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Items: 12

1.

PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

Melott JM, Weinstein JN, Broom BM.

Bioinformatics. 2016 Jan 15;32(2):312-4. doi: 10.1093/bioinformatics/btv554. Epub 2015 Sep 23.

2.

Inhibition of mTORC1/2 overcomes resistance to MAPK pathway inhibitors mediated by PGC1α and oxidative phosphorylation in melanoma.

Gopal YN, Rizos H, Chen G, Deng W, Frederick DT, Cooper ZA, Scolyer RA, Pupo G, Komurov K, Sehgal V, Zhang J, Patel L, Pereira CG, Broom BM, Mills GB, Ram P, Smith PD, Wargo JA, Long GV, Davies MA.

Cancer Res. 2014 Dec 1;74(23):7037-47. doi: 10.1158/0008-5472.CAN-14-1392. Epub 2014 Oct 8.

3.

A pan-cancer proteomic perspective on The Cancer Genome Atlas.

Akbani R, Ng PK, Werner HM, Shahmoradgoli M, Zhang F, Ju Z, Liu W, Yang JY, Yoshihara K, Li J, Ling S, Seviour EG, Ram PT, Minna JD, Diao L, Tong P, Heymach JV, Hill SM, Dondelinger F, Städler N, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB.

Nat Commun. 2014 May 29;5:3887. doi: 10.1038/ncomms4887. Erratum in: Nat Commun. 2015;6:4852.

4.

TCPA: a resource for cancer functional proteomics data.

Li J, Lu Y, Akbani R, Ju Z, Roebuck PL, Liu W, Yang JY, Broom BM, Verhaak RG, Kane DW, Wakefield C, Weinstein JN, Mills GB, Liang H.

Nat Methods. 2013 Nov;10(11):1046-7. doi: 10.1038/nmeth.2650. Epub 2013 Sep 15. No abstract available.

5.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ Jr, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G.

N Engl J Med. 2013 May 30;368(22):2059-74. doi: 10.1056/NEJMoa1301689. Epub 2013 May 1. Erratum in: N Engl J Med. 2013 Jul 4;369(1):98.

6.

Model averaging strategies for structure learning in Bayesian networks with limited data.

Broom BM, Do KA, Subramanian D.

BMC Bioinformatics. 2012;13 Suppl 13:S10. doi: 10.1186/1471-2105-13-S13-S10. Epub 2012 Aug 24.

7.

iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data.

Wang W, Baladandayuthapani V, Morris JS, Broom BM, Manyam G, Do KA.

Bioinformatics. 2013 Jan 15;29(2):149-59. doi: 10.1093/bioinformatics/bts655. Epub 2012 Nov 9.

8.

Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer.

Thompson PA, Brewster AM, Kim-Anh D, Baladandayuthapani V, Broom BM, Edgerton ME, Hahn KM, Murray JL, Sahin A, Tsavachidis S, Wang Y, Zhang L, Hortobagyi GN, Mills GB, Bondy ML.

PLoS One. 2011;6(8):e23543. doi: 10.1371/journal.pone.0023543. Epub 2011 Aug 12.

9.

Bayesian ensemble methods for survival prediction in gene expression data.

Bonato V, Baladandayuthapani V, Broom BM, Sulman EP, Aldape KD, Do KA.

Bioinformatics. 2011 Feb 1;27(3):359-67. doi: 10.1093/bioinformatics/btq660. Epub 2010 Dec 8.

10.

Bagged gene shaving for the robust clustering of high-throughput data.

Broom BM, Sulman EP, Do KA, Edgerton ME; Kenneth D. Aldape.

Int J Bioinform Res Appl. 2010;6(4):326-43.

11.
12.

Learning robust cell signalling models from high throughput proteomic data.

Koch M, Broom BM, Subramanian D.

Int J Bioinform Res Appl. 2009;5(3):241-53.

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