PUBLICATIONS
Publications with Lineberger Bioinformatics Core Co-authors

1. Akbay EA, Koyama S, Carretero J, Altabef A, Tchaicha JH, Christensen CL, Mikse OR, Cherniack AD, Beauchamp EM, Pugh TJ, Wilkerson MD, Fecci PE, Butaney M, Reibel JB, Soucheray M, Cohoon TJ, Janne PA, Meyerson M, Hayes DN, Shapiro GI, Shimamura T, Sholl LM, Rodig SJ, Freeman GJ, Hammerman PS, Dranoff G, Wong KK. Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors. Cancer Discov. 2013;3(12):1355-63. PMCID: PMC3864135.

2. Anders CK, Fan C, Parker JS, Carey LA, Blackwell KL, Klauber-DeMore N, Perou CM. Breast carcinomas arising at a young age: unique biology or a surrogate for aggressive intrinsic subtypes? J Clin Oncol. 2011;29(1):e18-20. PMCID: 3055864.

3. Ang MK, Patel MR, Yin XY, Sundaram S, Fritchie K, Zhao N, Liu Y, Freemerman AJ, Wilkerson MD, Walter V, Weissler MC, Shockley WW, Couch ME, Zanation AM, Hackman T, Chera BS, Harris SL, Miller CR, Thorne LB, Hayward MC, Funkhouser WK, Olshan AF, Shores CG, Makowski L, Hayes DN. High XRCC1 protein expression is associated with poorer survival in patients with head and neck squamous cell carcinoma. Clin Cancer Res. 2011;17(20):6542-52. PMCID: PMC3725262.

4. Bardowell SA, Parker J, Fan C, Crandell J, Perou CM, Swift-Scanlan T. Differential methylation relative to breast cancer subtype and matched normal tissue reveals distinct patterns. Breast Cancer Res Treat. 2013;142(2):365-80. PMCID: 3832780.

5. Beltran AS, Russo A, Lara H, Fan C, Lizardi PM, Blancafort P. Suppression of breast tumor growth and metastasis by an engineered transcription factor. PLoS One. 2011;6(9):e24595. PMCID: 3172243.

6. Bhati R, Patterson C, Livasy CA, Fan C, Ketelsen D, Hu Z, Reynolds E, Tanner C, Moore DT, Gabrielli F, Perou CM, Klauber-DeMore N. Molecular characterization of human breast tumor vascular cells. Am J Pathol. 2008;172(5):1381-90. PMCID: 2329846.

7. Bierie B, Chung CH, Parker JS, Stover DG, Cheng N, Chytil A, Aakre M, Shyr Y, Moses HL. Abrogation of TGF-beta signaling enhances chemokine production and correlates with prognosis in human breast cancer. J Clin Invest. 2009;119(6):1571-82. PMCID: PMC2689133.

8. Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Res. 2009;11(4):R55. PMCID: 2750116.

9. Bivona TG, Hieronymus H, Parker J, Chang K, Taron M, Rosell R, Moonsamy P, Dahlman K, Miller VA, Costa C, Hannon G, Sawyers CL. FAS and NF-kappaB signalling modulate dependence of lung cancers on mutant EGFR. Nature. 2011;471(7339):523-6. PMCID: PMC3541675.

10. Bolton KL, Chenevix-Trench G, Goh C, Sadetzki S, Ramus SJ, Karlan BY,Lambrechts D, Despierre E, Barrowdale D, McGuffog L, Healey S, Easton DF,Sinilnikova O, Benítez J, García MJ, Neuhausen S, Gail MH, Hartge P, Peock S,Frost D, Evans DG, Eeles R, Godwin AK, Daly MB, Kwong A, Ma ES, Lázaro C, Blanco I, Montagna M, D’Andrea E, Nicoletto MO, Johnatty SE, Kjær SK, Jensen A, Høgdall E, Goode EL, Fridley BL, Loud JT, Greene MH, Mai PL, Chetrit A, Lubin F,Hirsh-Yechezkel G, Glendon G, Andrulis IL, Toland AE, Senter L, Gore ME, Gourley C, Michie CO, Song H, Tyrer J, Whittemore AS, McGuire V, Sieh W, KristofferssonU, Olsson H, Borg Å, Levine DA, Steele L, Beattie MS, Chan S, Nussbaum RL,Moysich KB, Gross J, Cass I, Walsh C, Li AJ, Leuchter R, Gordon O, Garcia-Closas M, Gayther SA, Chanock SJ, Antoniou AC, Pharoah PD; EMBRACE; kConFabInvestigators; Cancer Genome Atlas Research Network. Association between BRCA1and BRCA2 mutations and survival in women with invasive epithelial ovariancancer. JAMA. 2012 Jan 25;307(4):382-90. doi: 10.1001/jama.2012.20. PubMed PMID: 22274685; PubMed Central PMCID: PMC3727895.

