{"id":9,"date":"2014-06-22T20:35:21","date_gmt":"2014-06-22T20:35:21","guid":{"rendered":"http:\/\/140.120.203.75\/wordpress\/?page_id=9"},"modified":"2026-04-28T02:41:47","modified_gmt":"2026-04-28T02:41:47","slug":"publications","status":"publish","type":"page","link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?page_id=9","title":{"rendered":"Publications"},"content":{"rendered":"\n

Our laboratory has published research in microbial genomics, antimicrobial resistance, outbreak investigation, and host-associated microbiology. Recent work includes both faculty-led and student-led studies in international journals.<\/p>\n\n\n\n

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 (\u4f9d\u767c\u8868\u65e5\u671f)<\/p>\n\n\n\n

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  1. Huang WK, Yang CH, Lee YC, Wu YC, Chen YT, Wan MS, Yeh WS, Hong YP, Wu TH, Li JC, Liu WL, Chen CH, Chen YT*. Adaptive sampling-based enrichment enables genome reconstruction of intracellular symbionts despite host background and reference divergence. 2026. bioRxiv 2026.03.25.714109; doi: https:\/\/doi.org\/10.64898\/2026.03.25.714109<\/a> <\/li>\n\n\n\n
  2. Dhital B, Pudasaini R, Hsieh JC, Pudasaini R, Chen YT<\/mark>, Chao DY, Chiang HI*. One Health Perspective on Antimicrobial Resistance in Bovine Mastitis Pathogens \u2014 A Narrative Review. 2026. Antibiotics. 15(1):84. https:\/\/doi.org\/10.3390\/antibiotics15010084<\/li>\n\n\n\n
  3. Wu TH, Wu YC, Yeh WS, Wan MS, Li RY<\/mark>, Lee CY, Fang YP, Yang YY, Chang YF, Chen YT<\/mark>.* Genomic and phylogenetic characterization of human-adapted methicillin-resistant Staphylococcus aureus clonal complex 398 lineages in Taiwan. 2025. Microbiol Spectr. 0:e02090-25.<\/li>\n\n\n\n
  4. Dhital B, Chen YT<\/mark>, Paudyal S, Pudasaini R, Chen YT, Chiang HI*. Genomic signatures of beta-lactam resistance and reversion in Staphylococcus aureus from bovine mastitis. Lett Appl Microbial. 2025. 78(10):ovaf107.<\/li>\n\n\n\n
  5. Huang CL, Chu HF, Wu CC, Deng FS, Wen PJ, Chien SP<\/mark>, Chao CH, Chen YT<\/mark>, Lu MK, Tsai TC*. Exopolysaccharide is the Potential Effector of Lactobacillus fermentum PS150, a Hypnotic Psychobiotic Strain. Front Microbial. 2023. 14:1209067.<\/li>\n\n\n\n
  6. Cheng YH, Ko YC, Ku HJ, Huang CC, Yao YC, Liao YT, Chen YT<\/mark>, Huang SF, Huang LR*. Novel paired cell lines for the study of lipid metabolism and cancer stemness of hepatocellular carcinoma. Front Cell Dev Biol. 2022. 10:821224.<\/li>\n\n\n\n
  7. Lee YL, Liu KM, Chang HL, Liao YC<\/mark>, Lin JS, Kung FY, Ho CM, Lin KH, Chen YT<\/mark>*. The evolutionary trend and genomic features of an emerging lineage of Elizabethkingia anophelis strains in Taiwan. Microbiol Spectr. 2022. 10(1):e01682-21.<\/li>\n\n\n\n
  8. Hong YP<\/mark>, Wang YW, Chen BH, Song HY, Chiou CS, Chen YT<\/mark>*. RamAp, an efflux pump regulator carried by an IncHI2 plasmid. Antimicrob Agents Chemother. 2022. 66(1):e01152-21.<\/li>\n\n\n\n
  9. Hong YP, Chen YT<\/mark>, 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. 65(5):e02634-20.<\/li>\n\n\n\n
  10. Huang YS, Tsai WC, Li JJ, Chen PY, Wang JT, <\/em>Chen YT<\/mark>, Chen FJ, Lauderdale TL, Chang SC. Increasing New Delhi metallo- \u03b2-lactamase-positive Escherichia coli among carbapenem non-susceptible Enterobacteriaceae in Taiwan during 2016 to 2018. Sci Rep. 2021. 11(1):2609.<\/li>\n\n\n\n
