新興病毒分子醫學國際碩士學位學程

研究方向及研究室特色(Lab & Research Interest)

「病原體親緣動力學之演化資料科學實驗室」專注於研究病原體演化及傳染病的複雜性。本實驗室的第一個研究方向著眼於分析基因序列及親緣關係樹，透過解讀新興病毒（如新冠病毒、流感病毒、腸病毒）的流行病學與演化模式，幫助理解病毒的傳播機制並提供應對未來疫情的依據，加強對病毒與宿主之間相互作用的認識。第二個研究方向利用次世代定序技術，專注於開發及優化數據分析流程，進而識別先前未被發現的病原體，此研究對迅速檢測新病原威脅尤為重要，使公共衛生機構能夠及時有效地做出反應。第三個方向則採用深度學習技術分析複雜的巨量基因數據，透過辨識重要的遺傳標誌及關鍵特徵，提供病原體演化的深入洞見。總結來說，這三項研究不僅推動了臨床診斷工具的開發，亦對傳染病研究具有深遠影響，為數據科學及全球公共衛生的進步貢獻良多。

論文與著作(Publication)

Publications (since 2019)

2024

Gong, Y. N., Yang, S. L., Chen, Y. C., Liu, Y. C., Huang, Y. C., & Tsao, K. C. (2024). Novel intertypic recombination of Echovirus 11 in the Enterovirus species B. J Med Virol, 96(1), e29323. https://doi.org/10.1002/jmv.29323 (First author)

Liu, H., Shaw-Saliba, K., Westerbeck, J., Jacobs, D., Fenstermacher, K., Chao, C. Y., Gong, Y. N., Powell, H., Ma, Z., Mehoke, T., Ernlund, A. W., Dziedzic, A., Vyas, S., Evans, J., Sauer, L. M., Wu, C. C., Chen, S. H., Rothman, R. E., Thielen, P., . . . Pekosz, A. (2024). Effect of human H3N2 influenza virus reassortment on influenza incidence and severity during the 2017-18 influenza season in the USA: a retrospective observational genomic analysis. Lancet Microbe. https://doi.org/10.1016/S2666-5247(24)00067-3

Pei, Y., Shum, M. H., Liao, Y., Leung, V. W., Gong, Y. N., Smith, D. K., Yin, X., Guan, Y., Luo, R., Zhang, T., & Lam, T. T. (2024). ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences. Microbiome, 12(1), 84. https://doi.org/10.1186/s40168-024-01805-0

2023

Shao, P. L.*, Tu, H. C.*, Gong, Y. N.*, Shu, H. Y., Kirby, R., Hsu, L. Y., Yeo, H. Y., Kuo, H. Y., Huang, Y. C., Lin, Y. F., Weng, H. Y., Wu, Y. L., Chen, C. C., Chen, T. W., Lee, K. M., Huang, C. G., Shih, S. R., Chen, W. J., Wu, C. C., . . . Tsai, S. F. (2023). Emergence and Persistent Dominance of SARS-CoV-2 Omicron BA.2.3.7 Variant, Taiwan. Emerg Infect Dis, 29(4), 792-796. https://doi.org/10.3201/eid2904.221497 (*Co-first authors)

Fall, A., Han, L., Yunker, M., Gong, Y. N., Li, T. J., Norton, J. M., Abdullah, O., Rothman, R. E., Fenstermacher, K. Z. J., Morris, C. P., Pekosz, A., Klein, E., & Mostafa, H. H. (2023). Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021-2023. Open Forum Infect Dis, 10(12), ofad577. https://doi.org/10.1093/ofid/ofad577

Han, Y. J., Lee, K. M., Wu, G. H., Gong, Y. N., Dutta, A., & Shih, S. R. (2023). Targeting influenza A virus by splicing inhibitor herboxidiene reveals the importance of subtype-specific signatures around splice sites. J Biomed Sci, 30(1), 10. https://doi.org/10.1186/s12929-023-00897-4

Huang, Y. C., Tu, H. C., Kuo, H. Y., Shao, P. L., Gong, Y. N., Weng, H. Y., Shu, H. Y., Kuo, C. H., Kuo, P. H., Chien, C. H., Wu, C. C., Chan, D. D., Tsai, M. K., Tsai, S. F., & Yu, C. J. (2023). Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission. J Microbiol Immunol Infect. https://doi.org/10.1016/j.jmii.2023.01.003