11. Brooks SA, Brannon AR, Parker JS, Fisher JC, Sen O, Kattan MW, Hakimi AA, Hsieh JJ, Choueiri TK, Tamboli P, Maranchie JK, Hinds P, Miller CR, Nielsen ME, Rathmell WK. ClearCode34: A Prognostic Risk Predictor for Localized Clear Cell Renal Cell Carcinoma. European urology. 2014.

12. Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN. ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. BMC Bioinformatics. 2012;13:221. PMCID: 3447716.

13. Cabanski CR, Qi Y, Yin X, Bair E, Hayward MC, Fan C, Li J, Wilkerson MD, Marron JS, Perou CM, Hayes DN. SWISS MADE: Standardized WithIn Class Sum of Squares to evaluate methodologies and dataset elements. PLoS One. 2010;5(3):e9905. PMCID: 2845619.

14. Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN. BlackOPs: increasing confidence in variant detection through mappability filtering. Nucleic Acids Res. 2013;41(19):e178. PMCID: 3799449.

15. Cancer Genome Atlas Network. Comprehensive molecular characterization of humancolon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi:10.1038/nature11252. PubMed PMID: 22810696; PubMed Central PMCID: PMC3401966.

16. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breasttumours. Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412. Epub 2012 Sep 23. PubMed PMID: 23000897; PubMed Central PMCID: PMC3465532.

17. Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD,Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, LairdPW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integratedgenomic characterization of endometrial carcinoma. Nature. 2013 May2;497(7447):67-73. doi: 10.1038/nature12113. Erratum in: Nature. 2013 Aug8;500(7461):242. PubMed PMID: 23636398; PubMed Central PMCID: PMC3704730.

18. Cancer Genome Atlas Research Network, 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.doi: 10.1038/ng.2764. PubMed PMID: 24071849; PubMed Central PMCID: PMC3919969.

19. Cancer Genome Atlas Research Network. Comprehensive genomic characterizationdefines human glioblastoma genes and core pathways. Nature. 2008 Oct23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4. Erratum in:ature. 2013 Feb 28;494(7438):506. PubMed PMID: 18772890; PubMed Central PMCID:PMC2671642.

20. Cancer Genome Atlas Research Network. Comprehensive genomic characterizationof squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25. doi:10.1038/nature11404. Epub 2012 Sep 9. Erratum in: Nature. 2012 Nov8;491(7423):288. Rogers, Kristen [corrected to Rodgers, Kristen]. PubMed PMID:PubMed Central PMCID: PMC3466113.

21. Cancer Genome Atlas Research Network. Comprehensive molecular characterizationof clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. doi:10.1038/nature12222. Epub 2013 Jun 23. PubMed PMID: 23792563; PubMed CentralPMCID: PMC3771322.

22. Cancer Genome Atlas Research Network. Comprehensive molecular characterizationof urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-22. doi:10.1038/nature12965. Epub 2014 Jan 29. PubMed PMID: 24476821; PubMed CentralPMCID: PMC3962515.

23. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes ofadult de novo acute myeloid leukemia. 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 Jul4;369(1):98. PubMed PMID: 23634996; PubMed Central PMCID: PMC3767041.

24. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovariancarcinoma. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166.Erratum in: Nature. 2012 Oct 11;490(7419):298. PubMed PMID: 21720365; PubMedCentral PMCID: PMC3163504.

25. Carretero J, Shimamura T, Rikova K, Jackson AL, Wilkerson MD, Borgman CL, Buttarazzi MS, Sanofsky BA, McNamara KL, Brandstetter KA, Walton ZE, Gu TL, Silva JC, Crosby K, Shapiro GI, Maira SM, Ji H, Castrillon DH, Kim CF, Garcia-Echeverria C, Bardeesy N, Sharpless NE, Hayes ND, Kim WY, Engelman JA, Wong KK. Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell. 2010;17(6):547-59. PMCID: PMC2901842.

26. Carson C, Omolo B, Chu H, Zhou Y, Sambade MJ, Peters EC, Tompkins P, Simpson DA, Thomas NE, Fan C, Sarasin A, Dessen P, Shields JM, Ibrahim JG, Kaufmann WK. A prognostic signature of defective p53-dependent G1 checkpoint function in melanoma cell lines. Pigment cell & melanoma research. 2012;25(4):514-26. PMCID: 3397470.