  11. Lee YL, Liu KM, Chang HL<\/mark>, Lin JS, Kung FY, Ho CM, Lin KS, Chen YT<\/mark>*. 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.<\/li>\n\n\n\n
  12. Lu MC, Chen YT<\/mark>, Tang HL, Liu YY, Chen BH, Wang YW, Chen YS, Teng RH, Hong YP, Chiou CS, Chiang MK, Lai YC*. Transmission and evolution of OXA-48-producing Klebsiella pneumoniae ST11 in a single hospital in Taiwan. J Antimicrob Chemother. 2020. 75(2):318-326.<\/li>\n\n\n\n
  13. Liu KM, Chang HL, Hsu MH, Lin YZ, Lee YL, Chen YT<\/mark>*. Complete Genome Sequencing of Elizabethkingia sp. Strain 2-6. Microbiol Resour Announc. 2019. 8(44). pii: e00805-19.<\/li>\n\n\n\n
  14. Wang YC, Tang HL, Liao YC, Chiou CS, Chen YT<\/mark>, Chiang MK, Lu MC, Lai YC. Cocarriage of Distinct blaKPC-2 and blaOXA-48 Plasmids in a Single Sequence Type 11 Carbapenem-Resistant Klebsiella pneumoniae Isolate. Antimicrob Agents Chemother. 2019. 63(6):e02282-18.<\/li>\n\n\n\n
  15. Dou HY, Lin CH, Chen YY, Yang SJ, Chang JR, Wu KM, Chen YT<\/mark>, Chin PJ, Liu YM, Su IJ, Tsai SF*. Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates. Sci Rep. 2017. 7(1):1425.<\/li>\n\n\n\n
  16. Chiou CS*, Chen YT<\/mark>, Wang YW, Liu YY, Kuo HC, Tu YH, Lin AC, Liao YS, Hong YP<\/mark>. Dissemination of mcr-1\u2013Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals, Taiwan. Antimicrobial Agents and Chemotherapy. 2017. 61:e00338-17.<\/li>\n\n\n\n
  17. Lu MC, Chen YT<\/mark>, 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. 7:103.<\/li>\n\n\n\n
  18. Chen YT<\/mark>, Lai YC, Tan MC, Hsieh LY, Wang JT, Shiau YR, Wang HY, Lin AC<\/mark>, Lai JF, Huang IW, Lauderdale TL*. Prevalence and characteristics of pks genotoxin gene cluster-positive clinical Klebsiella pneumoniae isolates in Taiwan. Sci Rep. 2017. 7:43120.<\/li>\n\n\n\n
  19. Chen YT<\/mark>, 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. 22:109-114.<\/li>\n\n\n\n
  20. Huang TW, Lauderdale TL, Liao TL, Hsu MC, Chang FY, Chang SC, Khong WX, Ng OT, Chen YT<\/mark>, 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. 70:2734-2738.<\/li>\n\n\n\n
  21. 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<\/mark>, 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 Journal. 2015. 38:221-228.<\/li>\n\n\n\n
  22. Tang HJ, Chen YT<\/mark>, 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. 44:431-435.<\/li>\n\n\n\n
  23. Chen CJ, Wu TL, Chen YT<\/mark>, 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. 9:e104899.<\/li>\n\n\n\n
  24. Lai YC, Lin AC<\/mark>, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, and Chen YT<\/mark>.* Genotoxic Klebsiella pneumoniae in Taiwan. PlosONE. 2014. 9:e96292.<\/li>\n\n\n\n
  25. Chen YT<\/mark>, 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. 2014. 69:628-631. <\/li>\n\n\n\n
  26. Huang TW, Wang JT, Lauderdale TL, Liao TL, Lai JF, Tan MJ, Lin AC, Chen YT<\/mark>, 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.<\/li>\n\n\n\n
  27. Huang TW, Chen TL, Chen YT<\/mark>, Lauderdale TL, Liao TL, Lee YT, Chen CP, Liu YM, Lin AC<\/mark>, 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.<\/li>\n\n\n\n
  28. Chen YT, Lin AC<\/mark>, Siu LK, Koh TH. Sequence of closely related plasmids encoding blaNDM-1 in two unrelated Klebsiella pneumoniae isolates in Singapore. PlosONE. 2012. 7:e48737.<\/li>\n\n\n\n
