Xie X - Search Results

1

Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1.

Chong HK, Infante AM, Seo YK, Jeon TI, Zhang Y, Edwards PA, Xie X, Osborne TF. Chong HK, et al. Among authors: xie x. Nucleic Acids Res. 2010 Oct;38(18):6007-17. doi: 10.1093/nar/gkq397. Epub 2010 May 18. Nucleic Acids Res. 2010. PMID: 20483916 Free PMC article.

2

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.

Seo YK, Chong HK, Infante AM, Im SS, Xie X, Osborne TF. Seo YK, et al. Among authors: xie x. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13765-9. doi: 10.1073/pnas.0904246106. Epub 2009 Aug 4. Proc Natl Acad Sci U S A. 2009. PMID: 19666523 Free PMC article.

3

Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy.

Seo YK, Jeon TI, Chong HK, Biesinger J, Xie X, Osborne TF. Seo YK, et al. Among authors: xie x. Cell Metab. 2011 Apr 6;13(4):367-375. doi: 10.1016/j.cmet.2011.03.005. Cell Metab. 2011. PMID: 21459322 Free PMC article.

4

Hobbes: optimized gram-based methods for efficient read alignment.

Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X. Ahmadi A, et al. Among authors: xie x. Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22. Nucleic Acids Res. 2012. PMID: 22199254 Free PMC article.

5

Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR.

Chong HK, Biesinger J, Seo YK, Xie X, Osborne TF. Chong HK, et al. Among authors: xie x. BMC Genomics. 2012 Feb 1;13:51. doi: 10.1186/1471-2164-13-51. BMC Genomics. 2012. PMID: 22296850 Free PMC article.

6

EXTREME: an online EM algorithm for motif discovery.

Quang D, Xie X. Quang D, et al. Among authors: xie x. Bioinformatics. 2014 Jun 15;30(12):1667-73. doi: 10.1093/bioinformatics/btu093. Epub 2014 Feb 14. Bioinformatics. 2014. PMID: 24532725 Free PMC article.

7

MotifMap: a human genome-wide map of candidate regulatory motif sites.

Xie X, Rigor P, Baldi P. Xie X, et al. Bioinformatics. 2009 Jan 15;25(2):167-74. doi: 10.1093/bioinformatics/btn605. Epub 2008 Nov 18. Bioinformatics. 2009. PMID: 19017655 Free PMC article.

8

Incorporating existing network information into gene network inference.

Christley S, Nie Q, Xie X. Christley S, et al. Among authors: xie x. PLoS One. 2009 Aug 27;4(8):e6799. doi: 10.1371/journal.pone.0006799. PLoS One. 2009. PMID: 19710931 Free PMC article.

9

AREM: aligning short reads from ChIP-sequencing by expectation maximization.

Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X. Newkirk D, et al. Among authors: xie x. J Comput Biol. 2011 Nov;18(11):1495-505. doi: 10.1089/cmb.2011.0185. Epub 2011 Oct 28. J Comput Biol. 2011. PMID: 22035330 Free PMC article.

10

MotifMap: integrative genome-wide maps of regulatory motif sites for model species.

Daily K, Patel VR, Rigor P, Xie X, Baldi P. Daily K, et al. Among authors: xie x. BMC Bioinformatics. 2011 Dec 30;12:495. doi: 10.1186/1471-2105-12-495. BMC Bioinformatics. 2011. PMID: 22208852 Free PMC article.

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