Page 88 - 2017 Brochure
P. 88
究員
蔡懷寬 Huai-Kuang Tsai
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/pages/hktsai
• Research Fellow, Institute of Information Science, Academia Sinica (2015-present)
• Professor (Joint appointment), Genome and Systems Biology degree program, National Taiwan University (2016-present)
• Professor (Joint appointment), Department of Biological Science and Technology, National Chiao-Tung University (2016-present)
• Professor (Joint appointment), Department of Computer Science and Engineering, National Ocean University (2016-present)
• Associate Professor (Adjunct), Institute of BioMedical Informatics, National Yang Ming University (2013-present)
• Associate Research Fellow, Institute of Information Science, Academia Sinica (2011-2015)
• Assistant Research Fellow, Institute of Information Science, Academia Sinica (2006-2011)
• Ph.D., Department of Computer Science and Information Engineering, National Taiwan University (1998-2003)
Research Description To further our understanding, we have begun to investigate
additional factors that play significant roles in gene regulatory
My research mainly focuses on understanding fundamental mechanisms, including epigenetic and DNA structural properties.
regulatory mechanisms in cells. I aim to understand the dynamic My research also includes projects on metagenomics, wherein we
interactions between cis- and trans- regulatory elements, analyze microbial samples directly taken from the environment.
the impact of these interactions on gene expression and the Our goal is to improve data processing methods for the noisy
evolutionary signatures of genes and genomes. As such, I apply metagenomics data and determine the systemic properties of
integrative approaches that combine computational techniques microbial communities. Our recent achievements in this field
and statistical methods to high-throughput experimental data include novel discoveries ranging from specific characterization
from a variety of organisms, including yeast, fruit fly, mouse and of elements to holistic examination of regulatory systems. These
human. My investigations include the identification of the function discoveries are driven by and have enabled us to create new tools
of transcription factors (TFs) and their binding sites (TFBSs), the and de novo methods for furthering the understanding of genetics,
impact of DNA binding position variants on gene expression, the genomics, transcriptomics, and metagenomics.
cis-regulatory modules of divergent gene pairs, the association
between nucleosome occupancy and the evolution of TFBSs, the
identification of interactions between TFs, the impact of TFs and
microRNA (miRNA) on protein evolutionary rates, the association
between non-B DNA structures and exon skipping, and the role of
enhancer transcripts in gene regulation.
Publications 7. Su, C.H., Hsu, M.T., Wang, T.Y., Weng, F., Kao, C.Y., Wang, D.
and Tsai, H.K.* (2011) MetaABC – an integrated Metagenomics
1. Cheng, J.H., Pan D., Tsai, Z.T.Y., and Tsai, H.K.* (2015) Genome- platform for data Adjustment, Binning, and Clustering, Bioinformatics,
wide analysis of enhancer RNA in gene regulation across 12 mouse 27,2298-2299.
tissues, Scientific Reports, 5, 12648.
8. Swamy, B.S. K.+, Cho, C.Y.+, Chiang, S., Tsai, Z. T.Y., and Tsai,
2. Tsai, Z.T.Y., Shiu, S.H.*, and Tsai, H.K.* (2015) Contribution of H.K.* (2009) Impact of DNA binding position variants on yeast gene
sequence motif, chromatin state, and DNA structure features to expression, Nucleic Acids Research, 37, 6991-7001.
predictive models of transcription factor binding in yeast, PLoS
Computational Biology, 11(8), e1004418. 9. Tsai, H.K.*, Chou, M.Y., Shih, C. H., Huang, Grace T. W., Chang,
T. H. and Li, W.H. (2007) MYBS: A comprehensive web server
3. Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.* (2014) for mining transcription factor binding sites in yeast, Nucleic Acids
Associations between intronic non-B DNA structures and exon Research, 35, W221-W226.
skipping, Nucleic Acids Research, 42(2):739-747.
10. Tsai, H.K., Lu, H.H. and Li, W.H. (2005) Statistical methods for
4. Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K.*, and Chuang T.J.* identifying yeast cell cycle transcription factors, Proc Natl Acad Sci
(2013) The Impact of Trans-Regulation on the Evolutionary Rates of USA, 102, 13532- 13537.
Metazoan Proteins, Nucleic Acids Research, 41(13):6371-80.
5. 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 novo motif
discovery facilitates identification of interactions between transcription
factors in Saccharomyces cerevisiae", Bioinformatics, 28, 701-708.
6. Wang, T.Y., Su, C.H. and Tsai, H.K.* (2011) MetaRank: a rank
conversion scheme for comparative analysis of microbial community
compositions, Bioinformatics, 27, 3341-3347, 2011.
