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Posts
Welcome to the EVO-PATH Lab Blog! 🧬✨
Published:
Hello world! Welcome to the official blog of the Evolutionary Data Science in Pathogen Phylodynamics (EVO-PATH) Lab at Chang Gung University.
Work in Progress….Coming Soon!
Published:
Work in Progress….Coming Soon!
portfolio
publications
A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses.
Published in Computational biology and chemistry, 2012
Recommended citation: Gong YN, Chen GW, Suchard MA (2012). Computational biology and chemistry. https://pubmed.ncbi.nlm.nih.gov/22858722/
Characterization of subtypes of the influenza A hemagglutinin (HA) gene using profile hidden Markov models.
Published in Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi, 2012
Recommended citation: Gong YN, Chen GW, Shih SR (2012). Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi. https://pubmed.ncbi.nlm.nih.gov/22197681/
Computational analysis and mapping of novel open reading frames in influenza A viruses.
Published in PloS one, 2014
Recommended citation: Gong YN, Chen GW, Chen CJ, Kuo RL, Shih SR (2014). PloS one. https://pubmed.ncbi.nlm.nih.gov/25506939/
Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis.
Published in Medicine, 2016
Recommended citation: Gong YN, Yang SL, Shih SR, Huang YC, Chang PY, Huang CG, Kao KC, Hu HC, Liu YC, Tsao KC (2016). Medicine. https://pubmed.ncbi.nlm.nih.gov/27495059/
A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity.
Published in PloS one, 2016
Recommended citation: Gong YN, Chen GW, Yang SL, Lee CJ, Shih SR, Tsao KC (2016). PloS one. https://pubmed.ncbi.nlm.nih.gov/26986479/
Erratum to: A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach.
Published in Archives of virology, 2017
Recommended citation: Gong YN, Yang SL, Chen GW, Chen YW, Huang YC, Ning HC, Tsao KC (2017). Archives of virology. https://pubmed.ncbi.nlm.nih.gov/28523519/
Centennial review of influenza in Taiwan.
Published in Biomedical journal, 2018
Recommended citation: Gong YN, Kuo RL, Chen GW, Shih SR (2018). Biomedical journal. https://pubmed.ncbi.nlm.nih.gov/30348266/
Clinical characteristics of patients with laboratory-confirmed influenza A(H1N1)pdm09 during the 2013/2014 and 2015/2016 clade 6B/6B.1/6B.2-predominant outbreaks.
Published in Scientific reports, 2018
Recommended citation: Hsieh YC, Tsao KC, Huang CT, Chang KY, Huang YC, Gong YN (2018). Scientific reports. https://pubmed.ncbi.nlm.nih.gov/30353096/
Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan.
Published in Journal of the Formosan Medical Association = Taiwan yi zhi, 2019
Recommended citation: Gong YN, Tsao KC, Chen GW (2019). Journal of the Formosan Medical Association = Taiwan yi zhi. https://pubmed.ncbi.nlm.nih.gov/29475785/
Population dynamics at neuraminidase position 151 of influenza A (H1N1)pdm09 virus in clinical specimens.
Published in The Journal of general virology, 2019
Recommended citation: Gong YN, Tsao KC, Chen GW, Wu CJ, Chen YH, Liu YC, Yang SL, Huang YC, Shih SR (2019). The Journal of general virology. https://pubmed.ncbi.nlm.nih.gov/30994443/
SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.
Published in Emerging microbes & infections, 2020
Recommended citation: Gong YN, Tsao KC, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR (2020). Emerging microbes & infections. https://pubmed.ncbi.nlm.nih.gov/32543353/
Evolution and Epidemiology of SARS-CoV-2 Virus.
Published in Methods in molecular biology (Clifton, N.J.), 2022
Recommended citation: Gong YN, Lee KM, Shih SR (2022). Methods in molecular biology (Clifton, N.J.). https://pubmed.ncbi.nlm.nih.gov/35554897/
Quantifying Neutralizing Antibodies in Patients with COVID-19 by a Two-Variable Generalized Additive Model.
