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BRADLEY MCINTOSH BROOM

TitleProfessor
InstitutionMD Anderson
DepartmentBioinformatics & Computational Biology
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Maximov PY, Abderrahman B, Hawsawi YM, Chen Y, Foulds CE, Jain A, Malovannaya A, Fan P, Curpan RF, Han R, Fanning SW, Broom BM, Quintana Rincon DM, Greenland JA, Greene GL, Jordan VC. The Structure-Function Relationship of Angular Estrogens and Estrogen Receptor Alpha to Initiate Estrogen-Induced Apoptosis in Breast Cancer Cells. Mol Pharmacol. 2020 May 03. PMID: 32362585.
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    2. Mokkapati S, Porten SP, Narayan VM, Lim AH, Jayaratna IS, Roth B, Cheng T, Navai N, Wszolek M, Melquist J, Manyam G, Choi W, Broom B, Pretzsch S, Czerniak B, McConkey DJ, Dinney CPN. TCF21 Promotes Luminal-Like Differentiation and Suppresses Metastasis in Bladder Cancer. Mol Cancer Res. 2020 Mar 02. PMID: 32122956.
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    3. Ryan MC, Stucky M, Wakefield C, Melott JM, Akbani R, Weinstein JN, Broom BM. Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Res. 2019; 8. PMID: 32269754.
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    4. Liu B, Li L, Yang G, Geng C, Luo Y, Wu W, Manyam GC, Korentzelos D, Park S, Tang Z, Wu C, Dong Z, Sigouros M, Sboner A, Beltran H, Chen Y, Corn PG, Tetzlaff MT, Troncoso P, Broom B, Thompson TC. PARP Inhibition Suppresses GR-MYCN-CDK5-RB1-E2F1 Signaling and Neuroendocrine Differentiation in Castration-Resistant Prostate Cancer. Clin Cancer Res. 2019 11 15; 25(22):6839-6851. PMID: 31439587.
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    5. Menter DG, Davis JS, Broom BM, Overman MJ, Morris J, Kopetz S. Back to the Colorectal Cancer Consensus Molecular Subtype Future. Curr Gastroenterol Rep. 2019 Jan 30; 21(2):5. PMID: 30701321.
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    6. 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. Targeting the MYCN-PARP-DNA Damage Response Pathway in Neuroendocrine Prostate Cancer. Clin Cancer Res. 2018 02 01; 24(3):696-707. PMID: 29138344.
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    7. Broom BM, Ryan MC, Brown RE, Ikeda F, Stucky M, Kane DW, Melott J, Wakefield C, Casasent TD, Akbani R, Weinstein JN. A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data. Cancer Res. 2017 11 01; 77(21):e23-e26. PMID: 29092932.
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    8. Thompson TC, Li L, Broom BM. Combining enzalutamide with PARP inhibitors: Pharmaceutically induced BRCAness. Oncotarget. 2017 Nov 07; 8(55):93315-93316. PMID: 29212150.
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    9. Clarke CN, Lee MS, Wei W, Manyam G, Jiang ZQ, Lu Y, Morris J, Broom B, Menter D, Vilar-Sanchez E, Raghav K, Eng C, Chang GJ, Simon I, Bernards R, Overman M, Mills GB, Maru D, Kopetz S. Proteomic Features of Colorectal Cancer Identify Tumor Subtypes Independent of Oncogenic Mutations and Independently Predict Relapse-Free Survival. Ann Surg Oncol. 2017 Dec; 24(13):4051-4058. PMID: 28936799.
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    10. 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. NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas. Cancer Res. 2017 09 15; 77(18):4835-4845. PMID: 28754676.
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    11. 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. Androgen receptor inhibitor-induced "BRCAness" and PARP inhibition are synthetically lethal for castration-resistant prostate cancer. Sci Signal. 2017 May 23; 10(480). PMID: 28536297.
