Publications

Preprints

2026
- Preprint Adaptive sampling–based enrichment enables genome reconstruction of intracellular symbionts despite host background and reference divergence
  Wei-Kang Huang, Cheng-Hao Yang, Hui Chung, Yen-Chen Lee, Yung-Chieh Wu, Yen-Tong Chen, Mei-Hsiu Wan, Wen-Sheng Yeh, Yu-Ping Hong, Tsung-Hua Wu, Jian-Chiuan Li, Wei-Liang Liu, Chun-Hong Chen, Ying-Tsong Chen
  DOI: 10.64898/2026.03.25.714109

Journal Articles

2026
- Journal Article Synergistic Bactericidal Effects of R- and F-Type Pyocin Cocktails Against Clinical Pseudomonas aeruginosa Isolates from Central Taiwan
  Yi-Luen Shen, Wen-Tong Xu, Zih-Ling Jiang, Nien-Jen Hu, Ying-Tsong Chen, Tze-Kiong Er, Chien-Wen Huang
  Antibiotics DOI: 10.3390/antibiotics15060596
- Journal Article Plasmid-borne transcriptional regulator RamAp modulates Salmonella genes for environmental and host adaptation
  Yu-Ping Hong, Wen-Sheng Yeh, Mei-Hsiu Wan, Yung-Chieh Wu, Yen-Tong Chen, Wei-Kang Huang, Cheng-Hao Yang, Liang-Yu Su, Yi-Min Hong, Pei-Ju Tsai, Yu-Ting Chen, Ching-Ting Lin, Yi-Chyi Lai, Chien-Shun Chiou, Ying-Tsong Chen
  Frontiers in Microbiology DOI: 10.3389/fmicb.2026.1842592
- Journal Article Establishment and characterization of a Wolbachia (wAlbB)-infected Aedes aegypti line (Tw-Kao) for dengue control
  Hui-Ying Yu, Bo-Yu Chen, Ying-Tsong Chen, Wei-Kang Huang, Cheng-Hao Yang, Yung-Chieh Wu, Mei-Hsiu Wan, Wen-Sheng Yeh, Feng-Guang Goh, Xinjun Hou, Pui-Kuan Toh, Sui-Hann Ng, Yu Cai, Jian-Chiuan Li, Chun-Hong Chen, Wei-Liang Liu
  PLOS Neglected Tropical Diseases DOI: 10.1371/journal.pntd.0014222
- Journal Article Genomic and phylogenetic characterization of human-adapted methicillin-resistant Staphylococcus aureus clonal complex 398 lineages in Taiwan
  Tsung-Hua Wu, Yung-Chieh Wu, Wen-Sheng Yeh, Mei-Hsiu Wan, Rou-Yi Li, Chun-Yi Lee, Yu-Ping Fang, Yu-Ying Yang, Yu-Fen Chang, Ying-Tsong Chen, Deena R. Altman
  Microbiology Spectrum DOI: 10.1128/spectrum.02090-25
- Journal Article One Health Perspective on Antimicrobial Resistance in Bovine Mastitis Pathogens—A Narrative Review
  Bigya Dhital, Rameshwor Pudasaini, Jui-Chun Hsieh, Ramchandra Pudasaini, Ying-Tsong Chen, Day-Yu Chao, Hsin-I Chiang
  Antibiotics DOI: 10.3390/antibiotics15010084
2025
- Journal Article Genomic signatures of beta-lactam resistance and reversion in Staphylococcus aureus from bovine mastitis
  Bigya Dhital, Ying-Tsong Chen, Sushil Paudyal, Rameshwor Pudasaini, Yi-Tzu Chen, Hsin-I Chiang
  Letters in Applied Microbiology DOI: 10.1093/lambio/ovaf107
- Journal Article Rapid antibiotic sensitivity prediction in Pseudomonas aeruginosa using UV–vis-NIR spectroscopy and gray-box one-vs-all models
  Tsung-Han Chou, Chi-Wei Chen, Su-Hua Huang, Ying-Tsong Chen, Yen-Wei Chu
  Journal of Microbiological Methods DOI: 10.1016/j.mimet.2025.107179
2024
- Journal Article Emergence and transmission of the high-risk ST78 clone of OXA-48-producing Enterobacter hormaechei in a single hospital in Taiwan
  Chih-Ming Chen, Hui-Ling Tang, Ying-Tsong Chen, Se-Chin Ke, Yi-Pei Lin, Bo-Han Chen, Ru-Hsiou Teng, Chien-Shun Chiou, Min-Chi Lu, Yi-Chyi Lai