27. Chao HH, He X, Parker JS, Zhao W, Perou CM. Micro-scale genomic DNA copy number aberrations as another means of mutagenesis in breast cancer. PLoS One. 2012;7(12):e51719. PMCID: 3524128.

28. Charles PC, Alder BD, Hilliard EG, Schisler JC, Lineberger RE, Parker JS, Mapara S, Wu SS, Portbury A, Patterson C, Stouffer GA. Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. BMC Med Genomics. 2008;1:38. PMCID: PMC2531187.

29. Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst. 2009;101(10):736-50. PMCID: 2684553.

30. Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd LE, Levine MN, Pritchard KI, Davies S, Stijleman IJ, Davis C, Ebbert MT, Parker JS, Ellis MJ, Bernard PS, Perou CM, Nielsen TO. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clin Cancer Res. 2012;18(8):2402-12. PMCID: 3743660.

31. Chen Z, Cheng K, Walton Z, Wang Y, Ebi H, Shimamura T, Liu Y, Tupper T, Ouyang J, Li J, Gao P, Woo MS, Xu C, Yanagita M, Altabef A, Wang S, Lee C, Nakada Y, Pena CG, Sun Y, Franchetti Y, Yao C, Saur A, Cameron MD, Nishino M, Hayes DN, Wilkerson MD, Roberts PJ, Lee CB, Bardeesy N, Butaney M, Chirieac LR, Costa DB, Jackman D, Sharpless NE, Castrillon DH, Demetri GD, Janne PA, Pandolfi PP, Cantley LC, Kung AL, Engelman JA, Wong KK. A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response. Nature. 2012;483(7391):613-7. PMCID: PMC3385933.

32. Chia SK, Bramwell VH, Tu D, Shepherd LE, Jiang S, Vickery T, Mardis E, Leung S, Ung K, Pritchard KI, Parker JS, Bernard PS, Perou CM, Ellis MJ, Nielsen TO. A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Clin Cancer Res. 2012;18(16):4465-72. PMCID: 3743663.

33. Chung CH, Pohlmann PR, Rothenberg ML, Burkey BB, Parker J, Palka K, Aulino J, Puzanov I, Murphy B. Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma. Head & neck. 2011;33(12):1804-8. PMCID: PMC3111896.

34. Cleary SP, Jeck WR, Zhao X, Chen K, Selitsky SR, Savich GL, Tan TX, Wu MC, Getz G, Lawrence MS, Parker JS, Li J, Powers S, Kim H, Fischer S, Guindi M, Ghanekar A, Chiang DY. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology (Baltimore, Md). 2013;58(5):1693-702. PMCID: PMC3830584.

35. Cohen EE, Zhu H, Lingen MW, Martin LE, Kuo WL, Choi EA, Kocherginsky M, Parker JS, Chung CH, Rosner MR. A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. Cancer Res. 2009;69(1):65-74. PMCID: PMC2746005.

36. Connor EE, Kahl S, Elsasser TH, Parker JS, Li RW, Van Tassell CP, Baldwin RLt, Barao SM. Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth. Functional & integrative genomics. 2010;10(1):39-51.

37. Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA,Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH; Cancer Genome AtlasResearch Network. Integrated analyses of microRNAs demonstrate their widespreadinfluence on gene expression in high-grade serous ovarian carcinoma. PLoS One.2012;7(3):e34546. doi: 10.1371/journal.pone.0034546. Epub 2012 Mar 29. PubMedPMID: 22479643; PubMed Central PMCID: PMC3315571.

38. Creighton CJ, Li X, Landis M, Dixon JM, Neumeister VM, Sjolund A, Rimm DL, Wong H, Rodriguez A, Herschkowitz JI, Fan C, Zhang X, He X, Pavlick A, Gutierrez MC, Renshaw L, Larionov AA, Faratian D, Hilsenbeck SG, Perou CM, Lewis MT, Rosen JM, Chang JC. Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features. Proc Natl Acad Sci U S A. 2009;106(33):13820-5. PMCID: 2720409.

39. Crowder RJ, Phommaly C, Tao Y, Hoog J, Luo J, Perou CM, Parker JS, Miller MA, Huntsman DG, Lin L, Snider J, Davies SR, Olson JA, Jr., Watson MA, Saporita A, Weber JD, Ellis MJ. PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in estrogen receptor-positive breast cancer. Cancer Res. 2009;69(9):3955-62. PMCID: 2811393.

