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.
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.
44.
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
45.
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.
46.
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. :::
47.
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. :::
48.
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. :::
49.
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. :::
50.
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.
51.
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. :::
52.
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.
53.
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.
54.
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.
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.
57.
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, B.S., Wong, J.Y., and Tsai, H.K.*, "Object detection on DNA sequences using DNA-DETR," 1st Asia and Pacific Bioinformatics Joint Conference, October 2024.
2.
Yu, S.Q., Wong, J.Y., and Tsai, H.K.*, "A simulated annealing-based algorithm with novel objective function for mapping protein complexes in different conditions," 1st Asia and Pacific Bioinformatics Joint Conference, October 2024.
3.
Zhu, K.Z., Wong, J.Y., and Tsai, H.K.*, "Simulating gene perturbation effect through hypergraph causal inference," 1st Asia and Pacific Bioinformatics Joint Conference, October 2024.
4.
Li, T.C., Tsai, C.H., Shiau, C.K., Huang, J.H., and Tsai, H.K.*, "Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning," GIW XXXI/ISCB-Asia V, December 2022.
5.
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," The 19th Asia Pacific Bioinformatics Conference, February 2021.
6.
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," The 19th Asia Pacific Bioinformatics Conference, January 2021.
7.
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.
8.
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.
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.
11.
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.
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.
14.
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.
15.
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.
16.
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.
17.
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.
18.
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.
19.
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.
20.
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.
21.
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.
22.
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.
23.
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.
24.
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.
25.
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.
26.
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.
27.
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.
28.
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.
29.
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.
30.
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.
31.
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.
32.
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.
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.
