中文版
English
研究員  |  蔡懷寬  
 
contact
vita
education
experience
interests
descriptions
activities
invited_talk
invited_visit
honors
grants
publications
software
others
supervised
lab (New window)
 
 
 
 
 
Publications
 
Journal Articles
 
1. Chen, Y.H., Chao, K.H., Wong, J.Y., Liu, C.F., , Leu, J.Y.* and Tsai, H.K.*, "A feature extraction free approach for protein interactome inference from co-elution data," Briefings in Bioinformatics, pages bbad229, June 2023.
2. Lin, T.C., Liu, Y.L., Liu, Y.T., Liu, W.H., Liu, Z.Y., Chang, K.L., Chang, C.Y., Ni, H.C., Huang, J.H., and Tsai, H.K.*, "TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes," NAR Genomics and Bioinformatics, volume 5, number 2, pages lqad043, May 2023.
3. Hung, P.H., Liao, C.W., Ko, F.H., Tsai, H.K.* and Leu, J.Y.*, "Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains," iScience, volume 26, pages 106635, May 2023.
4. Chang, K.L., Chen, J.H., Lin, T.C., Leu, J.Y., Kao, C.F., Wong, J.Y.*, Tsai, H.K.*, "Short human eccDNAs are predictable from sequences," Briefings in Bioinformatics, pages bbad147, April 2023.
5. Li, P.H., Chen, T.F., Yu, J.Y., Shih, S.H., Su, C.H., Lin, Y.H., Tsai, H.K., Juan, H.F., Chen, C.Y. and Huang, J.H., "pubmedKB: an interactive web server to explore biomedical entity relations from biomedical literature," Nucleic Acids Research, volume 50, number (W1), pages W616–W622, July 2022.
6. Liu, W.L., Hsu, C.W., Yen, P.S., Su, P., Li, J.C, Li, H.H., Tsai, H.K., Tsai, TY., Failloux, A.B., and Chen, C.H., "Transgenic refractory Aedes aegypti lines are resistant to multiple serotypes of dengue virus," Scientific Reports, volume 11, pages 23865, December 2021.
7. Shiau, C.K., Huang, J.H., Liu, Y.T. and Tsai, H.K.*, "Genome-wide identification of associations between enhancer and alternative splicing in human and mouse.," BMC Genomics, volume 22, pages 919, November 2021.
8. Tsai C.H., Lin T.Z., Chang Y.H., Tsai H.K.* and Huang J.H.*, "Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states.," BMC Genomics, volume 22, pages 917, November 2021.
9. Hsieh, W.C., Lai, E.Y., Liu, Y.T., Wang, Y.F., Tzeng, Y.S., Cui, L., Lai, Y.J., Huang, H.C., Huang, J.H., Ni, H.C., Tsai, D.Y., Liang, J.J., Liao, C.C., Lu, Y.T., Jiang, L., Liu, M.T., Wang, J.T., Chang, S.Y., Chen, C.Y., Tsai, H.C., Chang, Y.M., Wernig, G., Li, C.W., Lin, K.I., Lin, Y.L., Tsai, H.K., Huang, Y.T., Chen, S.Y., "NK cell receptor and ligand composition influences the clearance of SARS-CoV-2," The Journal of Clinical Investigation, volume 131, number 21, pages e146408, October 2021.
10. Lee, K.H., Chang, Y.C., Chen, T.F., Juan, H.F., Tsai, H.K., Chen, C.Y., "Connecting MHC-I-binding motifs with HLA alleles via deep learning," Communications Biology, volume 4, number 194, pages 194, October 2021.
11. Huang, J.H., Liu, Y.T., Ni, H.C., Chen, B.Y., Huang, S.Y., Tsai, H.K.*, and Li, H.F.*, "Termite pest identification method based on deep convolution neural networks," Journal of Economic Entomology, volume toab162, August 2021.
12. Huang J.H., Liao, Y.R., Lin, T.C., Tsai, C.H., Lai, W.Y., Chou, Y.K., Leu, J.Y., Tsai, H.K.*, and Kao, C.F.*, "iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover," Nucleic Acids Research, pages gkab555, July 2021.
13. Wu, M.J., Chen, C.J., Lin, T.Y.,Liu, Y.Y., Tseng, L.L., Cheng, M.L., Chuu, C.P., Tsai, H.K., Kuo, W.L., Kung, H.J., and Wang, W.C., "Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer," Theranostics, volume 11, number 16, pages 7779-7796, July 2021.
14. Chong, S.Y., Sutler, S., Lin, J.J., Tsai, C.H., Tsai, H.K., Biggins, S., Tsukiyama, T., Lo, Y.C., and Kao, C.F., "H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress," Nature Communications, volume 11, pages 809, February 2020.
15. Chiang, S., Shinohara, H., Huang, J.H., Tsai, H. K.*, and Okada, M.*, "Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach," FEBS Letters, volume doi: 10.1002/1873-3468, pages 13757, February 2020. :::icon
