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Results: 16

1.

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

Tsai ZT, Shiu SH, Tsai HK.

PLoS Comput Biol. 2015 Aug 20;11(8):e1004418. doi: 10.1371/journal.pcbi.1004418. eCollection 2015 Aug.

2.

Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues.

Cheng JH, Pan DZ, Tsai ZT, Tsai HK.

Sci Rep. 2015 Jul 29;5:12648. doi: 10.1038/srep12648.

3.

Associations between intronic non-B DNA structures and exon skipping.

Tsai ZT, Chu WY, Cheng JH, Tsai HK.

Nucleic Acids Res. 2014 Jan;42(2):739-47. doi: 10.1093/nar/gkt939. Epub 2013 Oct 22.

4.

The impact of trans-regulation on the evolutionary rates of metazoan proteins.

Chen YC, Cheng JH, Tsai ZT, Tsai HK, Chuang TJ.

Nucleic Acids Res. 2013 Jul;41(13):6371-80. doi: 10.1093/nar/gkt349. Epub 2013 May 8.

5.

Evolution of cis-regulatory elements in yeast de novo and duplicated new genes.

Tsai ZT, Tsai HK, Cheng JH, Lin CH, Tsai YF, Wang D.

BMC Genomics. 2012 Dec 21;13:717. doi: 10.1186/1471-2164-13-717.

6.

Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast.

Swamy KB, Chu WY, Wang CY, Tsai HK, Wang D.

BMC Evol Biol. 2011 May 31;11:150. doi: 10.1186/1471-2148-11-150.

7.

Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.

Weng FC, Su CH, Hsu MT, Wang TY, Tsai HK, Wang D.

BMC Bioinformatics. 2010 Nov 18;11:565. doi: 10.1186/1471-2105-11-565.

8.

Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.

Tsai HK, Huang PY, Kao CY, Wang D.

Int J Mol Sci. 2009 Aug 21;10(8):3658-70. doi: 10.3390/ijms10083658.

9.

Impact of DNA-binding position variants on yeast gene expression.

Swamy KB, Cho CY, Chiang S, Tsai ZT, Tsai HK.

Nucleic Acids Res. 2009 Nov;37(21):6991-7001. doi: 10.1093/nar/gkp743. Epub .

10.

Roles of trans and cis variation in yeast intraspecies evolution of gene expression.

Sung HM, Wang TY, Wang D, Huang YS, Wu JP, Tsai HK, Tzeng J, Huang CJ, Lee YC, Yang P, Hsu J, Chang T, Cho CY, Weng LC, Lee TC, Chang TH, Li WH, Shih MC.

Mol Biol Evol. 2009 Nov;26(11):2533-8. doi: 10.1093/molbev/msp171. Epub 2009 Jul 31.

11.

Evolutionary conservation of DNA-contact residues in DNA-binding domains.

Chang YL, Tsai HK, Kao CY, Chen YC, Hu YJ, Yang JM.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S3. doi: 10.1186/1471-2105-9-S6-S3.

12.

Discovering gapped binding sites of yeast transcription factors.

Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH.

Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2527-32. doi: 10.1073/pnas.0712188105. Epub 2008 Feb 13.

13.

Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system.

Tsai HK, Su CP, Lu MY, Shih CH, Wang D.

BMC Genomics. 2007 Oct 3;8:352.

14.

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.

Tsai HK, Chou MY, Shih CH, Huang GT, Chang TH, Li WH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W221-6. Epub 2007 May 30.

15.

Statistical methods for identifying yeast cell cycle transcription factors.

Tsai HK, Lu HH, Li WH.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13532-7. Epub 2005 Sep 12.

16.

GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations.

Yang JM, Tsai CH, Hwang MJ, Tsai HK, Hwang JK, Kao CY.

Protein Sci. 2002 Aug;11(8):1897-907.

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