International Master Degree Program for Molecular Medicine in Emerging Viral Infections

Lab & Research Interest

The “Evolutionary Data Science in Pathogen Phylodynamics” lab delves into the intricate pathogen evolution and infectious disease. Our first area of focus involves the analysis of genetic sequences and phylogenetic trees, aiming to unravel the epidemiological and evolutionary patterns of emerging viruses (e.g., SARS-CoV-2, influenza, and enterovirus). This approach not only sheds light on the mechanisms of virus evolution and transmission, but also aids in responding future outbreaks and understanding virus-host interactions. Our second research utilize capitalizes on the power of next-generation sequencing (NGS). By developing and refining NGS data analysis pipelines, we focus on the discovery of previously unidentified pathogens. This capability is crucial in the rapid identification of new pathogenic threats, enabling real-time and effective public health responses. Lastly, our lab employs advanced deep learning techniques to analyze complex genetic data. This innovative approach allows us to identify novel genetic markers and signatures that are key to understanding pathogen evolution. These insights are instrumental in developing cutting-edge diagnostic tools, which are essential for investigating infectious diseases. Through these efforts, our lab is not only contributing to the data scientific community, but also global health and infectious disease responses.

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