16. Lin, C.Y., Chao, J.L., Tsai, H.K., Chalker, D., and Yao, M.C., "Setting Boundaries for Genome-wide Heterochromatic DNA Deletions Through Flanking Inverted Repeats in Tetrahymena thermophila," Nucleic Acids Research, volume 47, number 10, pages 5181-92, June 2019.
17. Huang, J.H., Kwan, SY. Tsai, T.Y., Lin, T.C., and Tsai, H.K.*, "Borders of cis-regulatory DNA sequences preferentially harbor the divergent transcription factor binding motifs in the human genome," Frontiers in Genetics, volume 9, pages 571, November 2018.
18. Shiau, C.K., Huang, J.H. and Tsai, H.K.*, "CATANA: Comprehensive Alternative Transcript Atlas based oN Annotation," Bioinformatics, volume bty795, pages bty795, September 2018.
19. Liu, W.H., Tsai, Z. T., and Tsai, H. K.*, "Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs," BMC Genomics, volume 18, pages 786, October 2017. :::icon
20. Ng, I.M. , Huang, J.H., Tsai, S.C., and Tsai, H.K.*, "IsoPlot: a database for comparison of mRNA isoform variations in the fruit fly and mosquitoes," Database, volume Volume 2017,, pages bax069, August 2017.
21. Tsai, Z.T.Y., Shiu, S.H.*, and Tsai, H.K.*, "Contribution of sequence motif, chromatin state, and DNA structure features to predictive models of transcription factor binding in yeast," PLoS Computational Biology, volume 11, number 8, pages e1004418, August 2015. :::icon
22. Cheng, J.H., Pan D., Tsai, Z.T.Y., and Tsai, H.K.*, "Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues," Scientific Reports, volume 5, pages 12648, July 2015. :::icon
23. Hung, C.L., Cheng, H.H., Hsieh, W.C., Tsai, Z.T.Y., Tsai, H.K., Chu, C.H., Hsieh, W.P., Lai, C.H., and Wang, W.C.*, "The CrdRS two-component system in Helicobacter pylori responds to nitrosative stress," Molecular Microbiology, volume doi: 10.1111, pages /mmi.13089, June 2015.
24. Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.*, "Associations between intronic non-B DNA structures and exon skipping," Nucleic Acids Research, volume 42, number 2, pages 739-747, January 2014.
25. Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K.*, and Chuang T.J.*, "The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins," Nucleic Acids Research, volume 41, number 13, pages 6371-80, May 2013.
26. Tsai, Z.T.Y., Tsai, H.K.*, Cheng, J.H., Lin, C.H., Tsai, Y.F. and Wang, D.*, "Evolution of cis-regulatory elements in yeast de novo and duplicated new genes," BMC Genomics, volume 13, pages 717, December 2012.
27. Su, C.H., Wang, T.Y., Hsu, M.T., Weng, F., Kao, C.Y., Wang, D., and Tsai, H.K., "The impact of normalization and phylogenetic information on estimating the distance metrics for metagenomes," IEEE Transactions on Computational Biology and Bioinformatics, volume 9, number 2, pages 619-628, April 2012.
28. Chen, M.J., Chou, L.C., Hsieh, T.T., Lee, D.D., Liu, K.W., Yu, C.Y., Oyang, Y.J., Tsai, H.K.* and Chen, C.Y.*, "De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae," Bioinformatics, volume 28, pages 701-708, January 2012.
29. Chiang, S., Swamy, B.S. K., Hsu, T.W., Tsai, Z. T.Y., Lu, H.S., Wang, D., and Tsai, H.K.*, "Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast," Gene, volume 491, pages 237-245, January 2012.
30. Wang, T.Y., Su, C.H. and Tsai, H.K.*, "MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions," Bioinformatics, volume 27, number 24, pages 3341-3347, November 2011.
31. Su, C.H., Hsu, M.T., Wang, T.Y., Weng, F., Kao, C.Y., Wang, D., and Tsai, H.K.*, "MetaABC – an integrated Metagenomics platform for data Adjustment, Binning, and Clustering," Bioinformatics, volume 27, number 16, pages 2298-2299, June 2011.
32. Swamy, B.S. K., Chu, W.Y., Wang, C.Y., Tsai, H.K.*, and Wang, D., "Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast," BMC Evolutionary Biology, volume 11:150, May 2011.
33. Su, C.H., Shih, C.H., Chang, T.H. and Tsai, H.K.*, "Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast," Genomics, volume 96, pages 352-361, December 2010.
34. Weng, F., Su, C.-H., Hsu, M.-T., Wang, T.-Y., Tsai, H.-K.* and Wang, D.*, "Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency," BMC Bioinformatics, volume 11, number 565, November 2010.
