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Results: 16

1.

Recurrent read-through fusion transcripts in breast cancer.

Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM.

Breast Cancer Res Treat. 2014 Jul;146(2):287-97. doi: 10.1007/s10549-014-3019-2. Epub 2014 Jun 15.

PMID:
24929677
[PubMed - in process]
2.

Distinct properties of cell-type-specific and shared transcription factor binding sites.

Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM.

Mol Cell. 2013 Oct 10;52(1):25-36. doi: 10.1016/j.molcel.2013.08.037. Epub 2013 Sep 26.

PMID:
24076218
[PubMed - indexed for MEDLINE]
3.

Early de novo DNA methylation and prolonged demethylation in the muscle lineage.

Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M.

Epigenetics. 2013 Mar;8(3):317-32. doi: 10.4161/epi.23989. Epub 2013 Feb 15.

PMID:
23417056
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Dynamic DNA methylation across diverse human cell lines and tissues.

Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM.

Genome Res. 2013 Mar;23(3):555-67. doi: 10.1101/gr.147942.112. Epub 2013 Jan 16.

PMID:
23325432
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice.

Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q.

Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):21081-6. doi: 10.1073/pnas.1219280110. Epub 2012 Nov 30.

PMID:
23204437
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner.

Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM.

Genome Res. 2012 Nov;22(11):2153-62. doi: 10.1101/gr.135681.111. Epub 2012 Sep 26.

PMID:
23019147
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Widespread plasticity in CTCF occupancy linked to DNA methylation.

Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA.

Genome Res. 2012 Sep;22(9):1680-8. doi: 10.1101/gr.136101.111.

PMID:
22955980
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.

Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P.

BMC Genomics. 2012 Jun 15;13:249. doi: 10.1186/1471-2164-13-249.

PMID:
22703188
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM.

Genome Res. 2012 May;22(5):860-9. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

PMID:
22300769
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Transposase mediated construction of RNA-seq libraries.

Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM.

Genome Res. 2012 Jan;22(1):134-41. doi: 10.1101/gr.127373.111. Epub 2011 Nov 29. Erratum in: Genome Res. 2012 Mar;22(3):592.

PMID:
22128135
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM.

PLoS Genet. 2011 Aug;7(8):e1002228. doi: 10.1371/journal.pgen.1002228. Epub 2011 Aug 11.

PMID:
21852959
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

Varley KE, Mitra RD.

Genome Res. 2010 Sep;20(9):1279-87. doi: 10.1101/gr.101212.109. Epub 2010 Jul 13.

PMID:
20627893
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Nested Patch PCR for highly multiplexed amplification of genomic loci.

Varley KE, Mitra RD.

Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.prot5252. doi: 10.1101/pdb.prot5252.

PMID:
20147217
[PubMed - indexed for MEDLINE]
14.

Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing.

Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD.

Nucleic Acids Res. 2009 Aug;37(14):4603-12. doi: 10.1093/nar/gkp457. Epub 2009 Jun 3.

PMID:
19494183
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Quantification of rare allelic variants from pooled genomic DNA.

Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD.

Nat Methods. 2009 Apr;6(4):263-5. doi: 10.1038/nmeth.1307. Epub 2009 Mar 1.

PMID:
19252504
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes.

Varley KE, Mitra RD.

Genome Res. 2008 Nov;18(11):1844-50. doi: 10.1101/gr.078204.108. Epub 2008 Oct 10.

PMID:
18849522
[PubMed - indexed for MEDLINE]
Free PMC Article

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