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    12. 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. Modeling of Patient-Derived Xenografts in Colorectal Cancer. Mol Cancer Ther. 2017 07; 16(7):1435-1442. PMID: 28468778.
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    13. Karanika S, Karantanos T, Li L, Wang J, Park S, Yang G, Zuo X, Song JH, Maity SN, Manyam GC, Broom B, Aparicio AM, Gallick GE, Troncoso P, Corn PG, Navone N, Zhang W, Li S, Thompson TC. Targeting DNA Damage Response in Prostate Cancer by Inhibiting Androgen Receptor-CDC6-ATR-Chk1 Signaling. Cell Rep. 2017 02 21; 18(8):1970-1981. PMID: 28228262.
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    14. Overman MJ, Morris V, Moinova H, Manyam G, Ensor J, Lee MS, Eng C, Kee B, Fogelman D, Shroff RT, LaFramboise T, Mazard T, Feng T, Hamilton S, Broom B, Lutterbaugh J, Issa JP, Markowitz SD, Kopetz S. Phase I/II study of azacitidine and capecitabine/oxaliplatin (CAPOX) in refractory CIMP-high metastatic colorectal cancer: evaluation of circulating methylated vimentin. Oncotarget. 2016 Oct 11; 7(41):67495-67506. PMID: 27542211.
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    15. Raghav K, Morris V, Tang C, Morelli P, Amin HM, Chen K, Manyam GC, Broom B, Overman MJ, Shaw K, Meric-Bernstam F, Maru D, Menter D, Ellis LM, Eng C, Hong D, Kopetz S. MET amplification in metastatic colorectal cancer: an acquired response to EGFR inhibition, not a de novo phenomenon. Oncotarget. 2016 08 23; 7(34):54627-54631. PMID: 27421137.
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    16. Karantanos T, Karanika S, Wang J, Yang G, Dobashi M, Park S, Ren C, Li L, Basourakos SP, Hoang A, Efstathiou E, Wang X, Troncoso P, Titus M, Broom B, Kim J, Corn PG, Logothetis CJ, Thompson TC. Caveolin-1 regulates hormone resistance through lipid synthesis, creating novel therapeutic opportunities for castration-resistant prostate cancer. Oncotarget. 2016 Jul 19; 7(29):46321-46334. PMID: 27331874.
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    17. Ryan M, Wong WC, Brown R, Akbani R, Su X, Broom B, Melott J, Weinstein J. TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Res. 2016 Jan 04; 44(D1):D1018-22. PMID: 26602693.
      View in: PubMed
    18. Aparicio AM, Shen L, Tapia EL, Lu JF, Chen HC, Zhang J, Wu G, Wang X, Troncoso P, Corn P, Thompson TC, Broom B, Baggerly K, Maity SN, Logothetis CJ. Combined Tumor Suppressor Defects Characterize Clinically Defined Aggressive Variant Prostate Cancers. Clin Cancer Res. 2016 Mar 15; 22(6):1520-30. PMID: 26546618.
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    19. Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015 Nov; 21(11):1350-6. PMID: 26457759.
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    20. Melott JM, Weinstein JN, Broom BM. PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. Bioinformatics. 2016 Jan 15; 32(2):312-4. PMID: 26400039.
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    21. 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. Corrigendum: A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun. 2015 Jan 28; 6:4852. PMID: 25629879.
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    22. 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. Inhibition of mTORC1/2 overcomes resistance to MAPK pathway inhibitors mediated by PGC1a and oxidative phosphorylation in melanoma. Cancer Res. 2014 Dec 01; 74(23):7037-47. PMID: 25297634.
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    23. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31; 511(7511):543-50. PMID: 25079552.
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    24. 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. A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun. 2014 May 29; 5:3887. PMID: 24871328.
