國立中興大學基因體暨生物資訊學研究所

　　

　　 　　

　　　　　　　

　　　　　　　

　　　　　　　

基因體暨生物資訊學研究所

Graduate Institute of Genomics and Bioinformatics

Chinese
English

興大首頁

National Chung Hsing University

醫科博班

Doctoral Program in Medical Biotechnology

生命科學院

College of Life Sciences

Chen, Ying-Tsong

Lab: Microbial Genomics Core Laboratory

Experience

Title Department Period
Professor NCHU, Institute of Genomics and Bioinformatics 2022.08 –
Adjunct Associate Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2019.08-
Joint Associate Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2018 – 2019
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2015.02 – 2022.08
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2010.08 – 2015.01
Joint Assistant Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2011 – 2017
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2009 – 2010
Postdoctoral Fellow National Health Research Institutes,  The Division of Molecular and Genomic Medicine 2004~2009
PhD NCTU, Department of Biological Science & Technology

Research

Research Interests
  1. Bacterial Genomics
  2. Functional Genomics
  3. Comparative Genomics
  4. Plastid Research

Lectures:

Course

Biochemistry (University Department of Horticulture)
Cell Biology (University Biotechnology Program)
Bioinformatics and Internship (University Department of Life Sciences)
Interesting Talk on Life Science and Bioinformatics (University General Course)
Biochemistry (Department of Food and Biotechnology)
Shotgun Sequencing Principles and Practice (Fundamentals)
Functional Biology (Foundation Institute)
Special Discussion on Biomedical Big Data (1, 2) (Foundation Institute)
Microbial Genetics and Genomes (1, 2)
Applied Genomics and Bioinformatics cum Internship (GFSI)
Panel Discussion (GFSI)
Thematic Study E (Medical Courses)