86 研究人員 Research Faculty
蔡懷寬 Huai-Kuang Tsai
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/pages/hktsai
• Research Fellow, Institute of Information Science, Academia Sinica (2015-present)
• Professor (Joint appointment), Genome and Systems Biology degree program, National Taiwan University (2016-present)
• Professor (Joint appointment), Department of Biological Science and Technology, National Chiao-Tung University (2016-present)
• Professor (Joint appointment), Department of Computer Science and Engineering, National Ocean University (2016-present)
• Associate Professor (Adjunct), Institute of BioMedical Informatics, National Yang Ming University (2013-present)
• Associate Research Fellow, Institute of Information Science, Academia Sinica (2011-2015)
• Assistant Research Fellow, Institute of Information Science, Academia Sinica (2006-2011)
• Ph.D., Department of Computer Science and Information Engineering, National Taiwan University (1998-2003)
Research Description To further our understanding, we have begun to investigate
additional factors that play significant roles in gene regulatory
My research mainly focuses on understanding fundamental mechanisms, including epigenetic and DNA structural properties.
regulatory mechanisms in cells. I aim to understand the dynamic My research also includes projects on metagenomics, wherein we
interactions between cis- and trans- regulatory elements, analyze microbial samples directly taken from the environment.
the impact of these interactions on gene expression and the Our goal is to improve data processing methods for the noisy
evolutionary signatures of genes and genomes. As such, I apply metagenomics data and determine the systemic properties of
integrative approaches that combine computational techniques microbial communities. Our recent achievements in this field
and statistical methods to high-throughput experimental data include novel discoveries ranging from specific characterization
from a variety of organisms, including yeast, fruit fly, mouse and of elements to holistic examination of regulatory systems. These
human. My investigations include the identification of the function discoveries are driven by and have enabled us to create new tools
of transcription factors (TFs) and their binding sites (TFBSs), the and de novo methods for furthering the understanding of genetics,
impact of DNA binding position variants on gene expression, the genomics, transcriptomics, and metagenomics.
cis-regulatory modules of divergent gene pairs, the association
between nucleosome occupancy and the evolution of TFBSs, the
identification of interactions between TFs, the impact of TFs and
microRNA (miRNA) on protein evolutionary rates, the association
between non-B DNA structures and exon skipping, and the role of
enhancer transcripts in gene regulation.
Publications 7. Su, C.H., Hsu, M.T., Wang, T.Y., Weng, F., Kao, C.Y., Wang, D.
and Tsai, H.K.* (2011) MetaABC – an integrated Metagenomics
1. Cheng, J.H., Pan D., Tsai, Z.T.Y., and Tsai, H.K.* (2015) Genome- platform for data Adjustment, Binning, and Clustering, Bioinformatics,
wide analysis of enhancer RNA in gene regulation across 12 mouse 27,2298-2299.
tissues, Scientific Reports, 5, 12648.
8. Swamy, B.S. K.+, Cho, C.Y.+, Chiang, S., Tsai, Z. T.Y., and Tsai,
2. Tsai, Z.T.Y., Shiu, S.H.*, and Tsai, H.K.* (2015) Contribution of H.K.* (2009) Impact of DNA binding position variants on yeast gene
sequence motif, chromatin state, and DNA structure features to expression, Nucleic Acids Research, 37, 6991-7001.
predictive models of transcription factor binding in yeast, PLoS
Computational Biology, 11(8), e1004418. 9. Tsai, H.K.*, Chou, M.Y., Shih, C. H., Huang, Grace T. W., Chang,
T. H. and Li, W.H. (2007) MYBS: A comprehensive web server
3. Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.* (2014) for mining transcription factor binding sites in yeast, Nucleic Acids
Associations between intronic non-B DNA structures and exon Research, 35, W221-W226.
skipping, Nucleic Acids Research, 42(2):739-747.
10. Tsai, H.K., Lu, H.H. and Li, W.H. (2005) Statistical methods for
4. Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K.*, and Chuang T.J.* identifying yeast cell cycle transcription factors, Proc Natl Acad Sci
(2013) The Impact of Trans-Regulation on the Evolutionary Rates of USA, 102, 13532- 13537.
Metazoan Proteins, Nucleic Acids Research, 41(13):6371-80.
5. 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 novo motif
discovery facilitates identification of interactions between transcription
factors in Saccharomyces cerevisiae", Bioinformatics, 28, 701-708.
6. Wang, T.Y., Su, C.H. and Tsai, H.K.* (2011) MetaRank: a rank
conversion scheme for comparative analysis of microbial community
compositions, Bioinformatics, 27, 3341-3347, 2011.
86 研究人員 Research Faculty
