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副研究員
蔡懷寬 Huai-Kuang Tsai

Associate Research Fellow
Ph.D., Computer Science and Information Engineering,
National Taiwan University
Tel: +886-2-2788-3799 ext. 1718 Fax: +886-2-2782-4814
Email: hktsai@iis.sinica.edu.tw http://www.iis.sinica.edu.tw/~hktsai

● Associate Research Fellow, IIS, Research Description
Academia Sinica, 2011- present.
● Program coordinator, Taiwan My research focuses on gene regulatory mechanisms and transcriptomics, mostly in Sac-
International Graduate Program, charomyces cerevisiae and Homo sapiens. I apply computational techniques and statistical
Bioinformatics, Academia Sinica, methods to data obtained from high-throughput biological experiments. My investigations
2013- present.
include the identi cation of the function of transcription factors (TFs) and their binding sites

● Associate Professor (Joint (TFBSs), the impact of DNA binding position variants on gene expression, the cis-regulatory
appointment), Genome and modules of divergent gene pairs, the association between nucleosome occupancy and the
Systems Biology degree program, evolution of TFBSs, interactions between TFs, the impact of TFs and microRNA (miRNA) on
National Taiwan University, 2013-
present protein evolutionary rates, and the association between non-B DNA structures and exon
skipping. To further our understanding, we now investigate additional factors that play sig-
● Associate Professor (Joint ap- ni cant roles in regulatory mechanisms, including chromosome accessibility, noncoding

pointment), Department of
Computer Science and Engineer- RNAs, and DNA structure.
ing, National Ocean University, I also focus on metagenomics, which analyzes samples directly taken from the environ-
2012- present
ment. The data processing methodologies in metagenomics are yet to reach a consensus
● Associate Professor (Joint ap- for use by most researchers. I have thus tackled the important tasks of improving the data
pointment), Department of Bio- processing methods and developing statistical methods that characterize systemic proper-
logical Science and Technology,
National Chiao-Tung University, ties of microbial communities. Utilizing data produced from high-throughput sequencing

2011- present technology, I proposed a series of computational methods to discriminate the di erences
● Assistant Research Fellow, IIS,, between distinct microbial communities, and to enhance the accuracy of estimating the
Academia Sinica, 2006-2011. taxonomic compositions of metagenomes.

Publications

1. Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.* (2014) 6. Wang, T.Y., Su, C.H. and Tsai, H.K.* (2011) MetaRank: a
Associations between intronic non-B DNA structures and rank conversion scheme for comparative analysis of micro-
exon skipping, Nucleic Acids Research, 42(2):739-747. bial community compositions, Bioinformatics, 27, 3341-3347,
2011.
2. Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K.*, and Chuang
T.J.* (2013) The Impact of Trans-Regulation on the Evolu- 7. Su, C.H., Hsu, M.T., Wang, T.Y., Weng, F., Kao, C.Y., Wang,
tionary Rates of Metazoan Proteins, Nucleic Acids Research, D. and Tsai, H.K.* (2011) MetaABC – an integrated Metagen-
41(13):6371-80. omics platform for data Adjustment, Binning, and Clustering,
Bioinformatics, 27, 2298-2299.
3. 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.* (2012) “De 8. Swamy, B.S. K.+, Cho, C.Y.+, Chiang, S., Tsai, Z. T.Y., and

novo motif discovery facilitates identification of interactions Tsai, H.K.* (2009) Impact of DNA binding position variants
between transcription factors in Saccharomyces cerevisiae”, on yeast gene expression, Nucleic Acids Research, 37, 6991-
Bioinformatics, 28, 701-708. 7001.
4. Su, C.H., Wang, T.Y., Hsu, M.T., Weng, F., Kao, C.Y., Wang, 9. Tsai, H.K.*, Chou, M.Y., Shih, C. H., Huang, Grace T. W.,
D. and Tsai, H.K.* (2012) The impact of normalization and Chang, T. H. and Li, W.H. (2007) MYBS: A comprehensive
phylogenetic information on estimating the distance metrics web server for mining transcription factor binding sites in
for metagenomes, IEEE Transactions on Computational Biol- yeast, Nucleic Acids Research, 35, W221-W226.
ogy and Bioinformatics, 9, 619-628.
10. Tsai, H.K., Lu, H.H. and Li, W.H. (2005) Statistical methods
5. Chiang, S., Swamy, B.S. K., Hsu, T.W., Tsai, Z. T.Y., Lu, H.S., for identifying yeast cell cycle transcription factors, Proc Natl
Wang, D. and Tsai, H.K.* (2012) Analysis of the association Acad Sci USA, 102, 13532- 13537.
between transcription factor binding site variants and distinct
accompanying regulatory motifs in yeast, Gene, 491, 237-245.

90 研究人員 Research Faculty