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Items: 47

1.

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.

2.

Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.

3.

Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes.

McQuerry JA, Chang JT, Bowtell DDL, Cohen A, Bild AH.

J Mol Med (Berl). 2017 Nov;95(11):1167-1178. doi: 10.1007/s00109-017-1587-4. Epub 2017 Sep 4. Review.

PMID:
28871446
4.

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH.

Genome Med. 2017 Apr 26;9(1):40. doi: 10.1186/s13073-017-0429-x.

5.

A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia.

Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E; Cancer Prevention Network.

Cancer Prev Res (Phila). 2016 Dec;9(12):906-914. Epub 2016 Sep 22.

6.

The value of genomics in dissecting the RAS-network and in guiding therapeutics for RAS-driven cancers.

Shrestha G, MacNeil SM, McQuerry JA, Jenkins DF, Sharma S, Bild AH.

Semin Cell Dev Biol. 2016 Oct;58:108-17. doi: 10.1016/j.semcdb.2016.06.012. Epub 2016 Jun 20. Review.

7.

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

Piccolo SR, Hoffman LM, Conner T, Shrestha G, Cohen AL, Marks JR, Neumayer LA, Agarwal CA, Beckerle MC, Andrulis IL, Spira AE, Moos PJ, Buys SS, Johnson WE, Bild AH.

Mol Syst Biol. 2016 Mar 10;12(3):860. doi: 10.15252/msb.20156506.

8.

Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

Piccolo SR, Andrulis IL, Cohen AL, Conner T, Moos PJ, Spira AE, Buys SS, Johnson WE, Bild AH.

BMC Med Genomics. 2015 Nov 4;8:72. doi: 10.1186/s12920-015-0145-6.

9.

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.

Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR.

Bioinformatics. 2015 Nov 15;31(22):3666-72. doi: 10.1093/bioinformatics/btv377. Epub 2015 Jul 24.

10.

Inferring pathway dysregulation in cancers from multiple types of omic data.

MacNeil SM, Johnson WE, Li DY, Piccolo SR, Bild AH.

Genome Med. 2015 Jun 26;7(1):61. doi: 10.1186/s13073-015-0189-4. eCollection 2015.

11.

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.

Bioinformatics. 2015 Jun 1;31(11):1745-53. doi: 10.1093/bioinformatics/btv031. Epub 2015 Jan 22.

12.

Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer.

El-Chaar NN, Piccolo SR, Boucher KM, Cohen AL, Chang JT, Moos PJ, Bild AH.

Mol Oncol. 2014 Oct;8(7):1339-54. doi: 10.1016/j.molonc.2014.05.005. Epub 2014 May 20.

13.

Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition.

Zhang H, Cohen AL, Krishnakumar S, Wapnir IL, Veeriah S, Deng G, Coram MA, Piskun CM, Longacre TA, Herrler M, Frimannsson DO, Telli ML, Dirbas FM, Matin AC, Dairkee SH, Larijani B, Glinsky GV, Bild AH, Jeffrey SS.

Breast Cancer Res. 2014 Apr 7;16(2):R36. doi: 10.1186/bcr3640.

14.

A field guide to genomics research.

Bild AH, Chang JT, Johnson WE, Piccolo SR.

PLoS Biol. 2014 Jan;12(1):e1001744. doi: 10.1371/journal.pbio.1001744. Epub 2014 Jan 7. No abstract available.

15.

Multiplatform single-sample estimates of transcriptional activation.

Piccolo SR, Withers MR, Francis OE, Bild AH, Johnson WE.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17778-83. doi: 10.1073/pnas.1305823110. Epub 2013 Oct 15.

16.

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers.

Cohen AL, Piccolo SR, Cheng L, Soldi R, Han B, Johnson WE, Bild AH.

BMC Med Genomics. 2013 Sep 30;6:35. doi: 10.1186/1755-8794-6-35.

17.

A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment.

Steiling K, van den Berge M, Hijazi K, Florido R, Campbell J, Liu G, Xiao J, Zhang X, Duclos G, Drizik E, Si H, Perdomo C, Dumont C, Coxson HO, Alekseyev YO, Sin D, Pare P, Hogg JC, McWilliams A, Hiemstra PS, Sterk PJ, Timens W, Chang JT, Sebastiani P, O'Connor GT, Bild AH, Postma DS, Lam S, Spira A, Lenburg ME.

Am J Respir Crit Care Med. 2013 May 1;187(9):933-42. doi: 10.1164/rccm.201208-1449OC.

18.

SIRT1 pathway dysregulation in the smoke-exposed airway epithelium and lung tumor tissue.

Beane J, Cheng L, Soldi R, Zhang X, Liu G, Anderlind C, Lenburg ME, Spira A, Bild AH.