35. Swamy, B. S. K., Cho, C.Y., Chiang, S., Tsai, Z. T.Y., and Tsai, H.K. *, "Impact of DNA binding position variants on yeast gene expression," Nucleic Acids Research, volume 37, number 21, pages 6991-7001, December 2009. :::icon
36. Sung, H.M., Wang, T.Y., Wang, D., Huang, Y.S., Wu, J.P., Tsai, H.K., Tzeng, J., Huang, C.J., Lee, Y.C., Yang, P. et al., "Roles of Trans and Cis Variation in Yeast Intra-species Evolution of Gene Expression.," Molecular Biology and Evolution, volume 26, number 11, pages 2533-2538, November 2009. :::icon
37. Tsai, H.K.,, Huang, P.Y., Kao, C.Y. and Wang, Daryi, "Co-expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome," International Journal of Molecular Sciences, volume 10, pages 3658-3670, August 2009.
38. Chang, Y.L.*, Tsai, H.K*., Kao, C.Y., Chen, Y.C., and Yang, J.M. (*Contributed equally), "Evolutionary conservation of DNA-contact residues in DNA-binding domains," BMC Bioinformatics, volume 9, pages S3, May 2008.
39. Chen, C.Y., Tsai, H.K., Hsu, C.M., Chen, M.J. May, Hung, H.G., Huang, G.T., and Li, W.H., "Discovering gapped binding sites of yeast transcription factors," Proceedings of the National Academy of Sciences (USA), volume 105, number 7, pages 2527-2532, February 2008.
40. Tsai, H.K., Su, Cindy, P.C., Lu, M.J., Shih, C.H., and Wang, Daryi., "Co-expression of adjacent genes in yeast can not be simply attributed to shared regulatory system," BMC Genomics, volume 8:352., October 2007, http://www.biomedcentral.com/1471-2164/8/352/abstract
41. Tsai, H.K., Chou, M.Y., Shih, C. H., Huang, Grace T. W., Chang, T. H. and Li, W.H., "MYBS: A comprehensive web server for mining transcription factor binding sites in yeast," Nucleic Acids Research, volume 35, pages W221-W226, July 2007.
42. Tsai, H.K., Huang, Grace T., Chou, M.Y., Lu, Henry, H.S. and Li, W.H., "Method for identifying transcription factor binding sites in yeast," Bioinformatics, volume 22, pages 1675-1681, July 2006. :::icon
43. Tsai, H.K., Lu, H.H. and Li, W.H, "Statistical methods for identifying yeast cell cycle transcription factors," Proceedings of the National Academy of Sciences (USA), volume 102, pages 13532-13537, September 2005. :::icon
44. Zhao, E., Liu, H.L., Tsai, C.H., Tsai, H.K., Chan, C.H. and Kao, C.Y., "Cysteine separations profiles on protein sequences infer disulfide connectivity," Bioinformatics, volume 21, pages 1415-1420, 2005. :::icon
45. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y., "An evolutionary algorithm for large traveling salesman problems," IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics, volume 34, pages 1718-1729, 2004. :::icon
46. Huang Y.C., Chuang H.Y., Tsai, H.K., Chang C.F. and Kao C.Y., "Designing multiple-use primer set for multiplex PCR by using compact GAs," Lecture Notes in Computer Science, volume 3242, pages 511-523, 2004.
47. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y., "An evolutionary approach for gene expression patterns," IEEE Transactions on Information Technology in Biomedicine, volume 8, pages 69-78, 2004. :::icon
48. Tsai, Y.F., Tsai, H.K. and Kao, C.Y., "Clustering analysis of debris flow streams," International Journal of Sediment Research, volume 19, pages 37-46, 2004.
49. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y., "Some issues of designing genetic algorithms for traveling salesman problems," Soft Computing, volume 8, pages 689-697, 2004.
50. Chuang, H.Y., Tsai, H.K., Tsai, Y.F. and Kao, C.Y., "Ranking genes for discriminability on microarray data," Journal of Information Science and Engineering, volume 19, pages 953-966, 2003.
51. Tsai, H.K., Yang, J.M., Tsai, Y.F. and Kao, C.Y., "Heterogeneous selection genetic algorithms for traveling salesman problems," Engineering Optimization, volume 35, pages 297-311, 2003.
52. Yang, J.M., Tsai, C.H., Hwang, M.J., Tsai, H.K., Hwang, J.K. and Kao, C.Y., "GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations," Protein Science, volume 11, pages 1897-1907, 2002.
53. Tsai, Y.F., Tsai, H.K. and Shieh, C.L., "Hazard zone mapping of debris flow," The Chinese Journal of Mechanics, part B, volume 18, pages 91-102, 2002, (in Chinese)
 
