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Items: 24

1.

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs.

Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE.

Nature. 2019 Nov;575(7781):229-233. doi: 10.1038/s41586-019-1668-3. Epub 2019 Oct 16.

PMID:
31666694
2.

Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors.

Cejas P, Drier Y, Dreijerink KMA, Brosens LAA, Deshpande V, Epstein CB, Conemans EB, Morsink FHM, Graham MK, Valk GD, Vriens MR, Castillo CF, Ferrone CR, Adar T, Bowden M, Whitton HJ, Da Silva A, Font-Tello A, Long HW, Gaskell E, Shoresh N, Heaphy CM, Sicinska E, Kulke MH, Chung DC, Bernstein BE, Shivdasani RA.

Nat Med. 2019 Oct;25(10):1627. doi: 10.1038/s41591-019-0573-5.

PMID:
31501535
3.

Targeting FGFR overcomes EMT-mediated resistance in EGFR mutant non-small cell lung cancer.

Raoof S, Mulford IJ, Frisco-Cabanos H, Nangia V, Timonina D, Labrot E, Hafeez N, Bilton SJ, Drier Y, Ji F, Greenberg M, Williams A, Kattermann K, Damon L, Sovath S, Rakiec DP, Korn JM, Ruddy DA, Benes CH, Hammerman PS, Piotrowska Z, Sequist LV, Niederst MJ, Barretina J, Engelman JA, Hata AN.

Oncogene. 2019 Sep;38(37):6399-6413. doi: 10.1038/s41388-019-0887-2. Epub 2019 Jul 19.

4.

Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors.

Cejas P, Drier Y, Dreijerink KMA, Brosens LAA, Deshpande V, Epstein CB, Conemans EB, Morsink FHM, Graham MK, Valk GD, Vriens MR, Castillo CF, Ferrone CR, Adar T, Bowden M, Whitton HJ, Da Silva A, Font-Tello A, Long HW, Gaskell E, Shoresh N, Heaphy CM, Sicinska E, Kulke MH, Chung DC, Bernstein BE, Shivdasani RA.

Nat Med. 2019 Aug;25(8):1260-1265. doi: 10.1038/s41591-019-0493-4. Epub 2019 Jul 1. Erratum in: Nat Med. 2019 Oct;25(10):1627.

5.

Epithelial-to-Mesenchymal Transition Antagonizes Response to Targeted Therapies in Lung Cancer by Suppressing BIM.

Song KA, Niederst MJ, Lochmann TL, Hata AN, Kitai H, Ham J, Floros KV, Hicks MA, Hu H, Mulvey HE, Drier Y, Heisey DAR, Hughes MT, Patel NU, Lockerman EL, Garcia A, Gillepsie S, Archibald HL, Gomez-Caraballo M, Nulton TJ, Windle BE, Piotrowska Z, Sahingur SE, Taylor SM, Dozmorov M, Sequist LV, Bernstein B, Ebi H, Engelman JA, Faber AC.

Clin Cancer Res. 2018 Jan 1;24(1):197-208. doi: 10.1158/1078-0432.CCR-17-1577. Epub 2017 Oct 19.

6.

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer.

Shah N, Wang P, Wongvipat J, Karthaus WR, Abida W, Armenia J, Rockowitz S, Drier Y, Bernstein BE, Long HW, Freedman ML, Arora VK, Zheng D, Sawyers CL.

Elife. 2017 Sep 11;6. pii: e27861. doi: 10.7554/eLife.27861.

7.

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation.

Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CW.

Nat Genet. 2017 Feb;49(2):289-295. doi: 10.1038/ng.3746. Epub 2016 Dec 12.

8.

Genetic interrogation of circulating multiple myeloma cells at single-cell resolution.

Lohr JG, Kim S, Gould J, Knoechel B, Drier Y, Cotton MJ, Gray D, Birrer N, Wong B, Ha G, Zhang CZ, Guo G, Meyerson M, Yee AJ, Boehm JS, Raje N, Golub TR.

Sci Transl Med. 2016 Nov 2;8(363):363ra147.

9.

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE.

Nat Genet. 2016 Mar;48(3):265-72. doi: 10.1038/ng.3502. Epub 2016 Feb 1.

10.

Insulator dysfunction and oncogene activation in IDH mutant gliomas.

Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE.

Nature. 2016 Jan 7;529(7584):110-4. doi: 10.1038/nature16490. Epub 2015 Dec 23.

11.

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes.

van Galen P, Viny AD, Ram O, Ryan RJ, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE.

Mol Cell. 2016 Jan 7;61(1):170-80. doi: 10.1016/j.molcel.2015.11.003. Epub 2015 Dec 10.

12.

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.

Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE.

Cancer Discov. 2015 Oct;5(10):1058-71. doi: 10.1158/2159-8290.CD-15-0370. Epub 2015 Jul 30.

13.

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.

Gagliani N, Amezcua Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, Cotton MJ, Drier Y, Bernstein B, Geginat J, Stockinger B, Esplugues E, Huber S, Flavell RA.

Nature. 2015 Jul 9;523(7559):221-5. doi: 10.1038/nature14452. Epub 2015 Apr 29.

14.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G.

Nature. 2013 Jul 11;499(7457):214-218. doi: 10.1038/nature12213. Epub 2013 Jun 16.

15.

Punctuated evolution of prostate cancer genomes.

Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA.

Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021.

16.

Pathway-based personalized analysis of cancer.

Drier Y, Sheffer M, Domany E.

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6388-93. doi: 10.1073/pnas.1219651110. Epub 2013 Apr 1.

17.

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.

Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G.

Genome Res. 2013 Feb;23(2):228-35. doi: 10.1101/gr.141382.112. Epub 2012 Nov 2.

18.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

19.

Melanoma genome sequencing reveals frequent PREX2 mutations.

Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA.

Nature. 2012 May 9;485(7399):502-6. doi: 10.1038/nature11071.

20.

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.

Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG Jr, Spardy N, Hahn WC, Hoshida Y, Ogino S, DePinho RA, Chin L, Garraway LA, Fuchs CS, Baselga J, Tabernero J, Gabriel S, Lander ES, Getz G, Meyerson M.

Nat Genet. 2011 Sep 4;43(10):964-968. doi: 10.1038/ng.936.

21.

Two phases of mitogenic signaling unveil roles for p53 and EGR1 in elimination of inconsistent growth signals.

Zwang Y, Sas-Chen A, Drier Y, Shay T, Avraham R, Lauriola M, Shema E, Lidor-Nili E, Jacob-Hirsch J, Amariglio N, Lu Y, Mills GB, Rechavi G, Oren M, Domany E, Yarden Y.

Mol Cell. 2011 May 20;42(4):524-35. doi: 10.1016/j.molcel.2011.04.017.

22.

Initial genome sequencing and analysis of multiple myeloma.

Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR.

Nature. 2011 Mar 24;471(7339):467-72. doi: 10.1038/nature09837.

23.

Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes?

Drier Y, Domany E.

PLoS One. 2011 Mar 14;6(3):e17795. doi: 10.1371/journal.pone.0017795.

24.

The genomic complexity of primary human prostate cancer.

Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA.

Nature. 2011 Feb 10;470(7333):214-20. doi: 10.1038/nature09744.

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