Publications

Po-Hsiang Hung, Chia-Wei Liao, Fu-Hsuan Ko, Huai-Kuang Tsai, Jun-Yi Leu (2023). Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains. Iscience.

Kai-Li Chang, Jia-Hong Chen, Tzu-Chieh Lin, Jun-Yi Leu, Cheng-Fu Kao, Jin Yung Wong, Huai-Kuang Tsai (2023). Short human eccDNAs are predictable from sequences. Briefings in Bioinformatics.

Peng-Hsuan Li, Ting-Fu Chen, Jheng-Ying Yu, Shang-Hung Shih, Chan-Hung Su, Yin-Hung Lin, Huai-Kuang Tsai, Hsueh-Fen Juan, Chien-Yu Chen, Jia-Hsin Huang (2022). pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. Nucleic Acids Research.

Cheng-Kai Shiau, Jia-Hsin Huang, Yu-Ting Liu, Huai-Kuang Tsai (2022). Genome-wide identification of associations between enhancer and alternative splicing in human and mouse. BMC genomics.

Cheng-Hung Tsai, Tzu-Chieh Lin, Yi-Hsien Chang, Huai-Kuang Tsai, Jia-Hsin Huang (2022). Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states. BMC genomics.

Wei-Liang Liu, Chia-Wei Hsu, Shih-Peng Chan, Pei-Shi Yen, Matthew P. Su, Jian-Chiuan Li, Hsing-Han Li, Lie Cheng, Cheng-Kang Tang, Shih-Hsun Ko, Huai-Kuang Tsai, Zing Tsung-Yeh Tsai, Omar S. Akbari, Anna-Bella Failloux, Chun-Hong Chen (2021). Transgenic refractory Aedes aegypti lines are resistant to multiple serotypes of dengue virus.. Scientific Reports.

Wan-Chen Hsieh, En-Yu Lai, Yu-Ting Liu, Yi-Fu Wang, Yi-Shiuan Tzeng, Lu Cui, Yun-Ju Lai, Hsiang-Chi Huang, Jia-Hsin Huang, Hung-Chih Ni, Dong-Yan Tsai, Jian-Jong Liang, Chun-Che Liao, Ya-Ting Lu, Laurence Jiang, Ming-Tsan Liu, Jann-Tay Wang, Sui-Yuan Chang, Chung-Yu Chen, Hsing-Chen Tsai, Yao-Ming Chang, Gerlinde Wernig, Chia-Wei Li, Kuo-I Lin, Yi-Ling Lin, Huai-Kuang Tsai, Yen-Tsung Huang, Shih-Yu Chen (2021). NK cell receptor and ligand composition influences the clearance of SARS-CoV-2. The Journal of Clinical Investigation.

Ko-Han Lee, Yu-Chuan Chang, Ting-Fu Chen, Hsueh-Fen Juan, Huai-Kuang Tsai, Chien-Yu Chen (2021). Connecting MHC-I-binding motifs with HLA alleles via deep learning.. Communications Biology.

Jia-Hsin Huang, Yu-Ting Liu, Hung Chih Ni, Bo-Ye Chen, Shih-Ying Huang, Huai-Kuang Tsai, Hou-Feng Li (2021). Termite Pest Identification Method Based on Deep Convolution Neural Networks.. Journal of Economic Entomology.

Jia-Hsin Huang, You-Rou Liao, Tzu-Chieh Lin, Cheng-Hung Tsai, Wei-Yun Lai, Yang-Kai Chou, Jun-Yi Leu, Huai-Kuang Tsai, Cheng-Fu Kao (2021). iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover.. Nucleic Acids Research.

Meng-Jen Wu, Chih-Jung Chen, Ting-Yu Lin, Ying-Yuan Liu, Lin-Lu Tseng, Mei-Ling Cheng, Chih-Pin Chuu, Huai-Kuang Tsai, Wen-Ling Kuo, Hsing-Jien Kung, Wen-Ching Wang (2021). Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer.. Theranostics.

Sufeng Chiang, Hisaaki Shinohara, Jia Hsin Huang, Huai Kuang Tsai, Mariko Okada (2020). Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Letters.

Shin Yen Chong, Sam Cutler, Jing-Jer Lin, Cheng-Hung Tsai, Huai-Kuang Tsai, Sue Biggins, Toshio Tsukiyama, Yi-Chen Lo, Cheng-Fu Kao (2020). H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress.. Nature communications.

Chih-Yi Gabriela Lin, Ju-Lan Chao, Huai-Kuang Tsai, Douglas Chalker, Meng-Chao Yao (2019). Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophile. Nucleic Acids Research.

Cheng-Kai Shiau, Jia-Hsin Huang, Huai-Kuang Tsai (2018). CATANA: a tool for generating comprehensive annotations of alternative transcript events. Bioinformatics.

Jia-Hsin Huang, Ryan Shun-Yuen Kwan, Zing Tsung-Yeh Tsai, Tzu-Chieh Lin, Huai-Kuang Tsai (2018). Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome. Frontiers in Genetics.

I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Tsai (2017). IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes.. Database : the journal of biological databases and curation.

Wan Hsin Liu, Zing Tsung Yeh Tsai, Huai-Kuang Kuang Tsai, I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Kuang Tsai (2017). Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs. BMC Genomics.

Chiu-Lien Hung, Hsin-Hung Cheng, Wan-Chen Hsieh, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Chia-Han Chu, Wen-Ping Hsieh, Yi-Fan Chen, Yu Tsou, Chih-Ho Lai, Wen-Ching Wang (2015). The CrdRS two-component system in Helicobacter pylori responds to nitrosative stress.. Molecular microbiology.

