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Items: 1 to 20 of 33

1.

Mapping accessible chromatin regions using Sono-Seq.

Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran├žois P, Struhl K, Gerstein M, Snyder M.

Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. doi: 10.1073/pnas.0905443106.

2.

Extracting transcription factor targets from ChIP-Seq data.

Tuteja G, White P, Schug J, Kaestner KH.

Nucleic Acids Res. 2009 Sep;37(17):e113. doi: 10.1093/nar/gkp536.

3.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538. Review.

PMID:
19274049
4.

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.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

5.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518.

6.

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

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505.

7.

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites.

Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ.

Genome Res. 2008 Nov;18(11):1763-77. doi: 10.1101/gr.080622.108.

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.

Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137.

9.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

10.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488.

11.

Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes.

Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M.

PLoS Genet. 2008 Jul 25;4(7):e1000133. doi: 10.1371/journal.pgen.1000133.

12.

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.

Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA.

Nucleic Acids Res. 2008 Aug;36(14):4549-64. doi: 10.1093/nar/gkn382.

13.

Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells.

Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG.

Mol Cell Biol. 2008 Apr;28(8):2732-44. doi: 10.1128/MCB.02175-07.

14.

A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members.

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ.

Genome Res. 2007 Nov;17(11):1550-61.

15.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7.

PMID:
17558387
16.

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ.

PLoS Genet. 2007 Jun;3(6):e89.

17.

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

Johnson DS, Mortazavi A, Myers RM, Wold B.

Science. 2007 Jun 8;316(5830):1497-502.

18.

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.

Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K.

Mol Cell. 2006 Nov 17;24(4):593-602.

19.

Distinct and Overlapping Roles for E2F Family Members in Transcription, Proliferation and Apoptosis.

DeGregori J, Johnson DG.

Curr Mol Med. 2006 Nov;6(7):739-48. Review.

PMID:
17100600
20.

Suz12 binds to silenced regions of the genome in a cell-type-specific manner.

Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ.

Genome Res. 2006 Jul;16(7):890-900.

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