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Items: 21

1.

Systematic genomic and translational efficiency studies of uveal melanoma.

Johnson CP, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Lane AM, Gragoudas ES, Vazquez F, Nickerson E, Cibulskis K, McKenna A, Gabriel SB, Getz G, Van Allen EM, 't Hoen PAC, Garraway LA, Woodman SE.

PLoS One. 2017 Jun 8;12(6):e0178189. doi: 10.1371/journal.pone.0178189. eCollection 2017.

2.

The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis.

Gibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G, Carter SL, Beroukhim R, Salvesen HB.

Nat Genet. 2016 Aug;48(8):848-55. doi: 10.1038/ng.3602. Epub 2016 Jun 27.

3.

RNF43 is frequently mutated in colorectal and endometrial cancers.

Giannakis M, Hodis E, Jasmine Mu X, Yamauchi M, Rosenbluh J, Cibulskis K, Saksena G, Lawrence MS, Qian ZR, Nishihara R, Van Allen EM, Hahn WC, Gabriel SB, Lander ES, Getz G, Ogino S, Fuchs CS, Garraway LA.

Nat Genet. 2014 Dec;46(12):1264-6. doi: 10.1038/ng.3127. Epub 2014 Oct 26.

4.

Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters.

Zeevi D, Lubliner S, Lotan-Pompan M, Hodis E, Vesterman R, Weinberger A, Segal E.

Genome Res. 2014 Dec;24(12):1991-9. doi: 10.1101/gr.179259.114. Epub 2014 Oct 7.

5.

Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib.

Wagle N, Grabiner BC, Van Allen EM, Hodis E, Jacobus S, Supko JG, Stewart M, Choueiri TK, Gandhi L, Cleary JM, Elfiky AA, Taplin ME, Stack EC, Signoretti S, Loda M, Shapiro GI, Sabatini DM, Lander ES, Gabriel SB, Kantoff PW, Garraway LA, Rosenberg JE.

Cancer Discov. 2014 May;4(5):546-53. doi: 10.1158/2159-8290.CD-13-0353. Epub 2014 Mar 13.

6.

MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition.

Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, Rosenberg M, Goetz EM, Sullivan RJ, Farlow DN, Friedrich DC, Anderka K, Perrin D, Johannessen CM, McKenna A, Cibulskis K, Kryukov G, Hodis E, Lawrence DP, Fisher S, Getz G, Gabriel SB, Carter SL, Flaherty KT, Wargo JA, Garraway LA.

Cancer Discov. 2014 Jan;4(1):61-8. doi: 10.1158/2159-8290.CD-13-0631. Epub 2013 Nov 21.

7.

The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma.

Van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, Place CS, Taylor-Weiner A, Whittaker S, Kryukov GV, Hodis E, Rosenberg M, McKenna A, Cibulskis K, Farlow D, Zimmer L, Hillen U, Gutzmer R, Goldinger SM, Ugurel S, Gogas HJ, Egberts F, Berking C, Trefzer U, Loquai C, Weide B, Hassel JC, Gabriel SB, Carter SL, Getz G, Garraway LA, Schadendorf D; Dermatologic Cooperative Oncology Group of Germany (DeCOG).

Cancer Discov. 2014 Jan;4(1):94-109. doi: 10.1158/2159-8290.CD-13-0617. Epub 2013 Nov 21.

8.

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.

9.

Highly recurrent TERT promoter mutations in human melanoma.

Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA.

Science. 2013 Feb 22;339(6122):957-9. doi: 10.1126/science.1229259. Epub 2013 Jan 24.

10.

Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.

Machado AC, Saleebyan SB, Holmes BT, Karelina M, Tam J, Kim SY, Kim KH, Dror I, Hodis E, Martz E, Compeau PA, Rohs R.

Biochem Mol Biol Educ. 2012 Nov-Dec;40(6):400-1. doi: 10.1002/bmb.20650. Epub 2012 Oct 13.

11.

Proteopedia entry: "Tutorial: How we get the oxygen we breathe".

Prilusky J, Hodis E.

Biochem Mol Biol Educ. 2012 Sep-Oct;40(5):339. doi: 10.1002/bmb.20646. No abstract available.

12.

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.

Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M.

Cell. 2012 Sep 14;150(6):1107-20. doi: 10.1016/j.cell.2012.08.029.

13.

A landscape of driver mutations in melanoma.

Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander ES, Gabriel SB, Getz G, Garraway LA, Chin L.

Cell. 2012 Jul 20;150(2):251-63. doi: 10.1016/j.cell.2012.06.024.

14.

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.

15.

Proteopedia: A collaborative, virtual 3D web-resource for protein and biomolecule structure and function.

Hodis E, Prilusky J, Sussman JL.

Biochem Mol Biol Educ. 2010 Sep;38(5):341-2. doi: 10.1002/bmb.20431. No abstract available.

16.

Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules.

Prilusky J, Hodis E, Canner D, Decatur WA, Oberholser K, Martz E, Berchanski A, Harel M, Sussman JL.

J Struct Biol. 2011 Aug;175(2):244-52. doi: 10.1016/j.jsb.2011.04.011. Epub 2011 Apr 23.

PMID:
21536137
17.

Overlapping codes within protein-coding sequences.

Itzkovitz S, Hodis E, Segal E.

Genome Res. 2010 Nov;20(11):1582-9. doi: 10.1101/gr.105072.110. Epub 2010 Sep 14.

18.

An encyclopedic effort to make 3D structures easier to understand.

Hodis E, Sussman JL.

Trends Biochem Sci. 2009 Mar;34(3):100-1. doi: 10.1016/j.tibs.2009.01.001. Epub 2009 Feb 18. No abstract available.

PMID:
19230677
19.

Fabrication of a layered microstructured polycaprolactone construct for 3-D tissue engineering.

Sarkar S, Isenberg BC, Hodis E, Leach JB, Desai TA, Wong JY.

J Biomater Sci Polym Ed. 2008;19(10):1347-62. doi: 10.1163/156856208786052371.

20.

Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.

Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL.

Genome Biol. 2008;9(8):R121. doi: 10.1186/gb-2008-9-8-r121. Epub 2008 Aug 3.

21.

eMovie: a storyboard-based tool for making molecular movies.

Hodis E, Schreiber G, Rother K, Sussman JL.

Trends Biochem Sci. 2007 May;32(5):199-204. Epub 2007 Apr 19.

PMID:
17448663

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