2022

Liu, K. T.*, Gong, Y. N.*, Huang, C. G.*, Huang, P. N.*, Yu, K. Y., Lee, H. C., Lee, S. C., Chiang, H. J., Kung, Y. A., Lin, Y. T., Hsiao, M. J., Huang, P. W., Huang, S. Y., Wu, H. T., Wu, C. C., Kuo, R. L., Chen, K. F., Hung, C. T., Oguntuyo, K. Y., . . . Shih, S. R. (2022). Quantifying Neutralizing Antibodies in Patients with COVID-19 by a Two-Variable Generalized Additive Model. mSphere, 7(1), e0088321. https://doi.org/10.1128/msphere.00883-21 (*Co-first authors)

Chiu, Y. F., Huang, Y. W., Chen, C. Y., Chen, Y. C., Gong, Y. N., Kuo, R. L., Huang, C. G., & Shih, S. R. (2022). Visualizing Influenza A Virus vRNA Replication. Front Microbiol, 13, 812711. https://doi.org/10.3389/fmicb.2022.812711

Hsieh, H. S., Gong, Y. N., Chi, C. Y., Hsieh, S. Y., Chen, W. T., Ku, C. L., Cheng, H. T., Lin, L., & Sung, C. M. (2022). Gut microbiome profiles and associated metabolic pathways in patients of adult-onset immunodeficiency with anti-interferon-gamma autoantibodies. Sci Rep, 12(1), 9126. https://doi.org/10.1038/s41598-022-13289-9

Kung, Y. A., Chiang, H. J., Li, M. L., Gong, Y. N., Chiu, H. P., Hung, C. T., Huang, P. N., Huang, S. Y., Wang, P. Y., Hsu, T. A., Brewer, G., & Shih, S. R. (2022). Acyl-Coenzyme A Synthetase Long-Chain Family Member 4 Is Involved in Viral Replication Organelle Formation and Facilitates Virus Replication via Ferroptosis. mBio, e0271721. https://doi.org/10.1128/mbio.02717-21

2021

Liu, H.*, Gong, Y. N.*, Shaw-Saliba, K., Mehoke, T., Evans, J., Liu, Z. Y., Lewis, M., Sauer, L., Thielen, P., Rothman, R., Chen, K. F., & Pekosz, A. (2021). Differential disease severity and whole-genome sequence analysis for human influenza A/H1N1pdm virus in 2015-2016 influenza season. Virus Evol, 7(1), veab044. https://doi.org/10.1093/ve/veab044 (*Co-first authors)

Chen, Y. Y., Huang, C. T., Li, S. W., Pan, Y. J., Lin, T. L., Huang, Y. Y., Li, T. H., Yang, Y. C., Gong, Y. N., & Hsieh, Y. C. (2021). Bacterial factors required for Streptococcus pneumoniae coinfection with influenza A virus. J Biomed Sci, 28(1), 60. https://doi.org/10.1186/s12929-021-00756-0

Huang, S. Y., Kung, Y. A., Huang, P. N., Chang, S. Y., Gong, Y. N., Han, Y. J., Chiang, H. J., Liu, K. T., Lee, K. M., Chang, C. Y., Chang, C. C., Huang, C. G., & Shih, S. R. (2021). Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. mSphere, 6(2). https://doi.org/10.1128/mSphere.00104-21

Lin, J. Y., Weng, K. F., Chang, C. K., Gong, Y. N., Huang, G. J., Lee, H. L., Chen, Y. C., Huang, C. C., Lu, J. Y., Huang, P. N., Chiang, H. J., Chen, C. M., & Shih, S. R. (2021). Enterovirus A71 Induces Neurological Diseases and Dynamic Variants in Oral Infection of Human SCARB2-Transgenic Weaned Mice. J Virol, JVI0089721. https://doi.org/10.1128/JVI.00897-21