  Emerging Microbes & Infections DOI: 10.1080/22221751.2024.2404165
2023
- Journal Article Exopolysaccharide is the potential effector of Lactobacillus fermentum PS150, a hypnotic psychobiotic strain
  Chin-Lin Huang, Hsu-Feng Chu, Chien-Chen Wu, Fu-Sheng Deng, Pei-Jun Wen, Shao-Ping Chien, Chi-Hsein Chao, Ying-Tsong Chen, Mei-Kuang Lu, Ying-Chieh Tsai
  Frontiers in Microbiology DOI: 10.3389/fmicb.2023.1209067
2022
- Journal Article The Evolutionary Trend and Genomic Features of an Emerging Lineage of Elizabethkingia anophelis Strains in Taiwan
  Yu-Lin Lee, Kuan-Ming Liu, Hui-Lan Chang, Yi-Ci Liao, Jen-Shiou Lin, Fang-Yen Kung, Cheng-Mao Ho, Kai-Hsiang Lin, Ying-Tsong Chen, Tino Polen
  Microbiology Spectrum DOI: 10.1128/spectrum.01682-21
- Journal Article Novel Paired Cell Lines for the Study of Lipid Metabolism and Cancer Stemness of Hepatocellular Carcinoma
  Yun-Hsin Cheng, Ying-Chieh Ko, Hsiang-Ju Ku, Ching-Chun Huang, Yu-Ching Yao, Yi-Tzu Liao, Ying-Tsong Chen, Shiu-Feng Huang, Li-Rung Huang
  Frontiers in Cell and Developmental Biology DOI: 10.3389/fcell.2022.821224
- Journal Article RamAp Is an Efflux Pump Regulator Carried by an IncHI2 Plasmid
  Yu-Ping Hong, You-Wun Wang, Bo-Han Chen, Hui-Yung Song, Chien-Shun Chiou, Ying-Tsong Chen
  Antimicrobial Agents and Chemotherapy DOI: 10.1128/AAC.01152-21
2021
- Journal Article A dominant strain of Elizabethkingia anophelis emerged from a hospital water system to cause a three-year outbreak in a respiratory care center Journal of Hospital Infection DOI: 10.1016/j.jhin.2020.10.025
- Journal Article Increasing New Delhi metallo-β-lactamase-positive Escherichia coli among carbapenem non-susceptible Enterobacteriaceae in Taiwan during 2016 to 2018 Scientific Reports DOI: 10.1038/s41598-021-82166-8
- Journal Article Integrative and Conjugative Element-Mediated Azithromycin Resistance in Multidrug-Resistant Salmonella enterica Serovar Albany
  Yu-Ping Hong, Ying-Tsong Chen, You-Wun Wang, Bo-Han Chen, Ru-Hsiou Teng, Yi-Syong Chen, Chien-Shun Chiou
  Antimicrobial Agents and Chemotherapy DOI: 10.1128/AAC.02634-20
2020
- Journal Article Erratum for Wang et al., “Cocarriage of Distinct bla KPC-2 and bla OXA-48 Plasmids in a Single Sequence Type 11 Carbapenem-Resistant Klebsiella pneumoniae Isolate”
  Yao-Chen Wang, Hui-Ling Tang, Yu-Chieh Liao, Chien-Shun Chiou, Ying-Tsong Chen, Ming-Ko Chiang, Min-Chi Lu, Yi-Chyi Lai
  Antimicrobial Agents and Chemotherapy DOI: 10.1128/AAC.01546-20
2019
- Journal Article Complete Genome Sequencing of Elizabethkingia sp. Strain 2-6
  Kuan-Ming Liu, Hui-Lan Chang, Ming-Hong Hsu, Yi-Zhen Lin, Yu-Lin Lee, Ying-Tsong Chen, Irene L. G. Newton
  Microbiology Resource Announcements DOI: 10.1128/MRA.00805-19
- Journal Article Transmission and evolution of OXA-48-producing Klebsiella pneumoniae ST11 in a single hospital in Taiwan Journal of Antimicrobial Chemotherapy DOI: 10.1093/jac/dkz431
- Journal Article Cocarriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single sequence type 11 carbapenem-resistant klebsiella pneumoniae isolate
  Wang, Y.-C., Tang, H.-L., Liao, Y.-C., Chiou, C.-S., Chen, Y.-T., Chiang, M.-K., Lu, M.-C., Lai, Y.-C.
