Publications

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 ,Bioinformatics Advances ,3,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 & Bioscience ,13.

2022

• Wei-Jan Wang, Yeh Chen, Wen-Chi Su, Yen-Yi Liu (co-first author), Wan-Jou Shen, Wei-Chao Chang, Shen,Peimine inhibits variants of SARS-CoV-2 cell entry via blocking the interaction between viral spike protein and ACE2,Journal of Food Biochemistry.

• 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 Research,50.

• 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,17.

• 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,Journal of Microbiology, Immunology and Infection,55,102~106.

• Yi-Chuan Li, Hirohito Yamaguchi, Yen-Yi Liu (co-first author), Kai-Cheng Hsu, Ting-Hsuan Sun, Pei-Chi Sun, Mien-Chie H,Structural insights into EphA4 unconventional activation from prediction of the EphA4 and its complex with ribonuclease 1,American Journal of Cancer Research, 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 ,38,4428-4429.

• Hsiao-Fan Chen, Po-Ren Hsueh, Yen-Yi Liu (co-first author), Yeh Chen, Sui-Yuan Chang, Wei-Jan Wang, Chen-,Disulfiram blocked cell entry of SARS-CoV-2 via inhibiting the interaction of spike protein and ACE2 ,American Journal of Cancer Research ,12,3333-3346.

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, 16.

• 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, 9.

• 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,13.

2020

• Min-Chi Lu, Ying-Tsong Chen, Hui-Ling Tang, Yen-Yi Liu, Bo-Han Chen, You-Wun Wang, Yi-Syong Chen, Ru, Transmission and evolution of OXA-48-producing Klebsiella pneumoniae ST11 in a single hospital in Taiwan, Journal of Antimicrobial Chemotherapy, 75, 318~326.

2019

• Yueh-Hua Tu, Bo-Han Chen, Yu-Ping Hong, Ying-Shu Liao, Yi-Syong Chen, Yen-Yi Liu, Ru-Hsiou Teng, You,Emergence of Vibrio cholerae O1 sequence type 75 in Taiwan,Emerging infectious diseases,26,164-166.

• Ying-Shu Liao, Bo-Han Chen, Yu-Ping Hong, Ru-Hsiou Teng, You-Wun Wang, Shiu-Yun Liang, Yen-Yi Liu, Y,Emergence of multidrug-resistant Salmonella enterica serovar Goldcoast strains in Taiwan and international spread of the ST358 clone,Antimicrobial agents and chemotherapy,63.

• 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, 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 ,7.

• 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 ,7.

• Yen-Yi Liu, Ji-Wei Lin, Chih-Chieh Chen,cano-wgMLST_BacCompare: a bacterial genome analysis platform for epidemiological investigation and comparative genomic analysis,Frontiers in microbiology, 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-,Genetic relationships among multidrug-resistant Salmonella enterica serovar Typhimurium strains from humans and animals,Antimicrobial agents and chemotherapy,62.

2017

• Yen-Yi Liu, Chih-Chieh Chen,Computational analysis of the molecular mechanism of RamR mutations contributing to antimicrobial resistance in Salmonella enterica,Scientific reports,7,1~9.

• Ming-Hsin Tsai, Yen-Yi Liu (co-first author), Von-Wun Soo,PathoBacTyper: a web server for pathogenic bacteria identification and molecular genotyping,Frontiers in Microbiology,8.

• Chien-Shun Chiou, Ying-Tsong Chen, You-Wun Wang, Yen-Yi Liu, Hung-Chih Kuo, Yeuh-Hua Tu, Ann-Chi Lin,Dissemination of mcr-1-Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals in Taiwan,Antimicrobial agents and chemotherapy,61.

• 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,Emerging infectious diseases,23.

2016

• 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,Frontiers in microbiology,7.

• 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,Scientific reports,6,1~5.

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,International journal of food microbiology,214.

• Chien-Shun Chiou, Munirul Alam, Jung-Che Kuo, Yen-Yi Liu, Pei-Jen Wang,Chromosome-mediated multidrug resistance in Salmonella enterica serovar Typhi,Antimicrobial agents and chemotherapy,59,721~723.

2014

• Chiou CS, Lauderdale TL, Phung DC, Watanabe H, Kuo JC, Wang PJ, Liu YY, Liang SY, Chen PC. Antimicrobial resistance in Salmonella enterica Serovar Typhi isolates from Bangladesh, Indonesia, Taiwan, and Vietnam. Antimicrob Agents Chemother. 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. 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. 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. 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;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;416(1):27-36.