Publications

Journal (∗Corresponding author)
  1. Lee YL, Liu KM, Chang HL, Liao YC, Lin JS, Kung FY, Ho CM, Lin KH, Chen YT*. The evolutionary trend and genomic features of an emerging lineage of Elizabethkingia anophelis strains in Taiwan. Microbiol Spectr. 2022 [online]
  2. Hong YP, Wang YW, Chen BH, Song HY, Chiou CS, Chen YT*. RamAp, an efflux pump regulator carried by an IncHI2 plasmid. Antimicrob Agents Chenother. 2021 [Epub ahead of print]
  3. Hong YP, Chen YT, Wang YW, Chen BH, Teng RH, Chen YS, Chiou CS*. Integrative and conjugative element-mediated azithromycin resistance in multi drug-resistant Salmonella enterica serovar Albany. Antimicrob Agents Chemother. 2021 [Epub ahead of print]
  4. Lee YL, Liu KM, Chang HL, Lin JS, Kung FY, Ho CM, Lin KS, Chen YT*. A dominant strain of Elizabethkingia anophelis emerged from hospital water system to cause a three-year outbreak in a respiratory care center. J Hosp Infect. 2021. 108:43-51. PubMed PMID33157171.
  5. Yao-Chen Wang, Hui-Ling Tang, Yu-Chieh Liao, Chien-Shun Chiou, Ying-Tsong Chen, Ming-Ko Chiang, Min-Chi Lu, and Yi-Chyi Lai :Co-carriage of distinct blaKPC-2and blaOXA-48 plasmids in a single ST11 carbapenem-resistant Klebsiella pneumoniae isolate. Antimicrobial Agents and Chemotherapy(2019)
  6. Dou HY, Lin CH, Chen YY, Yang SJ, Chang JR, Wu KM, Chen YT, Chin PJ, Liu YM, Su IJ, Tsai SF: Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates. Scientific Reports(2017)
  7. Chiou CS, Chen YT, Wang YW, Liu YY, Kuo HC, Tu YH, Lin AC, Liao YS, Hong YP :Dissemination of mcr-1-Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals in Taiwan. Antimicrobial Agents and Chemotherapy(2017)
  8. Lu MC, Chen YT, Chiang MK, Wang YC, Hsiao PY, Huang YJ, Lin CT, Cheng CC, Liang CL, Lai YC: Colibactin contributes to the hyper virulence of pks+ K1 CC23 Klebsiella pneumoniae in mouse meningitis infections. Frontiers in Cellular and Infection Microbiology(2017)
  9. Chen YT, Lai YC, Tan MC, Hsieh LY, Wang JT, Shiau YR, Wang HY, Lin AC, Lai JF, Huang IW, Lauderdale TL: Prevalence and characteristics of pks genotoxin gene cluster-positive clinical Klebsiella pneumoniae isolates in Taiwan. Scientific Reports(2017)
  10. Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien- Hsing Lin, Keh-Ming Wu, Ming-Shian Lin, Ih-Jen Su and Shih-Feng Tsai: Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan. Evolutionary Bioinformatics(2016)
  11. Chen YT, Siu LK, Tsai YK, Lin FM, Koh TH, Chen JH: A Common Flanking Region in Promiscuous Plasmids Encoding blaNDM-1 in Klebsiella pneumoniae Isolated in Singapore. Microbial Drug Resistance(2016)
  12. Huang TW, Lauderdale TL, Liao TL, Hsu MC, Chang FY, Chang SC, Khong WX, Ng OT, Chen YT, Kuo SC, Chen TL, Mu JJ, Tsai SF: Effective transfer of a 47 kb NDM-1-positive plasmid among Acinetobacter species. Journal of Antimicrobial Chemotherapy(2015)
  13. Chang JW, Hou MM, Hsieh JJ, Cheung YC, Wang HM, Chen JS, Wang CH,Chen CH, Yeh KY, Ou LY, Hsieh CH, Wu HDI, Chen YT, Chang IC, Huang SF: Early radiographic response to epidermal growth factor receptor- tyrosine kinase inhibitor in non-small cell lung cancer patients with epidermal growth factor receptor mutations: A prospective study. Biomedical Journa(2015)
  14. Chen CJ, Wu TL, Chen YT, Fung CP, Chuang YC, Lin JC, and Siu LK: Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. PlosONE(2014)
  15. Tang HJ, Chen YT, Chiang T, Fung CP, Chuang YC, Siu LK: Identification of the first imported KPC-3 Klebsiella pneumoniae from the USA to Taiwan. International Journal of Antimicrobial Agents(2014)
  16. Lai YC, Lin AC, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, and Chen YT: Genotoxic Klebsiella pneumoniae in Taiwan. PlosONE(2014)
  17. Chen YT, Lin JC, Fung CP, Lu PL, Chuang YC, Wu TL, Siu LK: KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. Journal of Antimicrobial Chemotherapy