  Antimicrobial Agents and Chemotherapy DOI: 10.1128/AAC.02282-18
2017
- Journal Article Prevalence and characteristics of pks genotoxin gene cluster-positive clinical Klebsiella pneumoniae isolates in Taiwan Scientific Reports DOI: 10.1038/srep43120
- Journal Article Dissemination of mcr-1 -Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals in Taiwan Antimicrobial Agents and Chemotherapy DOI: 10.1128/aac.00338-17
- Journal Article Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates Scientific Reports DOI: 10.1038/s41598-017-01580-z
- Journal Article Colibactin Contributes to the Hypervirulence of pks+ K1 CC23 Klebsiella pneumoniae in Mouse Meningitis Infections Frontiers in Cellular and Infection Microbiology DOI: 10.3389/fcimb.2017.00103
2016
- Journal Article A Common Flanking Region in Promiscuous Plasmids Encoding blaNDM-1 in Klebsiella pneumoniae Isolated in Singapore
  Chen, Y.-T., Siu, L.K., Tsai, Y.-K., Lin, F.-M., Koh, T.H., Chen, J.-H.
  Microbial Drug Resistance DOI: 10.1089/mdr.2015.0132
- Journal Article Genomics study of Mycobacterium tuberculosis strains from different ethnic populations in Taiwan
  Dou, H.-Y., Chen, Y.-Y., Chen, Y.-T., Chang, J.-R., Lin, C.-H., Wu, K.-M., Lin, M.-S., Su, I.-J., Tsai, S.-F.
  Evolutionary Bioinformatics DOI: 10.4137/EBO.S40152
2015
- Journal Article Effective transfer of a 47 kb NDM-1-positive plasmid among Acinetobacter species.
  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
  DOI: 10.1093/jac/dkv191
- Journal Article A Common Flanking Region in Promiscuous Plasmids Encoding blaNDM-1 in Klebsiella pneumoniae Isolated in Singapore.
  Chen YT, Siu LK, Tsai YK, Lin FM, Koh TH, Chen JH
- Journal Article 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.
  Chang JW, Hou MM, Hsieh JJ, Cheung YC, Wang HM, Chen JS, Wang CH, Chen CH, Yeh KY, Ou LY, Hsieh CH, Wu HD, Chen YT, Chang IC, Huang SF
  DOI: 10.4103/2319-4170.138320
2014
- Journal Article Genotoxic Klebsiella pneumoniae in Taiwan.
  Lai YC, Lin AC, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, Chen YT
  DOI: 10.1371/journal.pone.0096292
- Journal Article KPC-2-encoding plasmids from escherichia coli and Klebsiella pneumoniae in Taiwan
  Chen, Y., Lin, J., Fung, C., Lu, P., Chuang, Y., Wu, T., Kristopher Siu, L.
  DOI: 10.1093/jac/dkt409
- Journal Article Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.
  Chen CJ, Wu TL, Lu PL, Chen YT, Fung CP, Chuang YC, Lin JC, Siu LK
  DOI: 10.1371/journal.pone.0104899
- Journal Article Identification of the first imported KPC-3 Klebsiella pneumoniae from the USA to Taiwan.
  Tang HJ, Chen YT, Chiang T, Fung CP, Chuang YC, Kristopher Siu L
  DOI: 10.1016/j.ijantimicag.2014.07.009
2013
- Journal Article Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate
  Huang, T.-W., Chen, T.-L., Chen, Y.-T., Lauderdale, T.-L., Liao, T.-L., Lee, Y.-T., Chen, C.-P., Liu, Y.-M., Lin, A.-C., Chang, Y.-H., Wu, K.-M., Kirby, R., Lai, J.-F., Tan, M.-C., Siu, L.-K., Chang, C.-M., Fung, C.-P., Tsai, S.-F.
  DOI: 10.1371/journal.pone.0062774
- Journal Article Complete sequences of two plasmids in a blandm-1-positive klebsiella oxytoca isolate from taiwan
  Huang, T.-W., Wang, J.-T., Lauderdale, T.-L., Liao, T.-L., Lai, J.-F., Tan, M.-C., Lin, A.-C., Chen, Y.-T., Tsai, S.-F., Chang, S.-C.
