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YinCheng Chen

Computational biology

Education

Institute of Biomedical Informatics

2022 - Present
National Yang Ming Chiao Tung University, Taipei, Taiwan
Ph.D. Candidate (Advisor Dr. Chen Ching Lin)
  • Single cell representation via self-supervised learning.
  • Feature engineering in sparse data.

Institute of Tropical Plant Sciences and Microbiology

2018 - 2020
National Cheng Kung University, Tainan, Taiwan
Masters (Advisor Chao-Li Huang)
  • Establishing a metagenomics-assisted approach for the isolation of sulfur oxidizing bacteria.
  • Fungal community succession through tea fermentation process.

Department of BioAgricultural Science

2013 - 2017
National Chiayi University, Chiayi, Taiwan
BA

Experiences

Intern

2025 Jun - 2025 Aug
University Hospital Dresden 'Carl Gustav Carus', Dresden, Germany
Institute for Clinical Genetics, Dr. Diana Le Duc

Research Assistant

2022 - Present
National Yang Ming Chiao Tung University, Taipei, Taiwan
Advisor Dr. Chen Ching Lin

Research Assistant

2020 - 2022
Chang Gung University, Taoyuan, Taiwan
Molecular Medicine Research Center

Publications

  • Fungal community succession in the fermentation of black and oolong teas
    • Chen, Y. C., Tran, H. T., Kuan, J. J., Chiang, T. Y., & Huang, C. L.
    LWT, 235, 2025
  • Respiratory microbiome and metabolome features associate with disease severity and doxycycline treatment requirement in children with macrolide-resistant Mycoplasma pneumoniae-mediated pneumonia
    • Liao, W. C., Li, S. W., Hsing, E. W., Chen Y. Y., Chang, Ian, Chen, Y. C., Yang C., Pan, Y. J.,Hsieh, Y. C.
    Frontiers in Cellular and Infection Microbiology, 15, 2025
  • PreLect : Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts
    • Chen, Y. C., Su, Y. Y., Chu, T. Y., Wu M. F., Huang, C. C. & Lin, C. C.
    npj Biofilms Microbiomes, 11(3), 2025
  • Global genome diversity and recombination in Mycoplasma pneumoniae
    • Hsieh, Y. C., Li, S. W., Chen, Y. Y., Kuo, C. C., Chen, Y. C., Chang, I. Y. F., ... & Liao, W. C.
    Emerging infectious diseases, 28(1), 111, 2022
  • An outbreak of tet (X6)-Carrying tigecycline-resistant Acinetobacter baumannii isolates with a new capsular type at a hospital in Taiwan
    • Hsieh, Y. C., Wu, J. W., Chen, Y. Y., Quyen, T. L. T., Liao, W. C., Li, S. W., Chen, Y. C. & Pan, Y. J.
    Antibiotics, 10(10), 1239, 2021

    Conference Presentations

  • PreEmbed : interpretable gene tokenization for enhanced single-cell representation
    • Chen, Y. C., Lin C. C.
    Oral presented at the 83rd Annual Meeting of the Japanese Cancer Association, 2024
  • Deciphering hepatitis B virus clearance genes in hepatocellular carcinoma via semi-supervised learning
    • Su, Y. Y, Chen, Y. C., Lin C. C.
    Poster presented at the 83rd Annual Meeting of the Japanese Cancer Association, 2024
  • Advancing precision oncology with a graph neural network framework for genetic mutation identification
    • Hsu, Y. T., Chen, Y. C., Lin C. C.
    Oral presented at the 83rd Annual Meeting of the Japanese Cancer Association, 2024
  • Adapted LASSO : A novel and robust approach for feature selection in microbiome data
    • Chen, Y. C., Lin C. C.
    Oral presented at the 82rd Annual Meeting of the Japanese Cancer Association, 2023
  • Three different amplicon unveils the changes of fungal community through tea fermentation process
    • Chen, Y. C., Huang C. L.
    Oral presented at Multiomics and precision medicine joint conference, Taiwan, 2019

    Software

    PreLect - Feature Engineering in Sparse Matrices
    PreLect PreLect PreLectR PreLectR
    vDiveR - A graphical user interface (GUI)-based web application hosted on R Shiny for the visualization of various diversity dynamics.
    vDiveR vDiveR vDiveR vDiveR

    Award and Grant

    Graduate research fellowship

    2025
    NSTC, Taiwan

    The graduate students study abroad program (千里馬)

    2025
    NSTC, Taiwan

    Doctoral dissertation scholarship, Finalist

    2025
    National Yang-Ming Chiao Tung University, Taiwan

    尹衍樑先生入學優異獎學金

    2022
    National Yang-Ming Chiao Tung University, Taiwan

    Oral presentation aware

    2019
    Multiomics and precision medicine joint conference, Taiwan

    Recommendations

    Dr. Chen Ching Lin

    Professor

    Institute of Biomedical Informatics

    National Yang Ming Chiao Tung University, Taipei, Taiwan

    Dr. Chao-Li Huang

    Associate professor

    Institute of Tropical Plant Sciences and Microbiology

    National Cheng Kung University Tainan, Taiwan