Johnson DS - Search Results

1

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM. Brunner AL, et al. Among authors: johnson ds. Genome Res. 2009 Jun;19(6):1044-56. doi: 10.1101/gr.088773.108. Epub 2009 Mar 9. Genome Res. 2009. PMID: 19273619 Free PMC article.

2

Sequence features that drive human promoter function and tissue specificity.

Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM. Landolin JM, et al. Among authors: johnson ds. Genome Res. 2010 Jul;20(7):890-8. doi: 10.1101/gr.100370.109. Epub 2010 May 25. Genome Res. 2010. PMID: 20501695 Free PMC article.

3

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Valouev A, et al. Among authors: johnson ds. Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246. Nat Methods. 2008. PMID: 19160518 Free PMC article.

4

Genome-wide mapping of in vivo protein-DNA interactions.

Johnson DS, Mortazavi A, Myers RM, Wold B. Johnson DS, et al. Science. 2007 Jun 8;316(5830):1497-502. doi: 10.1126/science.1141319. Epub 2007 May 31. Science. 2007. PMID: 17540862 Free article.

5

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Johnson DS, et al. Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7. Genome Res. 2008. PMID: 18258921 Free PMC article.

6

Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance.

Johnson DS, Davidson B, Brown CD, Smith WC, Sidow A. Johnson DS, et al. Genome Res. 2004 Dec;14(12):2448-56. doi: 10.1101/gr.2964504. Epub 2004 Nov 15. Genome Res. 2004. PMID: 15545496 Free PMC article.

7

De novo discovery of a tissue-specific gene regulatory module in a chordate.

Johnson DS, Zhou Q, Yagi K, Satoh N, Wong W, Sidow A. Johnson DS, et al. Genome Res. 2005 Oct;15(10):1315-24. doi: 10.1101/gr.4062605. Epub 2005 Sep 16. Genome Res. 2005. PMID: 16169925 Free PMC article.

8

Model-based analysis of ChIP-Seq (MACS).

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Zhang Y, et al. Among authors: johnson ds. Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. Genome Biol. 2008. PMID: 18798982 Free PMC article.

9

An integrated software system for analyzing ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. Ji H, et al. Among authors: johnson ds. Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505. Epub 2008 Nov 2. Nat Biotechnol. 2008. PMID: 18978777 Free PMC article.

10

Functional architecture and evolution of transcriptional elements that drive gene coexpression.

Brown CD, Johnson DS, Sidow A. Brown CD, et al. Among authors: johnson ds. Science. 2007 Sep 14;317(5844):1557-60. doi: 10.1126/science.1145893. Science. 2007. PMID: 17872446

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