2025
Zhong-Wei Ke, Chiu-Lan Hsieh, Yen-Yi Liu. Characterization of microbial communities degrading natural organic compounds in activated sludge through 16S rRNA sequencing and mass spectrometry. Environ Sci Pollut Res Int. 2025 Oct;32(46):26501-26512.
Yen-Yi Liu, Chi-Ching Lee, Pei-Hsuan Li, Sung-Huan Yu, Mien-Chie Hung, Hsin-Mien Hsu, Chih-Chao Yang, Chen-Chieh Huang, Pei-Yao Kuo, Yi-Chuan Li. AlphaPPIweb: an integration platform for protein-protein interaction prediction and evaluation. Am J Cancer Res. 2025 Sep 15;15(9):3980-3989.
2023
Yen-Yi Liu, Chu-Yi Hsu, Ya-Chu Yang, Chien-Hsun Huang, Chih-Chieh Chen, ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains. Bioinform Adv. 2023 Oct 18;3(1):vbad153.
Chen-Shiou Wu, Yi-Chuan Li, Shin-Lei Peng, Chung-Yu Chen, Hsiao-Fan Chen, Po-Ren Hsueh, Wei-Jan Wang, Yen-Yi Liu, Ciao-Ling Jiang, Wei-Chao Chang, Shao-Chun Wang & Mien-Chie Hung, Coffee as a dietary strategy to prevent SARS-CoV-2 infection. Cell Biosci. 2023 Nov 14;13(1):210.
2022
Wei-Jan Wang, Yeh Chen, Wen-Chi Su, Yen-Yi Liu, Wan-Jou Shen, Wei-Chao Chang, Sheng-Teng Huang, Cheng-Wen Lin, Yu-Chuan Wang, Chia-Shin Yang, Mei-Hui Hou, Yu-Chi Chou, Yang-Chang Wu, Shao-Chun Wang, Mien-Chie Hung, Peimine inhibits variants of SARS-CoV-2 cell entry via blocking the interaction between viral spike protein and ACE2. J Food Biochem. 2022 Oct;46(10):e14354.
Chih-Chieh Chen, Yen-Yi Liu, Ya-Chu Yang, Chu-Yi Hsu, 5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. Nucleic Acids Res. 2022 Jul 5;50(W1):W21-W28.
Yen-Yi Liu, Chih-Chieh Chen, Chien-Hua Yang, Hui-Yi Hsieh, Jia-Xin He, Hao-Hsuan Lin, Chi-Ching Lee, LmTraceMap: A Listeria monocytogenes fast-tracing platform for global surveillance. PLoS One. 2022 May 9;17(5):e0267972.
Yi-Syong Chen, Yueh-Hua Tu, Bo-Han Chen, Yen-Yi Liu, Yu-Ping Hong, Ru-Hsiou Teng, You-Wun Wang, Chie, cgMLST@Taiwan: A web service platform for Vibrio cholerae cgMLST profiling and global strain tracking. J Microbiol Immunol Infect. 2022 Feb;55(1):102-106.
Yi-Chuan Li, Hirohito Yamaguchi, Yen-Yi Liu (co-first author), Kai-Cheng Hsu, Ting-Hsuan Sun, Pei-Chi Sun, Mien-Chie Hung, Structural insights into EphA4 unconventional activation from prediction of the EphA4 and its complex with ribonuclease 1. Am J Cancer Res. 2022 Oct 15;12(10):4865-4878.
Chih-Hao Lu, Chih-Chieh Chen, Chin-Sheng Yu, Yen-Yi Liu, Jia-Jun Liu, Sung-Tai Wei, Yu-Feng Lin, MIB2: metal ion-binding site prediction and modeling server. Bioinformatics. 2022 Sep 15;38(18):4428-4429.
Hsiao-Fan Chen, Po-Ren Hsueh, Yen-Yi Liu (co-first author), Yeh Chen, Sui-Yuan Chang, Wei-Jan Wang, Chen-Shiou Wu, Ya-Min Tsai, Yu-Shu Liu, Wen-Chi Su, Yu-Chi Chou, Mien-Chie Hung, Disulfiram blocked cell entry of SARS-CoV-2 via inhibiting the interaction of spike protein and ACE2. Am J Cancer Res. 2022 Jul 15;12(7):3333-3346.
2021
Yen-Yi Liu, Chih-Chieh Chen, A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking. PLoS One. 2021 Nov 19;16(11):e0260293.
Yen-Yi Liu, Bo-Han Chen, Chih-Chieh Chen, Chien-Shun Chiou, Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. PeerJ. 2021 Aug 19;9:e11842.
Ming-Ko Chiang, Pei-Yi Hsiao, Yen-Yi Liu, Hui-Ling Tang, Chien-Shun Chiou, Min-Chi Lu, Yi-Chyi Lai, Two ST11 Klebsiella pneumoniae strains exacerbate colorectal tumorigenesis in a colitis-associated mouse model. Gut Microbes. 2021 Jan-Dec;13(1):1980348.
2020
Min-Chi Lu, Ying-Tsong Chen, Hui-Ling Tang, Yen-Yi Liu, Bo-Han Chen, You-Wun Wang, Yi-Syong Chen, Ru-Hsiou Teng, Yu-Ping Hong, Chien-Shun Chiou, Ming-Ko Chiang, Yi-Chyi Lai, 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.
Yueh-Hua Tu, Bo-Han Chen, Yu-Ping Hong, Ying-Shu Liao, Yi-Syong Chen, Yen-Yi Liu, Ru-Hsiou Teng, You-Wun Wang, Chien-Shun Chiou, Emergence of Vibrio cholerae O1 Sequence Type 75 in Taiwan. Emerg Infect Dis. 2020 Jan;26(1):164-166.
