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Items: 23

1.

Back to the Colorectal Cancer Consensus Molecular Subtype Future.

Menter DG, Davis JS, Broom BM, Overman MJ, Morris J, Kopetz S.

Curr Gastroenterol Rep. 2019 Jan 30;21(2):5. doi: 10.1007/s11894-019-0674-9. Review.

2.

Combining enzalutamide with PARP inhibitors: Pharmaceutically induced BRCAness.

Thompson TC, Li L, Broom BM.

Oncotarget. 2017 Oct 25;8(55):93315-93316. doi: 10.18632/oncotarget.22074. eCollection 2017 Nov 7. No abstract available.

3.

Targeting the MYCN-PARP-DNA Damage Response Pathway in Neuroendocrine Prostate Cancer.

Zhang W, Liu B, Wu W, Li L, Broom BM, Basourakos SP, Korentzelos D, Luan Y, Wang J, Yang G, Park S, Azad AK, Cao X, Kim J, Corn PG, Logothetis CJ, Aparicio AM, Chinnaiyan AM, Navone N, Troncoso P, Thompson TC.

Clin Cancer Res. 2018 Feb 1;24(3):696-707. doi: 10.1158/1078-0432.CCR-17-1872. Epub 2017 Nov 14.

4.

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data.

Broom BM, Ryan MC, Brown RE, Ikeda F, Stucky M, Kane DW, Melott J, Wakefield C, Casasent TD, Akbani R, Weinstein JN.

Cancer Res. 2017 Nov 1;77(21):e23-e26. doi: 10.1158/0008-5472.CAN-17-0318.

5.

NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas.

Su X, Zhang J, Mouawad R, Compérat E, Rouprêt M, Allanic F, Parra J, Bitker MO, Thompson EJ, Gowrishankar B, Houldsworth J, Weinstein JN, Tost J, Broom BM, Khayat D, Spano JP, Tannir NM, Malouf GG.

Cancer Res. 2017 Sep 15;77(18):4835-4845. doi: 10.1158/0008-5472.CAN-17-0143. Epub 2017 Jul 28.

6.

Androgen receptor inhibitor-induced "BRCAness" and PARP inhibition are synthetically lethal for castration-resistant prostate cancer.

Li L, Karanika S, Yang G, Wang J, Park S, Broom BM, Manyam GC, Wu W, Luo Y, Basourakos S, Song JH, Gallick GE, Karantanos T, Korentzelos D, Azad AK, Kim J, Corn PG, Aparicio AM, Logothetis CJ, Troncoso P, Heffernan T, Toniatti C, Lee HS, Lee JS, Zuo X, Chang W, Yin J, Thompson TC.

Sci Signal. 2017 May 23;10(480). pii: eaam7479. doi: 10.1126/scisignal.aam7479.

7.

Modeling of Patient-Derived Xenografts in Colorectal Cancer.

Katsiampoura A, Raghav K, Jiang ZQ, Menter DG, Varkaris A, Morelli MP, Manuel S, Wu J, Sorokin AV, Rizi BS, Bristow C, Tian F, Airhart S, Cheng M, Broom BM, Morris J, Overman MJ, Powis G, Kopetz S.

Mol Cancer Ther. 2017 Jul;16(7):1435-1442. doi: 10.1158/1535-7163.MCT-16-0721. Epub 2017 May 3.

8.

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.

9.

Corrigendum: 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. 2015 Jan 28;6:4852. doi: 10.1038/ncomms5852. No abstract available.

PMID:
25629879
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

Building networks with microarray data.

Broom BM, Rinsurongkawong W, Pusztai L, Do KA.

Methods Mol Biol. 2010;620:315-43. doi: 10.1007/978-1-60761-580-4_10.

PMID:
20652510
20.
21.

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.

22.

Predicting altered pathways using extendable scaffolds.

Broom BM, McDonnell TJ, Subramanian D.

Int J Bioinform Res Appl. 2006;2(1):3-18.

PMID:
18048150
23.

Genetic analysis of the age at menopause by using estimating equations and Bayesian random effects models.

Do KA, Broom BM, Kuhnert P, Duffy DL, Todorov AA, Treloar SA, Martin NG.

Stat Med. 2000 May 15;19(9):1217-35.

PMID:
10797518

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