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Items: 22


A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer.

Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS, Varley KE.

Cancer Res. 2019 Jul 1;79(13):3466-3478. doi: 10.1158/0008-5472.CAN-18-3014. Epub 2019 May 2.


Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development.

Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY, Fan C, Lasken R, Varley KE, Perou CM, Wahl GM, Spike BT.

Cell Rep. 2018 Aug 7;24(6):1653-1666.e7. doi: 10.1016/j.celrep.2018.07.025.


A novel AGGF1-PDGFRb fusion in pediatric T-cell acute lymphoblastic leukemia.

Zabriskie MS, Antelope O, Verma AR, Draper LR, Eide CA, Pomicter AD, Tran TH, Druker BJ, Tyner JW, Miles RR, Graham JM, Hwang JY, Varley KE, Toydemir RM, Deininger MW, Raetz EA, O'Hare T.

Haematologica. 2018 Feb;103(2):e87-e91. doi: 10.3324/haematol.2017.165282. Epub 2017 Dec 28. No abstract available.


Genomic regulation of invasion by STAT3 in triple negative breast cancer.

McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM.

Oncotarget. 2017 Jan 31;8(5):8226-8238. doi: 10.18632/oncotarget.14153.


Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes.

Forero A, Li Y, Chen D, Grizzle WE, Updike KL, Merz ND, Downs-Kelly E, Burwell TC, Vaklavas C, Buchsbaum DJ, Myers RM, LoBuglio AF, Varley KE.

Cancer Immunol Res. 2016 May;4(5):390-9. doi: 10.1158/2326-6066.CIR-15-0243. Epub 2016 Mar 15.


TBCRC 019: A Phase II Trial of Nanoparticle Albumin-Bound Paclitaxel with or without the Anti-Death Receptor 5 Monoclonal Antibody Tigatuzumab in Patients with Triple-Negative Breast Cancer.

Forero-Torres A, Varley KE, Abramson VG, Li Y, Vaklavas C, Lin NU, Liu MC, Rugo HS, Nanda R, Storniolo AM, Traina TA, Patil S, Van Poznak CH, Nangia JR, Irvin WJ Jr, Krontiras H, De Los Santos JF, Haluska P, Grizzle W, Myers RM, Wolff AC; Translational Breast Cancer Research Consortium (TBCRC).

Clin Cancer Res. 2015 Jun 15;21(12):2722-9. doi: 10.1158/1078-0432.CCR-14-2780. Epub 2015 Mar 16.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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