  29. Lin AC<\/mark>, Liao TL, Lin YC, Lai YC, Lu MC, Chen YT<\/mark>*. Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-negative K1 Clinical Strain. Journal of Bacteriology.  2012. 194:6316.<\/li>\n\n\n\n
  30. Liao TL, Lin AC<\/mark>, Chen E, Huang TW, Liu YM, Chang YH, Lai JF, Lauderdale TL, Wang JT, Chang SC, Tsai SF, Chen YT<\/mark>*. Complete genome sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-lactamase-1-producing nosocomial strain. Journal of Bacteriology.  2012. 194:5454.<\/li>\n\n\n\n
  31. Huang SH, Wang CK, Peng HL, Wu CC, Chen YT, Hong YM<\/mark>, 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.<\/li>\n\n\n\n
  32. Huang TW, Chen FJ, Miu WC, Liao TL, Lin AC<\/mark>, Huang IW, Wu KM, Tsai SF, Chen YT<\/mark>*, 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.<\/li>\n\n\n\n
  33. Chen YT, Chang WC J, Liu HP, Yu TF, Chiu YT, Hsieh JJ, Chen YT<\/mark>, 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.<\/li>\n\n\n\n
  34. Chang JR, Lin CH, Tsai SF, Su IJ, Tseng FC, Chen YT<\/mark>, Chiueh TS, Sun JR, Huang TS, Chen YS, Dou HY*. 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.<\/li>\n\n\n\n
  35. Hoang KC, Lai TH, Lin CS, Chen YT<\/mark>*, Liau CY*. The Chitinolytic Activities of Streptomyces sp. TH-11. International Journal of Molecular Sciences. 2011. 12:56-65.<\/li>\n\n\n\n
  36. Liu HP, Wu HDI, Chang JWC, MD, Wu YC, Yang HY, Chen YT, Hsieh WY, Chen YT<\/mark>, 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.<\/li>\n\n\n\n
  37. Tang HL, Chiang MK, Liou WJ, Chen YT<\/mark>, Peng HL, Chiou CS, Liu KS, Lu MC, Tung KC, Lai YC*. Correlation between Klebsiella pneumoniae carrying pLVPK-derived loci and abscess formation. European Journal of Clinical Microbiology & Infectious Diseases. 2010. 29:689-698.<\/li>\n\n\n\n
  38. Shu HY, Fung CP, Liu, YM, Wu, KM, Chen YT<\/mark>, Li LH, Liu TT, Kirby R, Tsai SF*. Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates. Microbiology. 2009. 155:4170-4183.<\/li>\n\n\n\n
  39. Chen YT<\/mark>, Liao TL, Wu, KM, Lauderdale, TL, Yan JJ, Huang IW, Lu MC, Lai YC, Liu, YM, Shu HY, Su IJ, Wang JT, Tsai SF*. Genomic diversity of citrate fermentation in Klebsiella pneumoniae. BMC Microbiology. 2009. 9:168.<\/li>\n\n\n\n
  40. 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<\/mark>, Shiau YR, Lauderdale TL, Su IJ, Kirby R*, 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.<\/li>\n\n\n\n
  41. Chen YT<\/mark>*, Liao TL, Liu YM, Lauderdale TL, Yan JJ, Tsai SF. Mobilization of qnrB2 and ISCR1 in Plasmids. Antimicrobial Agents and Chemotherapy. 2009. 53:1235-1237.<\/li>\n\n\n\n
  42. Chang JW, Liu HP, Hsieh MH, Fang YF, Hsieh MS, Hsieh JJ, Chiu YT, Tsai HY, Chen YH, Chen YT, Hsu HY, Chen YT<\/mark>, Tsai SF, Chen YR, Hsi BL, Huang SF*. Increased epidermal growth factor receptor (EGFR) gene copy number is strongly associated with EGFR mutations and adenocarcinoma in non-small cell lung cancers: A chromogenic in situ hybridization study of 182 patients. Lung Cancer. 2008. 61:328-339.<\/li>\n\n\n\n
  43. Chen YT<\/mark>*, Lauderdale TL, Liao TL, Shiao YR, Shu HY, Wu KM, Yan JJ, Su IJ, Tsai SF. Sequencing and Comparative Genomic Analysis of pK29, a 269-kb Conjugative Plasmid Encoding CMY-8 and CTX-M-3 \u03b2-lactamases from Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy. 2007. 51:3004-3007.<\/li>\n\n\n\n
