Clarke ND - Search Results

1

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. Chen X, et al. Among authors: clarke nd. Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043. Cell. 2008. PMID: 18555785 Free article.

2

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. Orlov Y, et al. J Integr Bioinform. 2012 Sep 18;9(2):211. doi: 10.2390/biecoll-jib-2012-211. J Integr Bioinform. 2012. PMID: 22987856

3

Inferring transcription factor targets from gene expression changes and predicted promoter occupancy.

Yeo ZX, Yeo HC, Yeo JK, Yeo AL, Li Y, Clarke ND. Yeo ZX, et al. Among authors: clarke nd. J Comput Biol. 2009 Feb;16(2):357-68. doi: 10.1089/cmb.2008.19TT. J Comput Biol. 2009. PMID: 19193152

4

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.

Chia NY, Chan YS, Feng B, Lu X, Orlov YL, Moreau D, Kumar P, Yang L, Jiang J, Lau MS, Huss M, Soh BS, Kraus P, Li P, Lufkin T, Lim B, Clarke ND, Bard F, Ng HH. Chia NY, et al. Among authors: clarke nd. Nature. 2010 Nov 11;468(7321):316-20. doi: 10.1038/nature09531. Epub 2010 Oct 17. Nature. 2010. PMID: 20953172

5

Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge.

Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND. Vega VB, et al. Among authors: clarke nd. Ann N Y Acad Sci. 2009 Mar;1158:215-23. doi: 10.1111/j.1749-6632.2008.03759.x. Ann N Y Acad Sci. 2009. PMID: 19348643

6

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND. Goh WS, et al. Among authors: clarke nd. PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649. PLoS Comput Biol. 2010. PMID: 20098497 Free PMC article.

7

Success in the DREAM3 signaling response challenge using simple weighted-average imputation: lessons for community-wide experiments in systems biology.

Clarke ND, Bourque G. Clarke ND, et al. PLoS One. 2010 Jan 26;5(1):e8417. doi: 10.1371/journal.pone.0008417. PLoS One. 2010. PMID: 20126276 Free PMC article.

8

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α.

Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, Ruan Y, Clarke ND, Prabhakar S, Cheung E, Liu ET. Joseph R, et al. Among authors: clarke nd. Mol Syst Biol. 2010 Dec 21;6:456. doi: 10.1038/msb.2010.109. Mol Syst Biol. 2010. PMID: 21179027 Free PMC article.

9

Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.

Guo G, Huss M, Tong GQ, Wang C, Li Sun L, Clarke ND, Robson P. Guo G, et al. Among authors: clarke nd. Dev Cell. 2010 Apr 20;18(4):675-85. doi: 10.1016/j.devcel.2010.02.012. Dev Cell. 2010. PMID: 20412781 Free article.

10

Assessment of CASP7 structure predictions for template free targets.

Jauch R, Yeo HC, Kolatkar PR, Clarke ND. Jauch R, et al. Among authors: clarke nd. Proteins. 2007;69 Suppl 8:57-67. doi: 10.1002/prot.21771. Proteins. 2007. PMID: 17894330

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