Journals


2018

Lin, C.Y., Chao, J.L., Tsai, H.K., Chalker, D., and Yao, M.C., (2019) Setting Boundaries for Genome-wide Heterochromatic DNA Deletions Through Flanking Inverted Repeats in Tetrahymena thermophila, Nucleic Acids Research, to appear.

Huang, J.H., Kwan, SY. Tsai, T.Y., and Tsai, H.K.*, (2018) Expansion of transcription factor binding sites for introducing lineage-specific motifs in the promoter regions, Frontiers in Genetics, 9, 571.

Shiau, C.K., Huang, J.H. and Tsai, H.K.*, (2018) CATANA: Comprehensive Alternative Transcript Atlas based oN Annotation,” Bioinformatics, volume bty795, pages bty795, September 2018.

Huang, J.H., Kwan, SY. Tsai, T.Y., Lin, T.C., and Tsai, H.K.*, (2018) 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.

2017

Liu, W.H., Tsai, Z.T.Y., and Tsai, H.K.* (2017) Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs, BMC Genomics, 18, 786.

Ng, I.M., Huang, J.H., Tsai, S.C. and Tsai, H.K. IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes. Database. Accepted 14th August, 2017.

2015

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.

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.

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.

2014

Tsai, Z.T.Y., Chu W.Y., Cheng, J.H., Tsai H.K. Associations between intronic non-B DNA structures and exon skipping. Nucleic Acid Research, 2014, 1-9.

2013

Lin, C.H., Tsai, Z.T.Y., Wang, D. Role of antisense RNAs in evolution of yeast regulatory complexity. Genomics, 102 (5-6), 484-490, 2013.

Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K., and Chuang, T.C. The impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins, Nucleic Acid Research, 41 (13), 6371-6380, 2013

2012

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, 13, 717, 2012.

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, 9, 619-628, 2012.

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, 28, 701-708, 2012.

Tsai, K.N., Wang, D., Identification of Activated Cryptic 5’ Splice Sites using Structure Profiles and Odds Measure, Nucleic Acids Res, 1-8, 2012.

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, 491, 237-245, 2012.

Chu, T.J., Wang, D., Haung, H.L., Lin, F.J. Tzeng, T.D., Population Structure and Historical Demography of the Whiskered Velvet Shrimp (Metapenaeopsis barbata) off China and Taiwan Inferred from the Mitochondrial Control Region, Zoological Studies, 51, 99-107, 2012.

2011

Wang, T.Y., Su, C.H. and Tsai, H.K., MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions, Bioinformatics, 27, 3341-3347, 2011.

Chu, T.J., Wang, D., Haung, H.L., Lin, F.J., Tzeng, T.D., Genetic variations and expansion of whiskered velvet shrimp (Metapenaeopsis barbata) off China and Taiwan inferred from intron sequence, Biochemical Systematics and Ecology, 39, 520-525, 2011.

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, 27, 2298-2299, 2011.

Chien, Y.I., Nonaka, I., Wang, D., Autosomal dominant late-onset quadriceps myopathy: three patients of a Taiwanese kindred, Internal Medicine, 50, 1175-1181, 2011.

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, 11, 150, 2011.

2010

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, 96, 352-361, 2010.

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, 11, 565, 2010.

2009

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 Res, 37, 6991-7001, 2009.

Sung, H.M., T.Y. Wang, D. Wang, Y.S. Huang, J.P. Wu, H.K. Tsai, J.Tseng, C,J, Huang, Y.C. Lee, P. Yang, J.H.T. Chang, C.Y. Cho, L.C. Weng, T.C. Lee, T.H. Chang, W.H. Li, M.C. Shih, Roles of Trans and Cis Variation in Yeast Intra-species Evolution of Gene Expression, To Appear in Molecular Biology and Evolution, 26, 2533-2538, 2009.

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, 10, 3658-3670, 2009.

Wang, Daryi, Wang, T.Y., Weng, L.C., Emori, Y., Tzeng, C.S. and Li, W.H., Evolution of Olfactory Receptor Genes in East Asian Loaches, Zoological Studies, 48, 223-237, 2009.

Wang, F.Y., Yan, H. Y., Chen, J.S.C., Wang, T.Y., Wang, Daryi, Adaptation of visual spectra and opsin genes in seabreams, Vision Research, 49,1860-1868, 2009.

2008

Chang, Y.L., Tsai, H.K., Kao, C.Y., Chen, Y.C., Hu, Y.J. and Yang, J.M., Evolutionary conservation of DNA-contact residues in DNA-binding domains, BMC bioinformatics, 9, S3-S3, 2008.

Chang, Y.W., Liu, R., Yu, N., Sung, H.M., Yang, P., Wang, D., Huang, C.J., Shih, M.C., Li, W.H., Roles of cis-and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast, Molecular Biology and Evolution, 25, 1863-1875, 2008.

Chaw, S.M., Shih, A.C.C., Wang, D., Wu, Y.W., Liu, S.M. and Chou, T.Y., The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites, Molecular Biology and Evolution, 25, 603-615, 2008.

Chen, C.Y., Tsai, H.K., Hsu, C.M., May Chen, M.J., Hung, H.G., Huang, G.T.W. and Li, W.H., Discovering gapped binding sites of yeast transcription factors, Proceedings of the National Academy of Sciences (USA), 105, 2527-2532, 2008.

Chen, J.S.C., Wang, T.Y., Tzeng, T.D., Wang, C.Y. and Wang, D., Evidence for positive selection in the TLR9 gene of teleosts, Fish & Shellfish Immunology, 24, 234-242, 2008.