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    25. Li L, Chang W, Yang G, Ren C, Park S, Karantanos T, Karanika S, Wang J, Yin J, Shah PK, Takahiro H, Dobashi M, Zhang W, Efstathiou E, Maity SN, Aparicio AM, Li Ning Tapia EM, Troncoso P, Broom B, Xiao L, Lee HS, Lee JS, Corn PG, Navone N, Thompson TC. Targeting poly(ADP-ribose) polymerase and the c-Myb-regulated DNA damage response pathway in castration-resistant prostate cancer. Sci Signal. 2014 May 20; 7(326):ra47. PMID: 24847116.
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    26. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20; 507(7492):315-22. PMID: 24476821.
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    27. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849.
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    28. 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. TCPA: a resource for cancer functional proteomics data. Nat Methods. 2013 Nov; 10(11):1046-7. PMID: 24037243.
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    29. Overman MJ, Zhang J, Kopetz S, Davies M, Jiang ZQ, Zhi-Qin J, Stemke-Hale K, Rümmele P, Pilarsky C, Grützmann R, Hamilton S, Hwang R, Abbruzzese JL, Varadhachary G, Broom B, Wang H. Gene expression profiling of ampullary carcinomas classifies ampullary carcinomas into biliary-like and intestinal-like subtypes that are prognostic of outcome. PLoS One. 2013; 8(6):e65144. PMID: 23776447.
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    30. Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73. PMID: 23636398.
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    31. Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ, 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. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013 05 30; 368(22):2059-74. PMID: 23634996.
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    32. Wang W, Baladandayuthapani V, Morris JS, Broom BM, Manyam G, Do KA. iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data. Bioinformatics. 2013 Jan 15; 29(2):149-59. PMID: 23142963.
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    33. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27; 489(7417):519-25. PMID: 22960745.
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    34. Broom BM, Do KA, Subramanian D. Model averaging strategies for structure learning in Bayesian networks with limited data. BMC Bioinformatics. 2012; 13 Suppl 13:S10. PMID: 23320818.
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    35. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407):330-7. PMID: 22810696.
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    36. 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. Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer. PLoS One. 2011; 6(8):e23543. PMID: 21858162.
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    37. Ahmed AA, Wang X, Lu Z, Goldsmith J, Le XF, Grandjean G, Bartholomeusz G, Broom B, Bast RC. Modulating microtubule stability enhances the cytotoxic response of cancer cells to Paclitaxel. Cancer Res. 2011 Sep 01; 71(17):5806-17. PMID: 21775522.
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    38. Bonato V, Baladandayuthapani V, Broom BM, Sulman EP, Aldape KD, Do KA. Bayesian ensemble methods for survival prediction in gene expression data. Bioinformatics. 2011 Feb 01; 27(3):359-67. PMID: 21148161.
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    39. Broom BM, Sulman EP, Do KA, Edgerton ME. Bagged gene shaving for the robust clustering of high-throughput data. Int J Bioinform Res Appl. 2010; 6(4):326-43. PMID: 20940121.
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    40. Broom BM, Rinsurongkawong W, Pusztai L, Do KA. Building networks with microarray data. Methods Mol Biol. 2010; 620:315-43. PMID: 20652510.
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    41. Sanga S, Broom BM, Cristini V, Edgerton ME. Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family. BMC Med Genomics. 2009 Sep 11; 2:59. PMID: 19747394.
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    42. Koch M, Broom BM, Subramanian D. Learning robust cell signalling models from high throughput proteomic data. Int J Bioinform Res Appl. 2009; 5(3):241-53. PMID: 19525198.
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    43. Deus HF, Stanislaus R, Behrens C, Wistuba II, Minna JD, Garner HR, Swisher SG, Roth JA, Correa AM, Broom B, Coombes K, Almeida JS. Data driven semantic integration of translational lung cancer research at MDAnderson Cancer Center. AMIA Annu Symp Proc. 2008 Nov 06; 927. PMID: 18999102.
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    44. Deus HF, Stanislaus R, Veiga DF, Behrens C, Wistuba II, Minna JD, Garner HR, Swisher SG, Roth JA, Correa AM, Broom B, Coombes K, Chang A, Vogel LH, Almeida JS. A Semantic Web management model for integrative biomedical informatics. PLoS One. 2008 Aug 13; 3(8):e2946. PMID: 18698353.
