Huntsman Cancer Institute Gertz Lab

Publications

Cooperative Dynamics of AR and ER Activity in Breast Cancer
D'Amato NC, Gordon MA, Babbs B, Spoelstra NS, Carson Butterfield KT, Torkko KC, Phan VT, Barton VN, Rogers TJ, Sartorius CA, Elias A, Gertz J, Jacobsen BM, Richer JK (2016).  
Mol Cancer Res, 14(11), 1054-1067.

MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition.
Mollaoglu G, Guthrie MR, Bohm S, Bragelmann J, Can I, Ballieu PM, Marx A, George J, Heinen C, Chalishazar MD, Cheng H, Ireland AS, Denning KE, Mukhopadhyay A, Vahrenkamp JM, Berrett KC, Mosbruger TL, Wang J, Kohan JL, Salama ME, Witt BL, Peifer M, Thomas RK, Gertz J, Johnson JE, Gazdar AF, Wechsler-Reya RJ, Sos ML, Oliver TG (2016).
LID - S1535-6108(16)30600-6 [pii]LID - 10.1016/j.ccell.2016.12.005 [doi]. Cancer Cell.

Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus.
Camp NJ, Lin WY, Bigelow A, Burghel GJ, Mosbruger TL, Parry MA, Waller RG, Rigas SH, Tai PY, Berrett K, Rajamanickam V, Cosby R, Brock IW, Jones B, Connley D, Sargent R, Wang G, Factor RE, Bernard PS, Cannon-Albright L, Knight S, Abo R, Werner TL, Reed MW, Gertz J, Cox A (2016).
Cancer Res, 76(7), 1916-25.

Multigene testing of moderate-risk genes: be mindful of the missense.
Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV (2016).
J Med Genet, 53(6), 366-76.

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites.
Savic D, Roberts BS, Carleton JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM.
Genome Res. 2015 Oct 20.

Improved survival among colon cancer patients with increased differentially expressed pathways.
Slattery ML, Herrick JS, Mullany LE, Gertz J, Wolff RK.
BMC Med. 2015 Apr 8;13:75. doi: 10.1186/s12916-015-0292-9.

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing.
Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ.
Genome Res. 2014 Mar;24(3):496-510.

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.

Mapping genome-wide transcription factor binding sites in frozen tissues.
Savic D, Gertz J, Jain P, Cooper GM, Myers RM.
Epigenetics Chromatin. 2013 Sep 16;6(1):30.

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.

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.

An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.
Nature. 2012 Sep 6;489(7414):57-74.

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.

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. Erratum in: Genome Res. 2012 Mar;22(3):592.

Research resource: enhanced genome-wide occupancy of estrogen receptor α by the cochaperone p23 in breast cancer cells.
Simpson NE, Gertz J, Imberg K, Myers RM, Garabedian MJ.
Mol Endocrinol. 2012 Jan;26(1):194-202.

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.

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.
Gertz J, Siggia ED, Cohen BA.
Nature. 2009 Jan 8;457(7226):215-8.

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.
Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA.
Genome Res. 2005 Aug;15(8):1145-52.