  18. Lai YC, Lin AC, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, and Chen YT*. Genotoxic Klebsiella pneumoniae in Taiwan. PlosONE. 2014. 9:e96292.
  19. Chen YT*, Lin JC, Fung CP, Lu PL, Chuang YC, Wu TL, Siu LK*. KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. Journal of Antimicrobial Chemotherapy. 2013. 69:628-631.
  20. Huang TW, Wang JT, Lauderdale TL, Liao TL, Lai JF, Tan MJ, Lin AC, Chen YT*, Tsai SF, Chang SC*. Complete sequences of two plasmids in an NDM-1 positive Klebsiella oxytoca isolated from Taiwan. Antimicrobial Agents and Chemotherapy. 2013. 57:4072-4076.
  21. Huang TW, Chen TL, Chen YT*, Lauderdale TL, Liao TL, Lee YT, Chen CP, Liu YM, Lin AC, Chang YH, Wu KM, Kirby R, Lai JF, Tan, MC, Siu, LK, Chang CM, Fung CP, Tsai SF. Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate. PlosONE. 2013. 8:e62774.
  22. Chen YT*, Lin AC, Siu LK, Koh TH. Sequence of closely related plasmids encoding blaNDM-1 in two unrelated Klebsiella pneumoniae isolates in Singapore. PlosONE. 2012. 7:e48737.
  23. Lin AC, Liao TL, Lin YC, Lai YC, Lu MC, Chen YT*. Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-negative K1 Clinical Strain. Journal of Bacteriology. 2012. 194:6316.
  24. Liao TL, Chen SY, Lin AC, Huang TW, Lauderdale TL, Tsai SF, and Chen YT*. Complete genome sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-lactamase-1-producing nosocomial strain. Journal of Bacteriology. 2012. 194:5454.
  25. Huang SH, Wang CK, Peng HL, Wu CC, Chen YT*, Hong YM, and Lin CT. Role of the small RNA RyhB in the Fur regulon in mediating the capsular polysaccharide biosynthesis and iron acquisition systems in Klebsiella pneumoniae. BMC Microbiology. 2012. 12:148.
  26. Huang TW, Chen FJ, Miu WC, Liao TL, Lin AC, Huang IW, Wu KM, Tsai SF, Chen YT*, and Lauderdale TL*. Complete Genome Sequence of Staphylococcus aureus M013, a pvl-positive ST59:SCCmec V Strain Isolated in Taiwan. Journal of Bacteriology. 2012. 194:1256-1257.
  27. Chen YT*, Chang WC J, Liu HP, Yu TF, Chiu YT, Hsieh JJ, Chen YT, Chen YR, Wu I HD, Huang SF*. Clinical implications of high MET gene dosage in non-small cell lung cancer patients without prior tyrosine kinase inhibitor treatment. Journal of Thoracic Oncology. 2011. 6:2027-2035.
  28. Chang JR, Lin CH, Tsai SF, Su IJ, Tseng FC, Chen YT*, Chiueh TS, Sun JR, Huang TS, Chen YS, and Dou HR*. Genotypic analysis of genes associated with transmission and drug resistance in the Beijing lineage of Mycobacterium tuberculosis. Clinical Microbiology and Infection. 2011. 17:1391-1396.
  29. Hoang KC, Lai TH, Lin CS, Chen YT*, and Liau CY*.The Chitinolytic Activities of Streptomyces sp. TH-11. International Journal of Molecular Sciences. 2011. 12:56-65.
  30. Liu HP, Wu HDI, Chang JWC, MD, Wu YC, Yang HY, Chen YT*, Hsieh WY, Chen YT, Chen YR, Huang SF*. Prognostic implications of EGFR and KRAS gene mutations, and EGFR gene copy numbers in Surgically Resectable Non-Small Cell Lung Cancer Patients in Taiwan. Journal of Thoracic Oncology. 2010. 5:1175-1184.
  31. Tang HL, Chiang MK, Liou WJ, Chen YT*, Peng HL, Chiou CS, Liu KS, Lu MC, Tung KC and Lai YC*. Correlation between Klebsiella pneumoniae carrying pLVPK-derived loci and abscess formation. European Journal of Clinical Microbiology & Infectious Diseases. 2010. 29:689-698.
  32. Shu HY, Fung CP, Liu, YM, Wu, KM, Chen YT*, Li LH, Liu TT, Kirby R, and Tsai SF*. Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates. Microbiology. 2009. 155:4170-4183.
  33. Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, Fung CP, Chen HJ, Liu YM, Wang JT, Fang CT, Chang SC, Shu HY, Liu TT, Chen YT*, Shiau YR, Lauderdale TL, Su IJ, Kirby R* and Tsai SF. Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis. Journal of Bacteriology. 2009. 191:4492-4501.
  34. Chen YT*, Liao TL, Liu YM, Lauderdale TL, Yan JJ, and Tsai SF. Mobilization of qnrB2 and ISCR1 in Plasmids. Antimicrobial Agents and Chemotherapy. 2009. 53:1235-1237.