Cancer Res. 2012 Nov 15;72(22):5702-11. doi: 10.1158/0008-5472.CAN-12-1043. Epub 2012 Sep 17.

19.

A single-sample microarray normalization method to facilitate personalized-medicine workflows.

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE.

Genomics. 2012 Dec;100(6):337-44. doi: 10.1016/j.ygeno.2012.08.003. Epub 2012 Aug 19.

20.

Major differences among chemopreventive organoselenocompounds in the sustained elevation of cytoprotective genes.

Poerschke RL, Franklin MR, Bild AH, Moos PJ.

J Biochem Mol Toxicol. 2012 Sep;26(9):344-53. doi: 10.1002/jbt.21427. Epub 2012 Jul 16.

21.

A genomic approach to predict synergistic combinations for breast cancer treatment.

Soldi R, Cohen AL, Cheng L, Sun Y, Moos PJ, Bild AH.

Pharmacogenomics J. 2013 Feb;13(1):94-104. doi: 10.1038/tpj.2011.48. Epub 2011 Nov 15.

22.

A pharmacogenomic method for individualized prediction of drug sensitivity.

Cohen AL, Soldi R, Zhang H, Gustafson AM, Wilcox R, Welm BE, Chang JT, Johnson E, Spira A, Jeffrey SS, Bild AH.

Mol Syst Biol. 2011 Jul 19;7:513. doi: 10.1038/msb.2011.47.

23.

Retraction: A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-80.

Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, Kratzke R, Watson MA, Kelley M, Ginsburg GS, West M, Harpole DH Jr, Nevins JR.

N Engl J Med. 2011 Mar 24;364(12):1176. doi: 10.1056/NEJMc1101915. Epub 2011 Mar 2.

24.

Retraction: Genomic signatures to guide the use of chemotherapeutics.

Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, Cragun J, Cottrill H, Kelley MJ, Petersen R, Harpole D, Marks J, Berchuck A, Ginsburg GS, Febbo P, Lancaster J, Nevins JR.

Nat Med. 2011 Jan;17(1):135. doi: 10.1038/nm0111-135. No abstract available.

PMID:
21217686
25.

Airway PI3K pathway activation is an early and reversible event in lung cancer development.

Gustafson AM, Soldi R, Anderlind C, Scholand MB, Qian J, Zhang X, Cooper K, Walker D, McWilliams A, Liu G, Szabo E, Brody J, Massion PP, Lenburg ME, Lam S, Bild AH, Spira A.

Sci Transl Med. 2010 Apr 7;2(26):26ra25. doi: 10.1126/scitranslmed.3000251.

26.

Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery.

Tejpar S, Bertagnolli M, Bosman F, Lenz HJ, Garraway L, Waldman F, Warren R, Bild A, Collins-Brennan D, Hahn H, Harkin DP, Kennedy R, Ilyas M, Morreau H, Proutski V, Swanton C, Tomlinson I, Delorenzi M, Fiocca R, Van Cutsem E, Roth A.

Oncologist. 2010;15(4):390-404. doi: 10.1634/theoncologist.2009-0233. Epub 2010 Mar 29. Review.

27.

An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer.

Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM.

Breast Cancer Res. 2009;11(4):R55. doi: 10.1186/bcr2344. Epub 2009 Jul 28. Erratum in: Breast Cancer Res. 2011;13(4):406.

28.

A genomic strategy to elucidate modules of oncogenic pathway signaling networks.

Chang JT, Carvalho C, Mori S, Bild AH, Gatza ML, Wang Q, Lucas JE, Potti A, Febbo PG, West M, Nevins JR.

Mol Cell. 2009 Apr 10;34(1):104-14. doi: 10.1016/j.molcel.2009.02.030.

29.

Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma.

Mori S, Rempel RE, Chang JT, Yao G, Lagoo AS, Potti A, Bild A, Nevins JR.

Cancer Res. 2008 Oct 15;68(20):8525-34. doi: 10.1158/0008-5472.CAN-08-1329.

30.

An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer.

Dressman HK, Berchuck A, Chan G, Zhai J, Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsburg GS, Potti A, West M, Nevins JR, Lancaster JM.

J Clin Oncol. 2007 Feb 10;25(5):517-25. Retraction in: J Clin Oncol. 2012 Feb 20;30(6):678.

PMID:
17290060
31.

Genomic signatures in non-small-cell lung cancer: targeting the targeted therapies.

Dressman HK, Bild A, Garst J, Harpole D Jr, Potti A.

Curr Oncol Rep. 2006 Jul;8(4):252-7. Review.

PMID:
17254524
32.

Genomic signatures to guide the use of chemotherapeutics.

Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, Cragun J, Cottrill H, Kelley MJ, Petersen R, Harpole D, Marks J, Berchuck A, Ginsburg GS, Febbo P, Lancaster J, Nevins JR.

Nat Med. 2006 Nov;12(11):1294-300. Epub 2006 Oct 22. Erratum in: Nat Med. 2007 Nov;13(11):1388. Nat Med. 2008 Aug;14(8):889. Retraction in: Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, Cragun J, Cottrill H, Kelley MJ, Petersen R, Harpole D, Marks J, Berchuck A, Ginsburg GS, Febbo P, Lancaster J, Nevins JR. Nat Med. 2011 Jan;17(1):135.

PMID:
17057710
33.

Linking oncogenic pathways with therapeutic opportunities.

Bild AH, Potti A, Nevins JR.

Nat Rev Cancer. 2006 Sep;6(9):735-41. Epub 2006 Aug 17. Review.

PMID:
16915294
34.

Compensation and specificity of function within the E2F family.

Kong LJ, Chang JT, Bild AH, Nevins JR.

Oncogene. 2007 Jan 18;26(3):321-7. Epub 2006 Aug 14.

PMID:
16909124
35.

A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer.

Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, Kratzke R, Watson MA, Kelley M, Ginsburg GS, West M, Harpole DH Jr, Nevins JR.

N Engl J Med. 2006 Aug 10;355(6):570-80. Retraction in: Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, Kratzke R, Watson MA, Kelley M, Ginsburg GS, West M, Harpole DH Jr, Nevins JR. N Engl J Med. 2011 Mar 24;364(12):1176. Erratum in: N Engl J Med. 2007 Jan 11;356(2):201-2.

36.

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.

Edelman E, Porrello A, Guinney J, Balakumaran B, Bild A, Febbo PG, Mukherjee S.

Bioinformatics. 2006 Jul 15;22(14):e108-16.

PMID:
16873460
37.

Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy.

Dressman HK, Hans C, Bild A, Olson JA, Rosen E, Marcom PK, Liotcheva VB, Jones EL, Vujaskovic Z, Marks J, Dewhirst MW, West M, Nevins JR, Blackwell K.

Clin Cancer Res. 2006 Feb 1;12(3 Pt 1):819-26.

38.

Oncogenic pathway signatures in human cancers as a guide to targeted therapies.

Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR.

Nature. 2006 Jan 19;439(7074):353-7. Epub 2005 Nov 6.

PMID:
16273092
39.

Gene-expression patterns predict phenotypes of immune-mediated thrombosis.

Potti A, Bild A, Dressman HK, Lewis DA, Nevins JR, Ortel TL.

Blood. 2006 Feb 15;107(4):1391-6. Epub 2005 Nov 1. Retraction in: Blood. 2011 Oct 20;118(16):4497.

40.

Application of a priori established gene sets to discover biologically important differential expression in microarray data.

Bild A, Febbo PG.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15278-9. Epub 2005 Oct 17. No abstract available.

41.

DIG--a system for gene annotation and functional discovery.

Delong M, Yao G, Wang Q, Dobra A, Black EP, Chang JT, Bild A, West M, Nevins JR, Dressman H.

Bioinformatics. 2005 Jul 1;21(13):2957-9. Epub 2005 May 3.

PMID:
15870167
42.

Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes.

Pittman J, Huang E, Dressman H, Horng CF, Cheng SH, Tsou MH, Chen CM, Bild A, Iversen ES, Huang AT, Nevins JR, West M.

Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8431-6. Epub 2004 May 19.

43.

Gene expression phenotypic models that predict the activity of oncogenic pathways.

Huang E, Ishida S, Pittman J, Dressman H, Bild A, Kloos M, D'Amico M, Pestell RG, West M, Nevins JR.

Nat Genet. 2003 Jun;34(2):226-30.

PMID:
12754511
44.

Gene expression predictors of breast cancer outcomes.

Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT.

Lancet. 2003 May 10;361(9369):1590-6.

PMID:
12747878
45.

MEKK1-induced apoptosis requires TRAIL death receptor activation and is inhibited by AKT/PKB through inhibition of MEKK1 cleavage.

Bild AH, Mendoza FJ, Gibson EM, Huang M, Villanueva J, Garrington TP, Jove R, Johnson GL, Gibson SB.

Oncogene. 2002 Sep 26;21(43):6649-56.

46.

Cytoplasmic transport of Stat3 by receptor-mediated endocytosis.

Bild AH, Turkson J, Jove R.

EMBO J. 2002 Jul 1;21(13):3255-63.

47.

Clathrin, adaptors and eps15 in endosomes containing activated epidermal growth factor receptors.

Sorkina T, Bild A, Tebar F, Sorkin A.

J Cell Sci. 1999 Feb;112 ( Pt 3):317-27.

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