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Items: 1 to 20 of 26

1.

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition.

Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H.

Nat Cell Biol. 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264.

2.

The NIH BD2K center for big data in translational genomics.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047.

3.

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants., Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC.

Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407.

4.
5.

Toward better benchmarking: challenge-based methods assessment in cancer genomics.

Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G.

Genome Biol. 2014 Sep 17;15(9):462. doi: 10.1186/s13059-014-0462-7.

6.

Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting.

Chaibub Neto E, Bare JC, Margolin AA.

PLoS One. 2014 Oct 7;9(10):e107957. doi: 10.1371/journal.pone.0107957.

7.

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning.

Gönen M, Margolin AA.

Bioinformatics. 2014 Sep 1;30(17):i556-63. doi: 10.1093/bioinformatics/btu464.

8.

Functional kinomics identifies candidate therapeutic targets in head and neck cancer.

Moser R, Xu C, Kao M, Annis J, Lerma LA, Schaupp CM, Gurley KE, Jang IS, Biktasova A, Yarbrough WG, Margolin AA, Grandori C, Kemp CJ, Méndez E.

Clin Cancer Res. 2014 Aug 15;20(16):4274-88. doi: 10.1158/1078-0432.CCR-13-2858.

9.

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network., Benz CC, Perou CM, Stuart JM.

Cell. 2014 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049.

10.

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H.

Nat Biotechnol. 2014 Jul;32(7):644-52. doi: 10.1038/nbt.2940.

11.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-9. doi: 10.1038/ng.2932. No abstract available.

12.

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.

Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA.

Pac Symp Biocomput. 2014:63-74.

14.

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.

Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA.

Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761.

15.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047.

16.

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.

Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL.

Sci Transl Med. 2013 Apr 17;5(181):181re1. doi: 10.1126/scitranslmed.3006112.

17.

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.

Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP.

Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.

18.

Chemical genomics identifies small-molecule MCL1 repressors and BCL-xL as a predictor of MCL1 dependency.

Wei G, Margolin AA, Haery L, Brown E, Cucolo L, Julian B, Shehata S, Kung AL, Beroukhim R, Golub TR.

Cancer Cell. 2012 Apr 17;21(4):547-62. doi: 10.1016/j.ccr.2012.02.028.

19.

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA.

Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003. Erratum in: Nature. 2012 Dec 13;492(7428):290.

20.

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.

Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R.

Blood. 2010 Feb 4;115(5):975-84. doi: 10.1182/blood-2009-06-227017.

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