 
Conference Papers
 
1. Huang JH, Liu YT, Ni HC, Chen BY, Huang SY, Tsai HK, and Li HF., "Smartphone image-based identification of four major termite pest species by using deep learning," Proceedings in the 13th Conference of The Pacific Rim Termite Research Group, pages 166-172, February 2020.
2. Kwan, S.Y., Huang, J.H., Tsai, Z.T.Y. and Tsai, H.K.*, "Dynamics of cis-regulatory regions for introducing the divergent transcription factor motifs in the human genome," 50th Anniversary of the Neutral Theory of Molecular Evolution (SMBE), Yokohama, Japan, July 2018.
3. Shiau, C.K., Huang, J.H. and Tsai, H.K.*, "CATANA: Comprehensive Alternative Transcript Atlas based oN Annotation," 50th Anniversary of the Neutral Theory of Molecular Evolution (SMBE), Yokohama, Japan, July 2018.
4. Chiang, S., Shimodaira, H., Tsai, H.K.*, and Okada M.*, "Dissecting the transcriptional response of the antigen-stimulated B cells using a generalized multiplicative decomposition model (GMDM)," The 17th International Conference on Systems Biology (ICSB), September 2016.
5. Hung, P.H., Tsai, H.K., and Leu, J.Y., "Identification of cryptic genetic variations buffered by HSP90 in wild yeast populations," The 17th International Conference on Systems Biology (ICSB), September 2016.
6. Liu, W.H., Tsai, Z. T., and Tsai, H. K.*, "Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs," RNA, June 2016.
7. Tsai, Z. T.Y., Huang, G. T.W., and Tsai, H.K.*, "Simultaneous identification for synergistic transcription factors and their transcription factor binding sites," The Fourth International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011), June 2011.
8. Chang, Y.L., Tsai, H.K., Kao, C.Y., Chen, Y.C., and Yang, J.M., "Evolutionary conservation of DNA-contact residues in DNA-binding domains," International Multi-Symposiums on Computer and Computational Sciences (IMSCCS 07), 2007.
9. Chan, C.H., Lee, S.A., Kao, C.Y. and Tsai, H.K., "Improving EAX with restricted 2-opt," Proceedings of the 2005 Genetic and Evolutionary Computation (GECCO), pages 1471-1476, 2005.
10. Huang, Y.C., Chao, Y.C., Lin, S.B., Tsai, H.K. and Kao C.Y., "A Tool to Determine the Specificity of Antisense Oligonucleotide," The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), pages 447-449, 2004.
11. Huang, Y.C., Tsai, H.K., Chuang, H.Y., Chang, C.F. and Kao, C.Y., "A Novel Method to speed up multiple-use PCR primer design," International conference on Computational Biology (RECOMB), Currents in Computational Molecular Biology., 2004.
12. Chiu, H.S., Chuang, H.Y., Tsai, H.K., Huang, T.W. and Kao, C.Y., "Discovering statistically significant clusters by using genetic algorithms in gene expression data," International conference on Computational Biology (RECOMB), Currents in Computational Molecular Biology, 2004.
13. Chuang, H.Y., Tsai, H.K. and Kao, C.Y., "Optimal designs for microarray experiments," The 7th International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN), pages 619-624, 2004.
