wu, Dingfeng; Tang, Kailin; Cao, Zhiwei (2019). DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination. BMC bioinformatics, 20, 1-9.
Yin, Zuojing; Cao, Zhiwei; Yan, Xinmiao; Yang, Yiyan; Sheng, Zhen (2017). Study of synergistic mechanism in the combination of berberine and evodiamine from the perspective of miRNA. Chinese Pharmacological Bulletin, 772-780.
Qiu, Tianyi; Qiu, Jingxuan; Feng, Jun; Wu, Dingfeng; Yang, Yiyan; Tang, Kailin; Cao, Zhiwei; Zhu, Ruixin (2017). The recent progress in proteochemometric modelling: focusing on target descriptors, cross-term descriptors and application scope. Briefings in Bioinformatics, 18(1), 125-136.
Yan, Xinmiao; Kang, Hong; Feng, Jun; Yang, Yiyan; Tang, Kailin; Zhu, Ruixin; Yang, Li; Wang, Zhengtao; Cao, Zhiwei (2016). Identification of toxic pyrrolizidine alkaloids and their common hepatotoxicity mechanism. International Journal of Molecular Sciences, 17(3), 318.
Qiu, Tianyi; Xiao, Han; Zhang, Qingchen; Qiu, Jingxuan; Yang, Yiyan; Wu, Dingfeng; Cao, Zhiwei;Zhu, Ruixin (2015). Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PLoS One, 10(4), p.e0122416.