2019
Ying-Shu Liao, Bo-Han Chen, Yu-Ping Hong, Ru-Hsiou Teng, You-Wun Wang, Shiu-Yun Liang, Yen-Yi Liu, Yueh-Hua Tu, Yi-Syong Chen, Jui-Hsien Chang, Chi-Sen Tsao, Chien-Shun Chiou, Emergence of Multidrug-Resistant Salmonella enterica Serovar Goldcoast Strains in Taiwan and International Spread of the ST358 Clone. Antimicrob Agents Chemother. 2019 Sep 23;63(10):e01122-19.
Ming-Hsin Tsai, Yen-Yi Liu (co-first author), Chih-Chieh Chen, OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling. PeerJ. 2019 Aug 28;7:e7600.
Ming-Hsin Tsai, Yen-Yi Liu (co-first author), Von-Wun Soo, Chih-Chieh Chen, A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy. Microorganisms. 2019 Jun 3;7(6):161.
Yen-Yi Liu, Ji-Wei Lin, Chih-Chieh Chen, The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains. Microorganisms. 2019 Apr 3;7(4):98.
Yen-Yi Liu, Ji-Wei Lin, Chih-Chieh Chen, cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis. Front Microbiol. 2019 Jul 24;10:1687.
2018
Yu-Ping Hong, You-Wun Wang, I-Hsiu Huang, Yu-Chieh Liao, Hung-Chih Kuo, Yen-Yi Liu, Yueh-Hua Tu, Bo-Han Chen, Ying-Shu Liao, Chien-Shun Chiou, Genetic Relationships among Multidrug-Resistant Salmonella enterica Serovar Typhimurium Strains from Humans and Animals. Antimicrob Agents Chemother. 2018 Apr 26;62(5):e00213-18.
2017
Yen-Yi Liu, Chih-Chieh Chen, Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica. Sci Rep. 2017 Oct 17;7(1):13418.
Ming-Hsin Tsai, Yen-Yi Liu (co-first author), PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping. Front Microbiol. 2017 Aug 3;8:1474.
Chien-Shun Chiou, Ying-Tsong Chen, You-Wun Wang, Yen-Yi Liu, Hung-Chih Kuo, Yeuh-Hua Tu, Ann-Chi Lin, Ying-Shu Liao, Yu-Ping Hong, Dissemination of mcr-1-Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals in Taiwan. Antimicrob Agents Chemother. 2017 Jun 27;61(7):e00338-17.
2016
Ying-Shu Liao, Yen-Yi Liu, Yi-Chun Lo, Chien-Shun Chiou, Azithromycin-Nonsusceptible Shigella flexneri 3a in Men Who Have Sex with Men, Taiwan, 2015-2016. Emerg Infect Dis. 2016 Feb;23(2):345-346.
Yen-Yi Liu, Chih-Chieh Chen, Chien-Shun Chiou, Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification. Front Microbiol. 2016 Dec 15;7:2010.
Yen-Yi Liu, Chien-Shun Chiou, Chih-Chieh Chen, PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing. Sci Rep. 2016 Nov 8;6:36213.
2015
Chien-Shun Chiou, Mia Torpdahl, Ying-Shu Liao, Chun-Hsing Liao, Chi-Sen Tsao, Shiu-Yun Liang, You-Wun Wang, Jung-Che Kuo, Yen-Yi Liu, Usefulness of pulsed-field gel electrophoresis profiles for the determination of Salmonella serovars. Int J Food Microbiol. 2015 Dec 2;214:1-3.
Chien-Shun Chiou, Munirul Alam, Jung-Che Kuo, Yen-Yi Liu, Pei-Jen Wang, Chromosome-mediated multidrug resistance in Salmonella enterica serovar Typhi. Antimicrob Agents Chemother. 2015 Jan;59(1):721-3.
2014
Chien-Shun Chiou, Tsai-Ling Lauderdale, Dac Cam Phung, Haruo Watanabe, Jung-Che Kuo, Pei-Jen Wang, Yen-Yi Liu, Shiu-Yun Liang, Pei-Chen Chen, Antimicrobial resistance in Salmonella enterica Serovar Typhi isolates from Bangladesh, Indonesia, Taiwan, and Vietnam. Antimicrob Agents Chemother. 2014 Nov;58(11):6501-7.
2013
Chih-Chieh Chen, Tze-Kiong Er, Yen-Yi Liu, Jenn-Kang Hwang, Maria Jesus Barrio, Maximiliano Rodrigo, Enrique Garcia-Toro, Marta Herreros-Villanueva. Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations. PLoS One. 2013;8(2):e55793.
2012
Wei-Cheng Lo, Li-Fen Wang, Yen-Yi Liu, Tian Dai, Jenn-Kang Hwang, Ping-Chiang Lyu. CPred: a web server for predicting viable circular permutations in proteins. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W232-7.
Wei-Cheng Lo, Tian Dai, Yen-Yi Liu, Li-Fen Wang, Jenn-Kang Hwang, Ping-Chiang Lyu. Deciphering the preference and predicting the viability of circular permutations in proteins. PLoS One. 2012;7(2):e31791.
2011
Tze-Kiong Er, Chih-Chieh Chen, Yen-Yi Liu, Hui-Chiu Chang, Yin-Hsiu Chien, Jan-Gowth Chang, Jenn-Kang Hwang, Yuh-Jyh Jong. Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC Struct Biol. 2011 Oct 21;11:43.
2008
Jung-Yu Tung, Margaret Dah-Tsyr Chang, Wei-I Chou, Yen-Yi Liu, Yi-Hung Yeh, Fan-Yu Chang, Shu-Chuan Lin, Zhen-Liang Qiu, Yuh-Ju Sun. Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path. Biochem J. 2008 Nov 15;416(1):27-36.