  DOI: 10.1128/AAC.02266-12
2012
- Journal Article Complete genome sequence of Staphylococcus aureus M013, a pvl-positive, ST59-SCCmec type V strain isolated in Taiwan
  Huang, T.-W., Chen, F.-J., Miu, W.-C., Liao, T.-L., Lin, A.-C., Huang, I.-W., Wu, K.-M., Tsai, S.-F., Chen, Y.-T., Lauderdale, T.-L.Y.
  DOI: 10.1128/JB.06666-11
- Journal Article Role of the small RNA RyhB in the fur regulon in mediating the capsular polysaccharide biosynthesis and iron acquisition systems in Klebsiella pneumoniae
  Huang, S.-H., Wang, C.-K., Peng, H.-L., Wu, C.-C., Chen, Y.-T., Hong, Y.-M., Lin, C.-T.
  DOI: 10.1186/1471-2180-12-148
- Journal Article Complete genome sequence of Klebsiella oxytoca E718, a New Delhi metallo-β-lactamase-1-producing nosocomial strain
  Liao, T.-L., Lin, A.-C., Chen, E., Huang, T.-W., Liu, Y.-M., Chang, Y.-H., Lai, J.-F., Lauderdale, T.-L., Wang, J.-T., Chang, S.-C., Tsai, S.-F., Chen, Y.-T.
  DOI: 10.1128/JB.01216-12
- Journal Article Complete genome sequence of Klebsiella pneumoniae 1084, a hypermucoviscosity-negative K1 clinical strain
  Lin, A.-C., Liao, T.-L., Lin, Y.-C., Lai, Y.-C., Lu, M.-C., Chen, Y.-T.
  DOI: 10.1128/JB.01548-12
- Journal Article Sequence of closely related plasmids encoding bla(NDM-1) in two unrelated Klebsiella pneumoniae isolates in Singapore.
  Chen, Y.T., Lin, A.C., Siu, L.K., Koh, T.H.
2011
- Journal Article The chitinolytic activities of Streptomyces sp. TH-11
  Hoang, K.-C., Lai, T.-H., Lin, C.-S., Chen, Y.-T., Liau, C.-Y.
  DOI: 10.3390/ijms12010056
- Journal Article Genotypic analysis of genes associated with transmission and drug resistance in the Beijing lineage of Mycobacterium tuberculosis
  Chang, J.-R., Lin, C.-H., Tsai, S.-F., Su, I.-J., Tseng, F.-C., Chen, Y.-T., Chiueh, T.-S., Sun, J.-R., Huang, T.-S., Chen, Y.-S., Dou, H.-Y.
  DOI: 10.1111/j.1469-0691.2010.03436.x
- Journal Article Clinical implications of high MET gene dosage in non-small cell lung cancer patients without previous tyrosine kinase inhibitor treatment
  Chen, Y.-T., Chang, J.W.-C., Liu, H.-P., Yu, T.-F., Chiu, Y.-T., Hsieh, J.-J., Chen, Y.-T., Chen, Y.-R., Isaac Wu, H.-D., Huang, S.-F.
  DOI: 10.1097/JTO.0b013e3182307e92
2010
- Journal Article Prognostic implications of epidermal growth factor receptor and KRAS gene mutations and epidermal growth factor receptor gene copy numbers in patients with surgically resectable non-small cell lung cancer in Taiwan
  Liu, H.-P., Isaac Wu, H.-D., Chang, J.W.-C., Wu, Y.-C., Yang, H.-Y., Chen, Y.-T., Hsieh, W.-Y., Chen, Y.-T., Chen, Y.-R., Huang, S.-F.
  DOI: 10.1097/JTO.0b013e3181e2f4d6
- Journal Article Correlation between Klebsiella pneumoniae carrying pLVPK-derived loci and abscess formation
  Tang, H.-L., Chiang, M.-K., Liou, W.-J., Chen, Y.-T., Peng, H.-L., Chiou, C.-S., Liu, K.-S., Lu, M.-C., Tung, K.-C., Lai, Y.-C.
  DOI: 10.1007/s10096-010-0915-1
2009
- Journal Article Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis
  Wu, K.-M., Li, N.-H., Yan, J.-J., Tsao, N., Liao, T.-L., Tsai, H.-C., Fung, C.-P., Chen, H.-J., Liu, Y.-M., Wang, J.-T., Fang, C.-T., Chang, S.-C., Shu, H.-Y., Liu, T.-T., Chen, Y.-T., Shiau, Y.-R., Lauderdale, T.-L., Su, I.-J., Kirby, R., Tsai, S.-F.
