微生物基因體核心研究室

Microbial Genomics Core Laboratory, Graduate Institute of Genomics and Bioinformatics, NCHU, Taiwan

Publications

您可以透過我們發表的學術期刊論文了解我們的研究興趣與方向。

學術期刊著作 (依發表日期) Publications:

  1. Huang CL, Chu HF, Wu CC, Deng FS, Wen PJ, Chien SP, Chao CH, Chen YT, Lu MK, Tsai TC*. Exopolysaccharide is the Potential Effector of Lactobacillus fermentum PS150, a Hypnotic Psychobiotic Strain. Front Microbial. 2023. 14.
  2. Cheng YH, Ko YC, Ku HJ, Huang CC, Yao YC, Liao YT, Chen YT, 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.
  3. 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. 10(1):e01682-21.
  4. 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. 2022. 66(1):e01152-21.
  5. 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. 65(5):e02634-20.
  6. Huang YS, Tsai WC, Li JJ, Chen PY, Wang JT*, Chen YT, Chen FJ, Lauderdale TL*, Chang SC. Increasing New Delhi metallo- β-lactamase-positive Escherichia coli among carbapenem non-susceptible Enterobacteriaceae in Taiwan during 2016 to 2018. Sci Rep. 2021. 11(1):2609
  7. 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.
  8. Lu MC, Chen YT, 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 Feb 1;75(2):318-326.
  9. Liu KM, Chang HL, Hsu MH, Lin YZ, Lee YL, Chen YT*. Complete Genome Sequencing of Elizabethkingia sp. Strain 2-6. Microbiol Resour Announc. 2019 Oct 31;8(44). pii: e00805-19.
  10. Wang YC, Tang HL, Liao YC, Chiou CS, Chen YT, 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 May 24;63(6):e02282-18.
  11. 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. Sci Rep. 2017 May 3;7(1):1425.
  12. 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, Taiwan. Antimicrobial Agents and Chemotherapy. 2017. 61:e00338-17.
  13. 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. 7:103.
  14. 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. Sci Rep. 2017. 7:43120.
  15. 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. 22:109-114.
  16. 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. 70:2734-2738.
  17. 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 Journal. 2015. 38:221-228.
  18. 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. 44:431-435.
  19. 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. 9:e104899.
  20. 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.
  21. 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. 2014. 69:628-631. 
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. Liao TL, Lin AC, Chen E, Huang TW, Liu YM, Chang YH, Lai JF, Lauderdale TL, Wang JT, Chang SC, 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.
  27. 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.
  28. 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.
  29. 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.
  30. Chang JR, Lin CH, Tsai SF, Su IJ, Tseng FC, Chen YT, Chiueh TS, Sun JR, Huang TS, Chen YS, and 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. Chen YT, Liao TL, Wu, KM, Lauderdale, TL, Yan JJ, Huang IW, Lu MC, Lai YC, Liu, YM, Shu HY, Su IJ, Wang JT, and Tsai SF*. Genomic diversity of citrate fermentation in Klebsiella pneumoniae. BMC Microbiology. 2009. 9:168.
  36. 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.
  37. 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.
  38. Chang JW, Liu HP, Hsieh MH, Fang YF, Hsieh MS, Hsieh JJ, Chiu YT, Tsai HY, Chen YH, Chen YT, Hsu HY, Chen YT, 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.
  39. Chen YT*, Lauderdale TL, Liao TL, Shiao YR, Shu HY, Wu KM, Yan JJ, Su IJ, and Tsai SF. Sequencing and Comparative Genomic Analysis of pK29, a 269-kb Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-lactamases from Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy. 2007. 51:3004-3007.
  40. Chen YT, Shu HY, Li LH, Liao TL, Wu KM, Shiao YR, Yan JJ, Su IJ, Tsai SF, and Lauderdale TL*. Complete nucleotide sequence of pK245, a 98-kilobase plasmid conferring quinolone-resistance and extended-spectrum β-lactamase activity in a clinical Klebsiella pneumoniae isolate. Antimicrobial Agents and Chemotherapy. 2006. 50:3861-3866.
  41. Liu CH, Hsu FR, Chang HY, Shia WC, Peng HL, Chen YT, Lin YL, and Tsai YT. Comparative analysis of alternative splicing events in human and mouse. WSEAS Transactions on Information Science and Applications. 2006. 3 (9):1772-1776.
  42. Hsieh MH, Fang YF, Chang WC, Kuo HP, Lin SY, Liu HP, Liu CL, Chen HC, Ku YC, Chen YT, Chang YH, Chen YT, Hsi BL, Tsai SF, and 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.
  43. Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, 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.
  44. Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, 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)
  45. Chen YT, 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.
  46. Chen YT, 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.
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