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Items: 45

1.

Addendum: 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. 2019 Jan;565(7738):E5-E6. doi: 10.1038/s41586-018-0722-x. No abstract available.

PMID:
30559381
2.

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC.

Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

3.

Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy.

Medler TR, Murugan D, Horton W, Kumar S, Cotechini T, Forsyth AM, Leyshock P, Leitenberger JJ, Kulesz-Martin M, Margolin AA, Werb Z, Coussens LM.

Cancer Cell. 2018 Oct 8;34(4):561-578.e6. doi: 10.1016/j.ccell.2018.09.003.

4.

SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks.

Burlingame EA, Margolin AA, Gray JW, Chang YH.

Proc SPIE Int Soc Opt Eng. 2018 Feb;10581. pii: 1058105. doi: 10.1117/12.2293249. Epub 2018 Mar 6.

5.

Valection: design optimization for validation and verification studies.

Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P'ng C, Houlahan KE, Caloian C, Fraser M; SMC-DNA Challenge Participants, Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Sep 25;19(1):339. doi: 10.1186/s12859-018-2391-z.

6.

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism.

Davis RJ, Gönen M, Margineantu DH, Handeli S, Swanger J, Hoellerbauer P, Paddison PJ, Gu H, Raftery D, Grim JE, Hockenbery DM, Margolin AA, Clurman BE.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5462-5467. doi: 10.1073/pnas.1718338115. Epub 2018 May 7.

7.

Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer.

Xu C, Nikolova O, Basom RS, Mitchell RM, Shaw R, Moser RD, Park H, Gurley KE, Kao MC, Green CL, Schaub FX, Diaz RL, Swan HA, Jang IS, Guinney J, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Méndez E.

Clin Cancer Res. 2018 Jun 15;24(12):2828-2843. doi: 10.1158/1078-0432.CCR-17-1339. Epub 2018 Mar 29.

8.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0.

9.

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.

Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.

Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.

10.

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.

Tsujikawa T, Kumar S, Borkar RN, Azimi V, Thibault G, Chang YH, Balter A, Kawashima R, Choe G, Sauer D, El Rassi E, Clayburgh DR, Kulesz-Martin MF, Lutz ER, Zheng L, Jaffee EM, Leyshock P, Margolin AA, Mori M, Gray JW, Flint PW, Coussens LM.

Cell Rep. 2017 Apr 4;19(1):203-217. doi: 10.1016/j.celrep.2017.03.037.

11.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL.

Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. No abstract available.

12.

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies.

Nikolova O, Moser R, Kemp C, Gönen M, Margolin AA.

Bioinformatics. 2017 May 1;33(9):1362-1369. doi: 10.1093/bioinformatics/btw836.

13.

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. Epub 2015 Nov 16.

14.

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. Epub 2015 Jul 13.

15.

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. Epub 2015 May 18.

16.
17.

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.

18.

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. eCollection 2014.

19.

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.

20.

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.

21.

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 MDM, 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):929-944. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7.

22.

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. Epub 2014 Jun 22.

23.

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):318-319. doi: 10.1038/ng.2932. No abstract available.

24.

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.

26.

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.

27.

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. Epub 2013 May 9.

28.

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.

29.

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. Epub 2012 Dec 26.

30.

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.

31.

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. Erratum in: Nature. 2019 Jan;565(7738):E5-E6.

32.

Multivariate dependence and genetic networks inference.

Margolin AA, Wang K, Califano A, Nemenman I.

IET Syst Biol. 2010 Nov;4(6):428-40. doi: 10.1049/iet-syb.2010.0009.

PMID:
21073241
33.

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. Epub 2009 Dec 3.

34.

Empirical Bayes analysis of quantitative proteomics experiments.

Margolin AA, Ong SE, Schenone M, Gould R, Schreiber SL, Carr SA, Golub TR.

PLoS One. 2009 Oct 14;4(10):e7454. doi: 10.1371/journal.pone.0007454.

35.

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A.

Nat Biotechnol. 2009 Sep;27(9):829-39. doi: 10.1038/nbt.1563. Epub 2009 Sep 9.

36.

Identifying the proteins to which small-molecule probes and drugs bind in cells.

Ong SE, Schenone M, Margolin AA, Li X, Do K, Doud MK, Mani DR, Kuai L, Wang X, Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub TR, Gould RJ, Schreiber SL, Carr SA.

Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4617-22. doi: 10.1073/pnas.0900191106. Epub 2009 Mar 2.

37.

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9. doi: 10.1073/pnas.0806445106. Epub 2008 Dec 31.

38.

Theory and limitations of genetic network inference from microarray data.

Margolin AA, Califano A.

Ann N Y Acad Sci. 2007 Dec;1115:51-72. Epub 2007 Oct 9. Review.

PMID:
17925348
39.

Reverse engineering cellular networks.

Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A.

Nat Protoc. 2006;1(2):662-71.

PMID:
17406294
40.

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.

41.

PEG10 is a c-MYC target gene in cancer cells.

Li CM, Margolin AA, Salas M, Memeo L, Mansukhani M, Hibshoosh H, Szabolcs M, Klinakis A, Tycko B.

Cancer Res. 2006 Jan 15;66(2):665-72.

42.

Boolean calculations made easy (for ribozymes).

Margolin AA, Stojanovic MN.

Nat Biotechnol. 2005 Nov;23(11):1374-6. No abstract available.

PMID:
16273066
43.

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.

Margolin AA, Greshock J, Naylor TL, Mosse Y, Maris JM, Bignell G, Saeed AI, Quackenbush J, Weber BL.

Bioinformatics. 2005 Aug 1;21(15):3308-11. Epub 2005 May 19.

PMID:
15905276
44.

Reverse engineering of regulatory networks in human B cells.

Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A.

Nat Genet. 2005 Apr;37(4):382-90. Epub 2005 Mar 20.

PMID:
15778709
45.

CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors.

Li CM, Kim CE, Margolin AA, Guo M, Zhu J, Mason JM, Hensle TW, Murty VV, Grundy PE, Fearon ER, D'Agati V, Licht JD, Tycko B.

Am J Pathol. 2004 Dec;165(6):1943-53.

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