Published in mSphere, 2022
Recommended citation: Liu KT, Gong YN, Huang CG, Huang PN, Yu KY, Lee HC, Lee SC, Chiang HJ, Kung YA, Lin YT, Hsiao MJ, Huang PW, Huang SY, Wu HT, Wu CC, Kuo RL, Chen KF, Hung CT, Oguntuyo KY, Stevens CS, Kowdle S, Chiu HP, Lee B, Chen GW, Shih SR (2022). mSphere. https://pubmed.ncbi.nlm.nih.gov/35107336/
Emergence and Persistent Dominance of SARS-CoV-2 Omicron BA.2.3.7 Variant, Taiwan
Published in Emerging Infectious Diseases, 2023
Recommended citation: Pei-Lan Shao*, Hsiao-Chen Tu*, Yu-Nong Gong*, Hung-Yu Shu, Ralph Kirby, Li-Yun Hsu, Hui-Yee Yeo, Han-Yueh Kuo, Yi-Chia Huang, Yung-Feng Lin, Hui-Ying Weng, Yueh-Lin Wu, Chien-Chih Chen, Tzen-Wen Chen, Kuo-Ming Lee, Chung-Guei Huang, Shin-Ru Shih, Wei J Chen, Chen-Chi Wu, Chong-Jen Yu, Shih-Feng Tsai (2023). Emerging Infectious Diseases 29(4):792–796. https://wwwnc.cdc.gov/eid/article/29/4/22-1497_article
Novel intertypic recombination of Echovirus 11 in the Enterovirus species B.
Published in Journal of medical virology, 2024
Recommended citation: Gong YN, Yang SL, Chen YC, Liu YC, Huang YC, Tsao KC (2024). Journal of medical virology. https://pubmed.ncbi.nlm.nih.gov/38164047/
Corrigendum to ‘Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan’ [J Formos Med Assoc 118 (2019) 116-124].
Published in Journal of the Formosan Medical Association = Taiwan yi zhi, 2024
Recommended citation: Gong YN, Tsao KC, Chen GW (2024). Journal of the Formosan Medical Association = Taiwan yi zhi. https://pubmed.ncbi.nlm.nih.gov/38307798/
Genomic surveillance of SARS-CoV-2 in Taiwan: A perspective on evolutionary data interpretation and sequencing issues
Published in Biomedical Journal, 2025
Recommended citation: Yu-Nong Gong, Nai-Yu Kuo, Ting-Syuan Yeh, Shin-Ru Shih, Guang-Wu Chen (2025). Biomedical Journal. 48(4), 100820. https://www.sciencedirect.com/science/article/pii/S2319417024001239
Visualizing and deciphering influenza A(H1N1) pdm09 reassortment in the 2019-23 seasons
Published in Virus Evolution, 2025
Recommended citation: Tai-Jung Li, Kuan-Fu Chen, Andrew Pekosz, Yu-Nong Gong (2025). Virus Evolution 11(1), veaf070. https://doi.org/10.1093/ve/veaf070
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Genomic Data Science, EMM111
graduate course, International Master Degree Program for Molecular Medicine in Emerging Viral Infections, 2023
Teaching objectives
Genomic data science is an interdisciplinary subject that applies data science and biostatistics to the field of genomics. This course is designed for students in virology or molecular biology related fields. It allows students to understand, analyze and interpret viral genome data in order to have skills of bioinformatic analysis and interdisciplinary Learning.
Deep Learning with Python, EMM112
graduate course, International Master Degree Program for Molecular Medicine in Emerging Viral Infections, 2023
Teaching objectives
This course trains students to have the concept of computational thinking and object-oriented programming. Taking viral and biomedical applications as examples, students will understand the fundamentals of machine and deep learning and the practice of model building.