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Items: 1 to 20 of 122

1.

Co-regulation in embryonic stem cells via context-dependent binding of transcription factors.

Lee Y, Zhou Q.

Bioinformatics. 2013 Sep 1;29(17):2162-8. doi: 10.1093/bioinformatics/btt365. Epub 2013 Jun 21.

2.

Identification of context-dependent motifs by contrasting ChIP binding data.

Mason MJ, Plath K, Zhou Q.

Bioinformatics. 2010 Nov 15;26(22):2826-32. doi: 10.1093/bioinformatics/btq546. Epub 2010 Sep 23.

3.

Detecting clustering and ordering binding patterns among transcription factors via point process models.

Cha M, Zhou Q.

Bioinformatics. 2014 Aug 15;30(16):2263-71. doi: 10.1093/bioinformatics/btu303. Epub 2014 Apr 29.

4.

COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.

Ha N, Polychronidou M, Lohmann I.

PLoS One. 2012;7(12):e52055. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.

5.

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells.

Chen G, Zhou Q.

BMC Genomics. 2011 Oct 20;12:515. doi: 10.1186/1471-2164-12-515.

6.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

7.

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.

Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043.

8.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

9.

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

10.

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.

Orlov Y, Xu H, Afonnikov D, Lim B, Heng JC, Yuan P, Chen M, Yan J, Clarke N, Orlova N, Huss M, Gunbin K, Podkolodnyy N, Ng HH.

J Integr Bioinform. 2012 Sep 18;9(2):211. doi: 10.2390/biecoll-jib-2012-211.

PMID:
22987856
11.

Genome-wide in silico prediction of gene expression.

McLeay RC, Lesluyes T, Cuellar Partida G, Bailey TL.

Bioinformatics. 2012 Nov 1;28(21):2789-96. doi: 10.1093/bioinformatics/bts529. Epub 2012 Sep 6.

12.

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.

Gong W, Koyano-Nakagawa N, Li T, Garry DJ.

BMC Bioinformatics. 2015 Mar 7;16:74. doi: 10.1186/s12859-015-0460-0.

13.

Inferring microRNA and transcription factor regulatory networks in heterogeneous data.

Le TD, Liu L, Liu B, Tsykin A, Goodall GJ, Satou K, Li J.

BMC Bioinformatics. 2013 Mar 11;14:92. doi: 10.1186/1471-2105-14-92.

14.

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.

Ouyang Z, Zhou Q, Wong WH.

Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21521-6. doi: 10.1073/pnas.0904863106. Epub 2009 Dec 7.

15.

Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells.

Kidder BL, Yang J, Palmer S.

PLoS One. 2008;3(12):e3932. doi: 10.1371/journal.pone.0003932. Epub 2008 Dec 11.

16.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

17.

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S.

BMC Genomics. 2009 Jul 20;10:327. doi: 10.1186/1471-2164-10-327.

18.

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.

PMID:
24042128
19.

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.

Jiang P, Singh M.

Nucleic Acids Res. 2014 Mar;42(5):2833-47. doi: 10.1093/nar/gkt1302. Epub 2013 Dec 23.

20.

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.

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