  44. Chen YT<\/mark>, Shu HY, Li LH, Liao TL, Wu KM, Shiao YR, Yan JJ, Su IJ, Tsai SF, Lauderdale TL*. Complete nucleotide sequence of pK245, a 98-kilobase plasmid conferring quinolone-resistance and extended-spectrum \u03b2-lactamase activity in a clinical Klebsiella pneumoniae isolate. Antimicrobial Agents and Chemotherapy. 2006. 50:3861-3866.<\/li>\n\n\n\n
  45. Liu CH, Hsu FR*, Chang HY, Shia WC, Peng HL, Chen YT<\/mark>, Lin YL, Tsai YT. Comparative analysis of alternative splicing events in human and mouse. WSEAS Transactions on Information Science and Applications. 2006. 3 (9):1772-1776.<\/li>\n\n\n\n
  46. Hsieh MH, Fang YF, Chang WC, Kuo HP, Lin SY, Liu HP, Liu CL, Chen HC, Ku YC, Chen YT, Chang YH, Chen YT<\/mark>, Hsi BL, Tsai SF, Huang SF*. Complex mutation patterns of epidermal growth factor receptor gene associated with variable responses to gefitinib treatment in patients with non-small cell lung cancer. Lung Cancer. 2006. 53:311-322.<\/li>\n\n\n\n
  47. Hsu FR*, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT<\/mark>, Cheng CY, Shih MY, Liu CH, and Chen CF. AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs. Bioinformation. 2005. 1(1):16-18.<\/li>\n\n\n\n
  48. Hsu FR*, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT<\/mark>, Chen CF, Cheng CY, Liu CH, and Shih MY. Genome-wide alternative splicing events detection through analysis of large scale ESTs. Forth IEEE Symposium on Bioinformatics and Bioengineering (BIBE’04). 2004. 310-316 (EI)<\/li>\n\n\n\n
  49. Chen YT<\/mark>, Chang HY, Lu CL, Peng HL. Evolutionary analysis of the two-component systems in Pseudomonas aeruginosa PAO1. Journal of Molecular Evolution. 2004. 59(6):725-37.<\/li>\n\n\n\n
  50. Chen YT<\/mark>, Chang HY, Lai YC, Pan CC, Tsai SF, Peng HL. Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene. 2004. 337:189-98.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    Our laboratory has published research in microbial genomics, antimicrobial resistance, outbreak investigation, and host-associated microbiology. Recent work includes both faculty-led<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","footnotes":""},"class_list":["post-9","page","type-page","status-publish","hentry"],"magazineBlocksPostFeaturedMedia":{"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"colormag-highlighted-post":false,"colormag-featured-post-medium":false,"colormag-featured-post-small":false,"colormag-featured-image":false,"colormag-default-news":false,"colormag-featured-image-large":false},"magazineBlocksPostAuthor":{"name":"onion","avatar":"https:\/\/secure.gravatar.com\/avatar\/a596197721c6296d27446d1377ed931e199d7d76ae4dedbebf95195b579de271?s=96&d=mm&r=g"},"magazineBlocksPostCommentsNumber":false,"magazineBlocksPostExcerpt":"Our laboratory has published research in microbial genomics, antimicrobial resistance, outbreak investigation, and host-associated microbiology. Recent work includes both faculty-led","magazineBlocksPostCategories":[],"magazineBlocksPostViewCount":0,"magazineBlocksPostReadTime":11,"_links":{"self":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/9","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=9"}],"version-history":[{"count":81,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/9\/revisions"}],"predecessor-version":[{"id":2177,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/pages\/9\/revisions\/2177"}],"wp:attachment":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}