  DOI: 10.1128/JB.00315-09
- Journal Article Genomic diversity of citrate fermentation in Klebsiella pneumoniae
  Chen, Y.-T., Liao, T.-L., Wu, K.-M., Lauderdale, T.-L., Yan, J.-J., Huang, I.-W., Lu, M.-C., Lai, Y.-C., Liu, Y.-M., Shu, H.-Y., Wang, J.-T., Su, I.-J., Tsai, S.-F.
  DOI: 10.1186/1471-2180-9-168
- Journal Article Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates
  Shu, H.-Y., Fung, C.-P., Liu, Y.-M., Wu, K.-M., Chen, Y.-T., Li, L.-H., Liu, T.-T., Kirby, R., Tsai, S.-F.
  DOI: 10.1099/mic.0.029017-0
- Journal Article Mobilization of qnrB2 and ISCR1 in plasmids
  Chen, Y.-T., Liao, T.-L., Liu, Y.-M., Lauderdale, T.-L., Yan, J.-J., Tsai, S.-F.
  DOI: 10.1128/AAC.00970-08
2008
- Journal Article 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
  Chang, J.W.-C., Liu, H.-P., Hsieh, M.-H., Fang, Y.-F., Hsieh, M.-S., Hsieh, J.-J., Chiu, Y.-T., Tsai, H.-Y., Chen, Y.-H., Chen, Y.-T., Hsu, H.-Y., Chen, Y.-T., Tsai, S.-F., Chen, Y.-R., Hsi, B.-L., Huang, S.-F.
  DOI: 10.1016/j.lungcan.2008.01.009
2007
- Journal Article Sequencing and comparative genomic analysis of pK29, a 269-kilobase conjugative plasmid encoding CMY-8 and CTX-M-3 β-lactamases in Klebsiella pneumoniae
  Chen, Y.-T., Lauderdale, T.-L., Liao, T.-L., Shiau, Y.-R., Shu, H.-Y., Wu, K.-M., Yan, J.-J., Su, I.-J., Tsai, S.-F.
  DOI: 10.1128/AAC.00167-07
2006
- Journal Article Complex mutation patterns of epidermal growth factor receptor gene associated with variable responses to gefitinib treatment in patients with non-small cell lung cancer
  Hsieh, M.-H., Fang, Y.-F., Chang, W.-C., Kuo, H.-P., Lin, S.-Y., Liu, H.-P., Liu, C.-L., Chen, H.-C., Ku, Y.-C., Chen, Y.-T., Chang, Y.-H., Chen, Y.-T., Hsi, B.-L., Tsai, S.-F., Huang, S.-F.
  DOI: 10.1016/j.lungcan.2006.06.005
- Journal Article Comparative analysis of alternative splicing events in human and mouse
  Liu, C.-H., Hsu, F.R., Chang, H.-Y., Shia, W.-C., Peng, H.-L., Chen, Y.T., Lin, Y.-L., Tsai, Y.-T.
- Journal Article Complete nucleotide sequence of pK245, a 98-kilobase plasmid conferring quinolone resistance and extended-spectrum-β-lactamase activity in a clinical Klebsiella pneumoniae isolate
  Chen, Y.-T., Shu, H.-Y., Li, L.-H., Liao, T.-L., Wu, K.-M., Shiau, Y.-R., Yan, J.-J., Su, I.-J., Tsai, S.-F., Lauderdale, T.-L.
  DOI: 10.1128/AAC.00456-06
2005
- Journal Article AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs
  Fang Rong Hsu, Hwan-You Chang, Yaw-Lin Lin, Yin-Te Tsai, Hui-Ling Peng, Ying Tsong Chen, Chia Yang Cheng, Min Yao Shih, Chia-Hung Liu, Chin-Feng Chen
  Bioinformation DOI: 10.6026/97320630001016
2004
- Journal Article Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43
  Chen, Y.-T., Chang, H.-Y., Lai, Y.-C., Pan, C.-C., Tsai, S.-F., Peng, H.-L.
  DOI: 10.1016/j.gene.2004.05.008
- Journal Article Evolutionary analysis of the two-component systems in Pseudomonas aeruginosa PAO1
  Chen, Y.-T., Chang, H.Y., Lu, C.L., Peng, H.-L.
  DOI: 10.1007/s00239-004-2663-2

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2026

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