Jen-Hao Cheng, David Zhi-Chao Pan, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai (2015). Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues. Scientific Reports.

Zing Tsung-Yeh Tsai, Shin-Han Shiu, Huai-Kuang Tsai (2015). Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. PLOS Computational Biology.

Zing Tsung-Yeh Tsai, Wen-Yi Chu, Jen-Hao Cheng, Huai-Kuang Tsai (2013). Associations between intronic non-B DNA structures and exon skipping. Nucleic Acids Research.

Yi-Ching Chen, Jen-Hao Cheng, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Trees-Juen Chuang (2013). The impact of trans-regulation on the evolutionary rates of metazoan proteins.. Nucleic acids research.

Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai (2012). The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes. IEEE/ACM Trans. Comput. Biol. Bioinformatics.

Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Jen-Hao Cheng, Chih-Hsu Lin, Yuan-Fan Tsai, Daryi Wang (2012). Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. BMC Genomics.

Mei-Ju May Chen, Lih-Ching Chou, Tsung-Ting Hsieh, Ding-Dar Lee, Kai-Wei Liu, Chi-Yuan Yu, Yen-Jen Oyang, Huai-Kuang Tsai, Chien-Yu Chen (2012). De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. Bioinformatics.

Sufeng Chiang, Krishna B S Swamy, Ting-Wei Hsu, Zing Tsung-Yeh Tsai, Henry Horng-Shing Lu, Daryi Wang, Huai-Kuang Tsai (2012). Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast.. Gene.

Tse-Yi Wang, Chien-Hao Su, Huai-Kuang Tsai (2011). MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions. Bioinformatics.

Chien-Hao Su, Ming-Tsung Hsu, Tse−Yi Wang, Sufeng Chiang, Jen-Hao Cheng, Francis C Weng, Cheng−Yan Kao, Daryi Wang, Huai-Kuang Tsai (2011). MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering. Bioinformatics.

Krishna B S Swamy, Wen-Yi Chu, Chun-Yi Wang, Huai-Kuang Tsai, Daryi Wang (2011). Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast. BMC Evolutionary Biology.

Chien-Hao Su, Ching-Hua Shih, Tien-Hsien Chang, Huai-Kuang Tsai (2010). Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast.. Genomics.

Francis C Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai, Daryi Wang (2010). Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.. BMC bioinformatics.

Krishna B S Swamy, Chung-Yi Cho, Sufeng Chiang, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai (2009). Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Research.

Huai-Kuang Tsai, Pei-Ying Huang, Cheng-Yan Kao, Daryi Wang (2009). Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.. International journal of molecular sciences.

Huang-Mo Sung, Tzi-Yuan Wang, Daryi Wang, Yu-Shan Huang, Jen-Pey Wu, Huai-Kuang Tsai, Jengnan Tzeng, Chih-Jen Huang, Yi-Chen Lee, Peggy Yang, Joyce Hsu, Tiffany Chang, Chung-Yi Cho, Li-Chuan Weng, Tso-Ching Lee, Tien-Hsien Chang, Wen-Hsiung Li, Ming-Che Shih (2009). Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene Expression. Molecular Biology and Evolution.

Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, Yuh-Jyh Hu, Jinn-Moon Yang (2008). Evolutionary conservation of DNA-contact residues in DNA-binding domains.. BMC bioinformatics.

Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, Mei-Ju May Chen, Hao-Geng Hung, Grace Tzu-Wei Huang, Wen-Hsiung Li (2008). Discovering gapped binding sites of yeast transcription factors.. Proceedings of the National Academy of Sciences of the United States of America.

Huai-Kuang Tsai, Cindy P C Su, Mei-Yeh J Lu, Ching-Hua Shih, Daryi Wang (2007). Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system.. BMC genomics.

Huai-Kuang Tsai, Meng-Yuan Chou, Ching-Hua Shih, Grace Tzu-Wei Huang, Tien-Hsien Chang, Wen-Hsiung Li (2007). MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.. Nucleic acids research.

Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing Lu, Wen-Hsiung Li (2006). Method for identifying transcription factor binding sites in yeast.. Bioinformatics (Oxford, England).

Huai-Kuang Tsai, Henry Horng-Shing Lu, Wen-Hsiung Li (2005). Statistical methods for identifying yeast cell cycle transcription factors.. Proceedings of the National Academy of Sciences of the United States of America.

East Zhao, Hsuan-Liang Liu, Chi-Hung Tsai, Huai-Kuang Tsai, Chen-hsiung Chan, Cheng-Yan Kao (2005). Cysteine separations profiles on protein sequences infer disulfide connectivity.. Bioinformatics (Oxford, England).

Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fang Tsai, Cheng-Yan Kao (2004). An evolutionary algorithm for large traveling salesman problems. IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fang Tsai, Cheng-Yan Kao (2004). An evolutionary approach for gene expression patterns.. IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society.

H.-K. Tsai, J.-M. Yang, Y.-F. Tsai, C.-Y. Kao (2004). Some issues of designing genetic algorithms for traveling salesman problems. Soft Computing.

Yu Cheng Huang, Han Yu Chuang, Huai Kuang Tsai, Chun Fan Chang, Cheng Yan Kao (2004). Designing multiple-use primer set for multiplex PCR by using compact GAs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).

Huai Kuang Tsai, Jinn Moon Yang, Yuan Fang Tsai, Cheng Yan Kao (2003). Heterogeneous selection genetic algorithms for traveling salesman problems. Engineering Optimization.

Jinn-Moon Yang, Chi-Hung Tsai, Ming-Jing Hwang, Huai-Kuang Tsai, Jenn-Kang Hwang, Cheng-Yan Kao (2002). GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations.. Protein science : a publication of the Protein Society.