 

Conference (*Invited speaker)
  1. YT Chen, CA Liao, XY Huang, AC Lin, TL Lauderdale: Identification and genomic analyses of an emerging virulent Klebsiella pneumoniae K62 clone in Taiwan. The 41th Annual Meeting of the Molecular Biology Society of Japan Yokohama/Japan
  2. Ying-Tsong Chen, Tsai-Ling Lauderdale, Xin-Ying Huang, Ann-Chi Lin: Population genetics studies of Klebsiella pneumoniae genotoxic K62 type in Taiwan. 4th Annual Microbiology & Infectious Diseases Asia Congress 7th Annual Next Generation Sequencing & Clinical Diagnostics Asia Congress 5th Annual Single Cell Analysis Asia Congress Singapore
  3. Yu-Han Liu, Ann-Chi Li, Chun-Hong Chen, Ying-Tsong Chen: Genomics Studies on the Ae. albopictus mitochondria. IMGM Poster Day NHRI/Taiwan
  4. XY Huang, AC Lin, TL Lauderdale, YT Chen: Complete Sequencing and Analyses of a Genotoxic Klebsiella pneumoniae K62 strain. 3rd Annual Microbiology & Infectious Diseases Asia Congress / 6th Annual Next Generation Sequencing Asia CongressSingapore
  5. YT Chen: 克雷白氏肺炎菌的基因體學研究(invited speech). 2016農業暨生物資訊分析前瞻與新知研討會
  6. YT Chen: 基因毒性與台灣的克雷白氏肺炎菌(invited speech). 2015細菌學研討會
  7. 洪義閔，陳盈璁: 克雷白氏肺炎桿菌基因體小島模組間交互作用與功能之探討. 2015細菌學研討會
  8. YT Chen: Genotoxic Klebsiella pneumoniae in Taiwan (invited speech). International Symposium on Evolutionary Genomics and Bioinformatics
  9. YT Chen: Functional Genomics Studies on Genotoxic Klebsiella pneumoniae in Taiwan (invited speech). 2014 Life Taiwan User Conference -The future of laboratory developed testing – The total solution powered by Roche
  10. TL Liao; TW Huang; KM Wu; CT Lee; YM Liu; AC Lin; YT Chen; TT Liu; N Bisharat; LI Hor; SF Tsai: A single chromosome of 5.2 Mb in Vibrio vulnificus biotype 3 strain CECT7356. IMGM Poster Day NHRI/Taiwan
  11. YC Lai; AC Lin; YT Chen: Genotoxicity of Klebsiella pneumoniae in Taiwan. IMGM Poster Day NHRI/Taiwan
  12. 洪義閔，黃意真，張詠鈞，賴怡琪，林靖婷，陳盈璁: 克雷白氏肺炎桿菌基因體小島KPHPI208的功能性研究. 2014細菌學研討會
  13. Genotoxicity of Klebsiella pneumoniae in Taiwan (2014) 2014 IMGM Poster Party, IMGM, NHRI, Taiwan
  14. A single chromosome of 5.2 Mb in Vibrio vulnificus biotype 3 strain CECT7356 (2014) IMGM Poster Party, IMGM, NHRI, Taiwan
  15. Complete genome sequence of Klebsiella pneumoniae 1084 and the identification of a genotoxin-encoding virulence genomic island (2013) 2013 IMGM Poster Party, IMGM, NHRI, Taiwan
  16. Missing pieces in Klebsiella pneumoniae genomes (2012) 2012第廿八屆生物夏令營
  17. Towards a database of antimicrobial resistance genes (2012) 2012 UST-UCSD I-RICE Symposium and Joint Biomedical Informatics Symposium between National Yang-Ming University (NYMU), and University of California, San Diego (UCSD)
  18. Using nalidixic acid-susceptibility and borderline resistance to identify plasmid-mediated quinolone resistance (PMQR) in Salmonella in Taiwan. (2012) 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans and the Environment, France. June 26-30.
  19. Multiplex sequencing of antimicrobial resistance genes by PGM. (2012) 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans and the Environment, France. June 26-30.
  20. Application of 454 in Bacterial Genomics (2012) 生物資訊研究中心學術研討會 國立交通大學 (受邀演講)
  21. Complete Sequencing and Annotation of Klebsiella oxytoca E718. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  22. Missing Pieces in Klebsiella pneumoniae genomes. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  23. Complete Sequencing and Annotation of MRSA strain M013 from Taiwan. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  24. Comparative analysis of three NDM-1 positive plasmids using personal sequencers. (2012) 2012 NHRI Research Day, Zhunan, Taiwan. March 22.
  25. 遺失的克雷白氏桿菌DNA序列 (2011) 2011年克雷白氏桿菌學術研討會 國家衛生研究院感染症與疫苗研究所與國防醫學院 (受邀演講)
  26. PMQR in Taiwan (2010) 系統生物學研討會 國家衛生研究院 (專題演講)