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Associate Research Fellow  |  Tsai, Huai-Kuang  
 
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Publications
 
Journal Articles
 
1. Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.*, "Associations between intronic non-B DNA structures and exon skipping," to appear in Nucleic Acids Research, volume doi: 10.1093/nar/gkt939.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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
13. 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
14. 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.
15. 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.
16. 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.
17. 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
18. 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.
19. 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
20. 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
21. 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
22. 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.
23. 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.
24. 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
25. 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.
26. 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
27. 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.
28. 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.
29. 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.
30. 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. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
 
 
 
 
 
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