2007

Tsai, H.K., Chou, M.Y., Shih, C.H., Huang, G.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, 35, W221-W226, 2007.

Tsai, H.K., Su, C.P.C., Lu, M.Y.J., Shih, C.H. and Wang, D., Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system, BMC genomics, 8, 352-352, 2007.

Wang, D., Sung, H.M., Wang, T.Y., Huang, C.J., Yang, P., Chang, T., Wang, Y.C., Tseng, D.L., Wu, J.P. and Lee, T.C., Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors, Genome research, 17, 1161-1161, 2007.

Wang, D., Wu, Y.W., Shih, A.C.C., Wu, C.S., Wang, Y.N. and Chaw, S.M., Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA, Molecular Biology and Evolution, 24, 2040-2048, 2007.

2006

Tsai, H.K., Huang, G.T.W., Chou, M.Y., Lu, H.H.S. and Li, W.H., Method for identifying transcription factor binding sites in yeast, Bioinformatics, 22, 1675-1681, 2006.

2005

Tsai, H.K., Lu, H.H.S. and Li, W.H., Statistical methods for identifying yeast cell cycle transcription factors, Proceedings of the National Academy of Sciences (USA), 102, 13532-13537, 2005.

Wang, D., Hsieh, M. and Li, W.H., A general tendency for conservation of protein length across eukaryotic kingdoms, Molecular Biology and Evolution, 22, 142-147, 2005.

Zhao, E., Liu, H.L., Tsai, C.H., Tsai, H.K., Chan, C. and Kao, C.Y., Cysteine separations profiles on protein sequences infer disulfide connectivity, Bioinformatics, 21, 1415-1420, 2005.

2002-2004

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, 511-521, 2004.

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, 34, 1718-1729, 2004.

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, 8, 69-78, 2004.

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-A Fusion of Foundations, Methodologies and Applications, 8, 689-697, 2004.

Tsai, Y.F., Tsai, H.K. and Kao, C.Y., Clustering Analysis of Debris-Flow Streams, International Journal of Sediment Research, 19, 37-46, 2004.

Wang, D., T. Oakley, J. Mower, L.C. Shimmin, S. Yim, R.L. Honeycutt, H. Tsao, W.H. Li., Molecular evolution of bat color vision genes, Mol. Biol. Evol., 21: 295-302, 2004.

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, 19, 953-966, 2003.

Tsai, H.K., Jm, Y., Yf, T. and Cy, K.A.O., Heterogeneous selection genetic algorithms for traveling salesman problems, Engineering Optimization, 35, 297-311, 2003.

Tsai, Y.F., Tsai, H.K. and Shieh, C.L., Hazard zone mapping of debris flow, The Chinese Journal of Mechanics, part B, 18, 91-102, 2002.

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: A Publication of the Protein Society, 11, 1897-1907, 2002.

 

 

Conferences

2001-2018

Shiau, C.K., Huang, J.H. and Tsai, H.K.* (2018) CATANA: Comprehensive Alternative Transcript Atlas based oN Annotation, 50th Anniversary of the Neutral Theory of Molecular Evolution (SMBE), Yokohama, Japan (poster).

Kwan, S.Y., Huang, J.H., Tsai, Z.T.Y. and Tsai, H.K.* (2018) 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(poster).

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.

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.

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

Ng, I.M, Huang, J.H, Tsai, H.K. IsoPlot: a web-based tool for visualization and exploration of alternative splicing events from annotation and RNA-seq data, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2016.

Kwan, S.Y, Huang, J.H, Tsai, H.K. Expansion of transcription factor binding specificities in the promoters of humans, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2016.

Tsai, Z.T.Y., Kwan, S.Y., Tsai, H.K. Expression data-driven identification of regulatory elements in sequenced species without regulatory genomic resources, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2014.

Liu, W.H. Tsai, Z.T.Y., Tsai H.K. Investigating evolutionary relationship between human lincRNA and protein-coding gene by comparative genomics, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2014.

Cheng, J.H., Pan D.Z., Tsai, Z.T.Y., Tsai H.K. Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2014.

Tsai, Z.T.Y, Chu W.Y., Cheng, J.H., Tsai H.K. Associations between intronic non-B DNA structures and exon skipping, The Eleventh Annual Bioinformatics and Systems Biology in Taiwan, 2013.

Tsai, Z.T.Y., Tsai, H.K., and Wang, D., The evolution of cis-regulatory elements in yeast de novo genes, The Fifth Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, 2012.

Tsai, Z.T.Y., Tsai, H.K., and Wang, D., Evolution of cis-regulatory features in yeast de novo genes, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB), 2012.

Swamy, K.B.S., Su, C.H., Tsai H.K., and Wang, D., Reevaluating duplicate gene evolution from the perspective of phylogenetic origin, Society for Molecular Biology and Evolution (SMBE), 2012.

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.

Chang, Y.L., Tsai, H.K., Kao, C.Y., Chen, Y.C., Hu, Y.J. and Yang, J.M., Evolutionary conservation of DNA-contact residues in DNA-binding domains, International Multi-Symposiums on Computer and Computational Sciences (IMSCCS), 2007.

Chan, C., Lee, S.A., Kao, C.Y. and Tsai, H.K., Improving EAX with restricted 2-opt, Proceedings of the 2005 conference on Genetic and evolutionary computation (GECCO), ACM New York, NY, USA, 1471-1476, 2005.

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), 619-624, 2004.

Huang, Y.C., Chao, Y.C., Lin, S.B., Tsai, H.K., Chang, C.F., Lee, S.A. 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), 447-449, 2004.

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), 511-521, 2004.

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), 391-395, 2004.

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), 610-617, 2002.

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), 1290–1295, 2002.

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), 2001.