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Items: 1 to 50 of 56

1.

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines.

Carleton JB, Berrett KC, Gertz J.

J Vis Exp. 2018 Jun 2;(136). doi: 10.3791/57883.

PMID:
29912188
2.

Endocytosed factor V is trafficked to CD42b+ proplatelet extensions during differentiation of human umbilical cord blood-derived megakaryocytes.

Gertz JM, McLean KC, Bouchard BA.

J Cell Physiol. 2018 May 15. doi: 10.1002/jcp.26749. [Epub ahead of print]

PMID:
29761851
3.

Clinical and Genomic Crosstalk between Glucocorticoid Receptor and Estrogen Receptor α In Endometrial Cancer.

Vahrenkamp JM, Yang CH, Rodriguez AC, Almomen A, Berrett KC, Trujillo AN, Guillen KP, Welm BE, Jarboe EA, Janat-Amsbury MM, Gertz J.

Cell Rep. 2018 Mar 13;22(11):2995-3005. doi: 10.1016/j.celrep.2018.02.076.

4.

GIGGLE: a search engine for large-scale integrated genome analysis.

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR.

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.

5.

Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers.

Carleton JB, Berrett KC, Gertz J.

Cell Syst. 2017 Oct 25;5(4):333-344.e5. doi: 10.1016/j.cels.2017.08.011. Epub 2017 Sep 27.

PMID:
28964699
6.

Post-mortem molecular profiling of three psychiatric disorders.

Ramaker RC, Bowling KM, Lasseigne BN, Hagenauer MH, Hardigan AA, Davis NS, Gertz J, Cartagena PM, Walsh DM, Vawter MP, Jones EG, Schatzberg AF, Barchas JD, Watson SJ, Bunney BG, Akil H, Bunney WE, Li JZ, Cooper SJ, Myers RM.

Genome Med. 2017 Jul 28;9(1):72. doi: 10.1186/s13073-017-0458-5.

7.

Simultaneous flow cytometric analysis of megakaryocyte polyploidy and a labile intracellular protein using zinc-based fixation.

Gertz JM, Meuser M, Bouchard BA.

Cytometry A. 2017 Jul;91(7):713-720. doi: 10.1002/cyto.a.23161. Epub 2017 Jul 10.

8.

CRISPR Epigenome Editing of AKAP150 in DRG Neurons Abolishes Degenerative IVD-Induced Neuronal Activation.

Stover JD, Farhang N, Berrett KC, Gertz J, Lawrence B, Bowles RD.

Mol Ther. 2017 Sep 6;25(9):2014-2027. doi: 10.1016/j.ymthe.2017.06.010. Epub 2017 Jul 1.

PMID:
28676344
9.

MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition.

Mollaoglu G, Guthrie MR, Böhm S, Brägelmann 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.

Cancer Cell. 2017 Feb 13;31(2):270-285. doi: 10.1016/j.ccell.2016.12.005. Epub 2017 Jan 12.

10.

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.

11.

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.

Mol Cancer Res. 2016 Nov;14(11):1054-1067. Epub 2016 Aug 26.

12.

Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation.

Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM.

Genome Med. 2016 Jul 11;8(1):74. doi: 10.1186/s13073-016-0328-6.

13.

RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4.

Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM.

Mol Oncol. 2016 Oct;10(8):1169-82. doi: 10.1016/j.molonc.2016.05.004. Epub 2016 May 26.

14.

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.

Cancer Res. 2016 Apr 1;76(7):1916-25. doi: 10.1158/0008-5472.CAN-15-1629. Epub 2016 Jan 21.

15.

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; Breast Cancer Family Registry, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV.

J Med Genet. 2016 Jun;53(6):366-76. doi: 10.1136/jmedgenet-2015-103398. Epub 2016 Jan 19.

16.

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 Dec;25(12):1791-800. doi: 10.1101/gr.191593.115. Epub 2015 Oct 20.

17.

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.

18.

Mechanisms Regulating Acquisition of Platelet-Derived Factor V/Va by Megakaryocytes.

Gertz JM, Bouchard BA.

J Cell Biochem. 2015 Oct;116(10):2121-6. doi: 10.1002/jcb.25163.

PMID:
25800007
19.

Comparison of [¹¹C]choline ([¹¹C]CHO) and S(+)-β-methyl-[¹¹C]choline ([¹¹C]SMC) as imaging probes for prostate cancer in a PC-3 prostate cancer xenograft model.