14. Huang, Y.C., Chuang, H.Y., Tsai, H.K., Chang, C.F. and Kao, C.Y., "Designing multiple-use primer set for multiplex PCR by using compact GAs," The 8th International Conference on Parallel Problem Solving from Nature (PPSN), pages 511-521, 2004.
15. Chiu, HS, Chuang, HY, Tsai HK, Huang TW, and Kao CH, "Discovering statistically significant clusters by using iterative genetic algorithms in gene expression data," Proceedings of International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), 2004.
16. Tsai, C.H., Tsai, H.K., Chen, S.C. and Kao, C.Y., "Disulfide connectivity prediction using support vector machine and novel features," The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), pages 391-395, 2004.
17. Chen, S.C., Tsai, C.H., Tsai, H.K. and Kao, C.Y., "Prediction of disulfide connectivity patterns in proteins," International Conference on Intelligent Systems for Molecular Biology (ISMB), 2003.
18. Chuang, H.Y., Chiu, H.S., Tsai, H.K. and Kao, C. Y., "An automatic and unbiased GA for finding the most discriminant gene sets on Microarray," International Conference on Intelligent Systems for Molecular Biology (ISMB), 2003.
19. Tsai, H.K., Yang, J.M. and Kao, C.Y., "Applying genetic algorithms to finding the optimal gene order in displaying the microarray data," Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), pages 610-617, 2002.
20. Tsai, C.H., Tsai, H.K. and Kao, C. Y., "Side-Chain Conformation Prediction with Support Vector Machines," International Conference on Intelligent Systems for Molecular Biology (ISMB), 2002.
21. Tsai, H.K., Yang, J.M. and Kao, C.Y., "Solving traveling salesman problems by combining global and local search mechanisms," Congress of Evolutionary Computation (CEC), pages 1290-1295, 2002.
22. Tsai, H.K., Chuang, H.Y., Chao, Y.C. and Kao, C. Y., "An intuitive way for selecting informative genes from microarray data," International conference on Computational Biology (RECOMB), Currents in Computational Molecular Biology, 2002.
23. Tsai, H.K., Yang, J.M., and Kao, C.Y., "A genetic algorithm for traveling salesman problems," Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), pages 687-693, 2001.
24. Tsai, C.H., Yang, J.M., Hwang, M.J., Tsai, H.K. and Kao, C. Y., "Protein Side-chain Prediction by Evolutionary Algorithm," Medical Infromatics Symposium/Show(MIST2001), Taipei, 2001.
25. Tsai, H.K. and Kao, C. Y., "Using Genetic Algorithms to Construct Physical Maps of Chromosomes with Unique Probes," Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), 2000.
26. Tsai, H.K. and Kao, C.Y., "Using Genetic Algorithms to Construct Physical Maps of Chromosomes with Unique Probes," International conference on Computational Biology (RECOMB), Currents in Computational Molecular Biology, 2000.
 
 
 
Book & Book Chapters
 
1. Wang, T.Y. and Tsai, H.K.*,, chapter "MetaRank: Ranking Microbial Taxonomic Units or Functional Groups for Comparative Analysis of Metagenomes," Encyclopedia of Metagenomics, Nelson and Karen E., editors, pages 1-7, Springer, 2014.
 
 
 
bg