Xie D - Search Results

1

Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.

Chen CC, Xiao S, Xie D, Cao X, Song CX, Wang T, He C, Zhong S. Chen CC, et al. Among authors: xie d. PLoS Comput Biol. 2013;9(12):e1003367. doi: 10.1371/journal.pcbi.1003367. Epub 2013 Dec 5. PLoS Comput Biol. 2013. PMID: 24339764 Free PMC article.

2

Towards an evolutionary model of transcription networks.

Xie D, Chen CC, He X, Cao X, Zhong S. Xie D, et al. PLoS Comput Biol. 2011 Jun;7(6):e1002064. doi: 10.1371/journal.pcbi.1002064. Epub 2011 Jun 9. PLoS Comput Biol. 2011. PMID: 21695281 Free PMC article.

3

Comparative epigenomic annotation of regulatory DNA.

Xiao S, Xie D, Cao X, Yu P, Xing X, Chen CC, Musselman M, Xie M, West FD, Lewin HA, Wang T, Zhong S. Xiao S, et al. Among authors: xie d, xie m. Cell. 2012 Jun 8;149(6):1381-92. doi: 10.1016/j.cell.2012.04.029. Cell. 2012. PMID: 22682255 Free PMC article.

4

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.

Xie D, Cai J, Chia NY, Ng HH, Zhong S. Xie D, et al. Genome Res. 2008 Aug;18(8):1325-35. doi: 10.1101/gr.072769.107. Epub 2008 May 15. Genome Res. 2008. PMID: 18490265 Free PMC article.

5

Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells.

Hong F, Fang F, He X, Cao X, Chipperfield H, Xie D, Wong WH, Ng HH, Zhong S. Hong F, et al. Among authors: xie d. PLoS Comput Biol. 2009 Dec;5(12):e1000607. doi: 10.1371/journal.pcbi.1000607. Epub 2009 Dec 18. PLoS Comput Biol. 2009. PMID: 20019792 Free PMC article.

6

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species.

Xie D, Chen CC, Ptaszek LM, Xiao S, Cao X, Fang F, Ng HH, Lewin HA, Cowan C, Zhong S. Xie D, et al. Genome Res. 2010 Jun;20(6):804-15. doi: 10.1101/gr.100594.109. Epub 2010 Mar 10. Genome Res. 2010. PMID: 20219939 Free PMC article.

7

Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.

Cai J, Xie D, Fan Z, Chipperfield H, Marden J, Wong WH, Zhong S. Cai J, et al. Among authors: xie d. PLoS Comput Biol. 2010 Mar 12;6(3):e1000707. doi: 10.1371/journal.pcbi.1000707. PLoS Comput Biol. 2010. PMID: 20300647 Free PMC article.

8

Mapping personal functional data to personal genomes.

Rivas-Astroza M, Xie D, Cao X, Zhong S. Rivas-Astroza M, et al. Among authors: xie d. Bioinformatics. 2011 Dec 15;27(24):3427-9. doi: 10.1093/bioinformatics/btr578. Epub 2011 Oct 17. Bioinformatics. 2011. PMID: 22006915 Free PMC article.

9

Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework.

Zhong S, Xie D. Zhong S, et al. Among authors: xie d. Artif Intell Med. 2007 Oct;41(2):105-15. doi: 10.1016/j.artmed.2007.08.002. Artif Intell Med. 2007. PMID: 17913480

10

TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays.

Kim C, Kim S, Dorer R, Xie D, Han J, Zhong S. Kim C, et al. Among authors: xie d. BMC Bioinformatics. 2007 Apr 18;8:128. doi: 10.1186/1471-2105-8-128. BMC Bioinformatics. 2007. PMID: 17442117 Free PMC article.

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