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    45. Broom BM, McDonnell TJ, Subramanian D. Predicting altered pathways using extendable scaffolds. Int J Bioinform Res Appl. 2006; 2(1):3-18. PMID: 18048150.
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    46. Do KA, Broom BM, Kuhnert P, Duffy DL, Todorov AA, Treloar SA, Martin NG. Genetic analysis of the age at menopause by using estimating equations and Bayesian random effects models. Stat Med. 2000 May 15; 19(9):1217-35. PMID: 10797518.
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    47. Broom B, Lond MB. Oxygen therapy--QED? N Engl J Med. 1968 Apr 18; 278(16):917. PMID: 5641178.
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    48. BROOM B. EFFECT OF HYPOXIA ON THE RABBIT DURING EXPOSURE TO COLD. Nature. 1964 Aug 01; 203:498-9. PMID: 14202370.
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    49. BROOM B. EFFECTS OF AIR, OXYGEN AND 20 PER CENT CARBON DIOXIDE ON THE RABBIT DURING SURFACE COOLING DOWN TO CARDIAC ARREST. Nature. 1963 Sep 21; 199:1155-8. PMID: 14072030.
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    50. BROOM B. Effects of 20 per cent carbon dioxide in oxygen, and 25 per cent air in oxygen, on the body temperature of the rat during surface cooling. Nature. 1962 Mar 31; 193:1262-3. PMID: 13873485.
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    51. The consensus molecular subtypes of colorectal cancer. Nature Medicine. 21:1350-1356.
    52. Implementation of a secure version of NFS including RBAC. Australian Computer Journal. 31:54-60.
    53. Design rationale for a language-based editor. Software - Practice and Experience. 21:923-948.
    54. Corrigendum. Nature Communications. 6.
    55. A uniform approach to securing unix applications using sesame. 24-35.
    56. An implementation of a secure version of NFS including RBAC. Journal of Research and Practice in Information Technology. 31:54-59.
    57. Telescoping languages. Journal of Parallel and Distributed Computing. 61:1803-1826.
    58. Phase I/II study of azacitidine and capecitabine/oxaliplatin (CAPOX) in refractory CIMP-high metastatic colorectal cancer. Oncotarget. 7:67495-67506.
    59. Erratum. PLoS One. 8.
    60. Advanced optimization strategies in the Rice dHPF compiler. Concurrency Computation Practice and Experience. 14:741-767.
    61. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 163:1011-1025.
    62. Importance bootstrap resampling for proportional hazards regression. Communications in Statistics - Theory and Methods. 30:2173-2188.
    63. Combined tumor suppressor defects characterize clinically defined aggressive variant prostate cancers. Clinical Cancer Research. 22:1520-1530.
    64. MET amplification in metastatic colorectal cancer. Oncotarget. 7:54627-54631.
    65. An implementation of a secure version of NFS including RBAC. 213-227.
    66. Sequential linearization of empirical likelihood constraints with application to U-statistics. Journal of Computational and Graphical Statistics. 5:365-385.
    67. ANOTHER APPROACH TO LITERATE PROGRAMMING. 257-268.
    68. Caveolin-1 regulates hormone resistance through lipid synthesis, creating novel therapeutic opportunities for castration-resistant prostate cancer. Oncotarget. 7:46321-46334.
    69. TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Research. 44:D1018-D1022.
    70. PathwaysWeb. Bioinformatics. 32:312-314.
    71. Statistical Methods for Biomarker Discovery Using Mass Spectrometry. 465-486.
    72. Comprehensive molecular portraits of human breast tumours. Nature. 490:61-70.
    73. Telescoping languages. Proceedings of the IEEE. 93:387-408.
    74. KelpIO. Future Generation Computer Systems. 18:449-460.
    75. KelpIO. 148-155.
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