微生物基因體研究室 Microbial Genomics Lab

Using genomics and bioinformatics to understand antimicrobial resistance, outbreaks, and emerging microbial threats

Principle Investigator

研究室主持人

Ying-Tsong Chen 陳盈璁

國立中興大學 生命科學院 基因體暨生物資訊研究所 教授 (2022-)

Professor, Graduate Institute of Genomics and Bioinformatics, College of Life Sciences, National Chung Hsing University, Taiwan

國家衛生研究院 分子與基因醫學研究所 兼任研究員(2023-)

Adjunct Investigator, Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan

onion@nchu.edu.tw

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我相信好的研究來自好奇心、扎實訓練與長期投入。
Good science begins with curiosity, grows through discipline, and succeeds through persistence.

About Professor Chen

Prof. Ying-Tsong Chen is a faculty member at the Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University.

His research centers on microbial genomics, antimicrobial resistance, pathogen evolution, and host-associated microbes. By integrating genome sequencing, bioinformatics, and molecular microbiology, his group investigates how microbes acquire resistance, virulence, and adaptive traits through genomic change and mobile genetic elements.

Recent interests include outbreak genomics of emerging pathogens, One Health microbiology, and genomic applications of endosymbionts such as Wolbachia.

Prof. Chen is committed to mentoring students through rigorous research training, interdisciplinary thinking, and problem-driven scientific inquiry.

陳教授現任國立中興大學生命科學院基因體暨生物資訊研究所教師，研究領域涵蓋微生物基因體學、抗生素抗藥性、病原體演化，以及宿主相關微生物。

研究團隊結合基因體定序、生物資訊分析與分子微生物學方法，探討微生物如何透過基因體變異與可移動遺傳因子獲得抗藥性、致病能力及環境適應特徵。

近年研究方向包括新興病原體群聚事件基因體分析、One Health 微生物學，以及 Wolbachia 等共生菌之基因體應用。

研究室重視學生的研究訓練與獨立思考能力，鼓勵跨領域合作與實務問題導向的科學探索，歡迎對研究充滿熱忱的同學加入團隊。

我的研究工作，在於連結微生物基因體學與實驗創造力。很多時候，我所做的是尋找各種連結——分子機制與生物意義之間、數據與理解之間，以及科學與實踐科學的人之間。

My work bridges microbial genomics and experimental creativity. Much of it is about finding connections—between molecular mechanisms and biological meaning, between data and understanding, and between science and the people who do it.

Career, Education and Honors

Graduate Institute of Genomics and Bioinformatics, COLS, NCHU
國立中興大學 生命科學院 基因體暨生物資訊研究所

  • Associate Professor 副教授 (2014-2022)
  • Assistant Professor 助理教授 (2010-2014)

Institute of Molecular and Genomic Medicine, NHRI
國家衛生研究院 分子與基因醫學研究所

  • Adjunct Associate Investigator 兼任副研究員(2019-2023)
  • Joint Associate Investigator 合聘副研究員(2018-2019)
  • Joint Assistant Investigator 合聘助研究員(2011-2017)
  • PostDoc 博士後研究 (2004-2010)

PhD, Department of Biological Science and Technology, National Chiao Tung University
國立交通大學 生物科技系 博士 (2000-2004)
MS, Institute of Genetics, National Yang-Ming University
國立陽明大學 遺傳學研究所 碩士 (1994-1996)
BE, Department of Bioengineering, Tatung Institute of Technology
大同工學院 生物工程系 學士 (1990-1994)

109年資深優良教師(2020)
生科院推薦優聘教師(2018)
國立中興大學優良通識教師獎(2015)
傑出青年教師獎勵(2014)

Featured publications

Hypervirulent Klebsiella pneumoniae plasmid pLVPK

Gene (2004)
One of the early complete analyses of a major virulence plasmid, revealing how mobile genetic elements contribute to hypervirulence.

NDM-1 plasmid dissemination in Klebsiella pneumoniae

PLOS ONE (2012)
Showed that carbapenem resistance can spread through epidemic plasmids shared across unrelated bacterial strains.

Elizabethkingia anophelis outbreak from hospital water system

Journal of Hospital Infection (2021)
Identified a persistent hospital water reservoir responsible for a multi-year outbreak using comparative genomics.

RamAp regulator carried by IncHI2 plasmid in Salmonella enterica

Antimicrobial Agents and Chemotherapy (2022)
Discovered a plasmid-borne regulator linking horizontal gene transfer with antimicrobial resistance and virulence control.

Adaptive sampling for Wolbachia genome reconstruction

bioRxiv (2026)
Developed a nanopore sequencing strategy for recovering intracellular symbiont genomes directly from host tissues.

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