Schwarzenböck SM, Gertz J, Souvatzoglou M, Kurth J, Sachs D, Nawroth R, Treiber U, Schuster T, Senekowitsch-Schmidtke R, Schwaiger M, Ziegler SI, Henriksen G, Wester HJ, Krause BJ.

Mol Imaging Biol. 2015 Apr;17(2):248-56. doi: 10.1007/s11307-014-0782-8.

PMID:
25163420
20.

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.

21.

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. doi: 10.1101/gr.161034.113. Epub 2013 Dec 3.

22.

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. doi: 10.1186/1756-8935-6-30.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

29.

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.

30.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

31.

The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes.

Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM.

Mol Cell Biol. 2012 Sep;32(18):3756-67. doi: 10.1128/MCB.00062-12. Epub 2012 Jul 16.

32.

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.

33.

IκB kinase epsilon (IKK(epsilon)) regulates the balance between type I and type II interferon responses.

Ng SL, Friedman BA, Schmid S, Gertz J, Myers RM, Tenoever BR, Maniatis T.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21170-5. doi: 10.1073/pnas.1119137109. Epub 2011 Dec 14.

34.

Platelet shape change and spreading.

Aslan JE, Itakura A, Gertz JM, McCarty OJ.

Methods Mol Biol. 2012;788:91-100. doi: 10.1007/978-1-61779-307-3_7.

PMID:
22130702
35.

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.

36.

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. doi: 10.1210/me.2011-1068. Epub 2011 Nov 10.

37.

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.

38.

Allele-specific distribution of RNA polymerase II on female X chromosomes.

Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF.

Hum Mol Genet. 2011 Oct 15;20(20):3964-73. doi: 10.1093/hmg/ddr315. Epub 2011 Jul 26.

39.

Innate immune responses and permissiveness to ranavirus infection of peritoneal leukocytes in the frog Xenopus laevis.

Morales HD, Abramowitz L, Gertz J, Sowa J, Vogel A, Robert J.

J Virol. 2010 May;84(10):4912-22. doi: 10.1128/JVI.02486-09. Epub 2010 Mar 3.

40.

Platelets and megakaryocytes contain functional nuclear factor-kappaB.

Spinelli SL, Casey AE, Pollock SJ, Gertz JM, McMillan DH, Narasipura SD, Mody NA, King MR, Maggirwar SB, Francis CW, Taubman MB, Blumberg N, Phipps RP.

Arterioscler Thromb Vasc Biol. 2010 Mar;30(3):591-8. doi: 10.1161/ATVBAHA.109.197343. Epub 2009 Dec 30.

41.

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions.

Gertz J, Gerke JP, Cohen BA.

Theor Popul Biol. 2010 Feb;77(1):1-5. doi: 10.1016/j.tpb.2009.10.002. Epub 2009 Oct 8.

42.

Identification of coagulation factor XI as a ligand for platelet apolipoprotein E receptor 2 (ApoER2).

White-Adams TC, Berny MA, Tucker EI, Gertz JM, Gailani D, Urbanus RT, de Groot PG, Gruber A, McCarty OJ.

Arterioscler Thromb Vasc Biol. 2009 Oct;29(10):1602-7. doi: 10.1161/ATVBAHA.109.187393. Epub 2009 Aug 6.

43.

Environment-specific combinatorial cis-regulation in synthetic promoters.

Gertz J, Cohen BA.

Mol Syst Biol. 2009;5:244. doi: 10.1038/msb.2009.1. Epub 2009 Feb 17.

44.

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.

Gertz J, Siggia ED, Cohen BA.

Nature. 2009 Jan 8;457(7226):215-8. doi: 10.1038/nature07521. Epub 2008 Nov 23.

45.

15-deoxy-delta12,14-PGJ2 enhances platelet production from megakaryocytes.

O'Brien JJ, Spinelli SL, Tober J, Blumberg N, Francis CW, Taubman MB, Palis J, Seweryniak KE, Gertz JM, Phipps RP.

Blood. 2008 Nov 15;112(10):4051-60. doi: 10.1182/blood-2008-05-158535. Epub 2008 Aug 28.

46.

A cis-regulatory logic simulator.

Zeigler RD, Gertz J, Cohen BA.

BMC Bioinformatics. 2007 Jul 27;8:272.

47.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

48.
49.

Inferring protein interactions from phylogenetic distance matrices.

Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B.

Bioinformatics. 2003 Nov 1;19(16):2039-45.

PMID:
14594708
50.

Pupil increment thresholds are influenced by color opponent mechanisms.

Krastel H, Alexandridis E, Gertz J.

Ophthalmologica. 1985;191(1):35-8.

PMID:
4034163

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