2020

Gong, Y. N.*, Tsao, K. C.*, Hsiao, M. J., Huang, C. G., Huang, P. N., Huang, P. W., Lee, K. M., Liu, Y. C., Yang, S. L., Kuo, R. L., Chen, K. F., Liu, Y. C., Huang, S. Y., Huang, H. I., Liu, M. T., Yang, J. R., Chiu, C. H., Yang, C. T., Chen, G. W., & Shih, S. R. (2020). SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerg Microbes Infect, 9(1), 1457-1466. https://doi.org/10.1080/22221751.2020.1782271 (*Co-first authors)

Chen, B. S., Lee, H. C., Lee, K. M., Gong, Y. N., & Shih, S. R. (2020). Enterovirus and Encephalitis. Front Microbiol, 11, 261. https://doi.org/10.3389/fmicb.2020.00261

Chen, Y. Y., Hsieh, Y. C., Gong, Y. N., Liao, W. C., Li, S. W., Chang, I. Y., Lin, T. L., Huang, C. T., Chiu, C. H., Wu, T. L., Su, L. H., Li, T. H., & Huang, Y. Y. (2020). Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain(23F)-ST81, Taiwan. Emerg Infect Dis, 26(4), 711-720. https://doi.org/10.3201/eid2604.190717

Huang, C. G., Lee, K. M., Hsiao, M. J., Yang, S. L., Huang, P. N., Gong, Y. N., Hsieh, T. H., Huang, P. W., Lin, Y. J., Liu, Y. C., Tsao, K. C., & Shih, S. R. (2020). Culture-Based Virus Isolation To Evaluate Potential Infectivity of Clinical Specimens Tested for COVID-19. J Clin Microbiol, 58(8). https://doi.org/10.1128/JCM.01068-20

2019

Gong, Y. N., Tsao, K. C., & Chen, G. W. (2019). Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan. J Formos Med Assoc, 118(1 Pt 1), 116-124. https://doi.org/10.1016/j.jfma.2018.01.019 (First author)

Gong, Y. N.*, Tsao, K. C.*, Chen, G. W., Wu, C. J., Chen, Y. H., Liu, Y. C., Yang, S. L., Huang, Y. C., & Shih, S. R. (2019). Population dynamics at neuraminidase position 151 of influenza A (H1N1)pdm09 virus in clinical specimens. J Gen Virol, 100(5), 752-759. https://doi.org/10.1099/jgv.0.001258 (*Co-first authors)

Chen, Y. Y., Wang, J. T., Lin, T. L., Gong, Y. N., Li, T. H., Huang, Y. Y., & Hsieh, Y. C. (2019). Prophage Excision in Streptococcus pneumoniae Serotype 19A ST320 Promote Colonization: Insight Into Its Evolution From the Ancestral Clone Taiwan 19F-14 (ST236). Front Microbiol, 10, 205. https://doi.org/10.3389/fmicb.2019.00205

Hung, H. M., Yang, S. L., Chen, C. J., Chiu, C. H., Kuo, C. Y., Huang, K. A., Lin, T. Y., Hsieh, Y. C., Gong, Y. N., Tsao, K. C., & Huang, Y. C. (2019). Molecular epidemiology and clinical features of rhinovirus infections among hospitalized patients in a medical center in Taiwan. J Microbiol Immunol Infect, 52(2), 233-241. https://doi.org/10.1016/j.jmii.2018.08.009

Lee, K. M., Gong, Y. N., & Shih, S. R. (2019). Methods for detection and study of virus-derived small RNAs produced from the intramolecular base-pairing region of the picornavirus genome. Methods. https://doi.org/10.1016/j.ymeth.2019.08.011

Sung, C. M., Lin, Y. F., Chen, K. F., Ke, H. M., Huang, H. Y., Gong, Y. N., Tsai, W. S., You, J. F., Lu, M. J., Cheng, H. T., Lin, C. Y., Kuo, C. J., Tsai, I. J., & Hsieh, S. Y. (2019). Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome. Cell Mol Gastroenterol Hepatol, 8(2), 301-318 e302. https://doi.org/10.1016/j.jcmgh.2019.04.008

Woodman, A., Lee, K. M., Janissen, R., Gong, Y. N., Dekker, N. H., Shih, S. R., & Cameron, C. E. (2019). Predicting Intraserotypic Recombination in Enterovirus 71. J Virol, 93(4). https://doi.org/10.1128/JVI.02057-18