91猫先生

研究方向及研究室特色(Lab & Research Interest)

「病原体亲缘动力学之演化资料科学实验室」专注於研究病原体演化及传染病的复杂性。本实验室的第一个研究方向着眼於分析基因序列及亲缘关係树，透过解读新兴病毒（如新冠病毒、流感病毒、肠病毒）的流行病学与演化模式，帮助理解病毒的传播机制并提供应对未来疫情的依据，加强对病毒与宿主之间相互作用的认识。第二个研究方向利用次世代定序技术，专注於开发及优化数据分析流程，进而识别先前未被发现的病原体，此研究对迅速检测新病原威胁尤為重要，使公共卫生机构能够及时有效地做出反应。第叁个方向则採用深度学习技术分析复杂的巨量基因数据，透过辨识重要的遗传标誌及关键特徵，提供病原体演化的深入洞见。总结来说，这叁项研究不仅推动了临床诊断工具的开发，亦对传染病研究具有深远影响，為数据科学及全球公共卫生的进步贡献良多。

论文与着作(笔耻产濒颈肠补迟颈辞苍)

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. (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. 

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. 

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.  (*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. 

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. 

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.

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. (*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.

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.

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.

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. (*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. 

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).

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.

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. (*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.

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.

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).

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. (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. (*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. 

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. 

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. 

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. 

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).