40. Dahlman KB, Parker JS, Shamu T, Hieronymus H, Chapinski C, Carver B, Chang K, Hannon GJ, Sawyers CL. Modulators of prostate cancer cell proliferation and viability identified by short-hairpin RNA library screening. PLoS One. 2012;7(4):e34414. PMCID: PMC3324507.

41. Damrauer JS, Hoadley KA, Chism DD, Fan C, Tiganelli CJ, Wobker SE, Yeh JJ, Milowsky MI, Iyer G, Parker JS, Kim WY. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc Natl Acad Sci U S A. 2014;111(8):3110-5. PMCID: PMC3939870.

42. DiMeo TA, Anderson K, Phadke P, Fan C, Perou CM, Naber S, Kuperwasser C. A novel lung metastasis signature links Wnt signaling with cancer cell self-renewal and epithelial-mesenchymal transition in basal-like breast cancer. Cancer Res. 2009;69(13):5364-73. PMCID: 2782448.

43. Dunbier AK, Anderson H, Ghazoui Z, Folkerd EJ, A’Hern R, Crowder RJ, Hoog J, Smith IE, Osin P, Nerurkar A, Parker JS, Perou CM, Ellis MJ, Dowsett M. Relationship between plasma estradiol levels and estrogen-responsive gene expression in estrogen receptor-positive breast cancer in postmenopausal women. J Clin Oncol. 2010;28(7):1161-7. PMCID: 2834467.

44. Dunbier AK, Anderson H, Ghazoui Z, Salter J, Parker JS, Perou CM, Smith IE, Dowsett M. Association between breast cancer subtypes and response to neoadjuvant anastrozole. Steroids. 2011;76(8):736-40.

45. Ellis MJ, Suman VJ, Hoog J, Lin L, Snider J, Prat A, Parker JS, Luo J, DeSchryver K, Allred DC, Esserman LJ, Unzeitig GW, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Watson MA, Leitch M, Hunt K, Olson JA. Randomized phase II neoadjuvant comparison between letrozole, anastrozole, and exemestane for postmenopausal women with estrogen receptor-rich stage 2 to 3 breast cancer: clinical and biomarker outcomes and predictive value of the baseline PAM50-based intrinsic subtype–ACOSOG Z1031. J Clin Oncol. 2011;29(17):2342-9. PMCID: PMC3107749.

46. Elloumi F, Hu Z, Li Y, Parker JS, Gulley ML, Amos KD, Troester MA. Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples. BMC Med Genomics. 2011;4:54. PMCID: 3151208.

47. Ezhkova E, Pasolli HA, Parker JS, Stokes N, Su IH, Hannon G, Tarakhovsky A, Fuchs E. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell. 2009;136(6):1122-35. PMCID: PMC2716120.

48. Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics. 2011;4:3. PMCID: 3025826.

49. Fannin RD, Russo M, O’Connell TM, Gerrish K, Winnike JH, Macdonald J, Newton J, Malik S, Sieber SO, Parker J, Shah R, Zhou T, Watkins PB, Paules RS. Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation. Hepatology (Baltimore, Md). 2010;51(1):227-36. PMCID: PMC2925683.

50. Frost D, Evans DG, Eeles R, Godwin AK, Daly MB, Kwong A, Ma ES, Lázaro C, Blanco I, Montagna M, D’Andrea E, Nicoletto MO, Johnatty SE, Kjær SK, Jensen A, Høgdall E, Goode EL, Fridley BL, Loud JT, Greene MH, Mai PL, Chetrit A, Lubin F, Hirsh-Yechezkel G, Glendon G, Andrulis IL, Toland AE, Senter L, Gore ME, Gourley C, Michie CO, Song H, Tyrer J, Whittemore AS, McGuire V, Sieh W, Kristoffersson U, Olsson H, Borg Å, Levine DA, Steele L, Beattie MS, Chan S, Nussbaum RL, Moysich KB, Gross J, Cass I, Walsh C, Li AJ, Leuchter R, Gordon O, Garcia Closas M, Gayther SA, Chanock SJ, Antoniou AC, Pharoah PD; EMBRACE; kConFab Investigators; Cancer Genome Atlas Research Network. Association between BRCA1 and BRCA2 mutations and survival in women with invasive epithelial ovarian cancer. JAMA. 2012 Jan 25;307(4):382-90. doi: 10.1001/jama.2012.20. PubMed PMID: 22274685; PubMed Central PMCID: PMC3727895.

51. Gohlke JM, Armant O, Parham FM, Smith MV, Zimmer C, Castro DS, Nguyen L, Parker JS, Gradwohl G, Portier CJ, Guillemot F. Characterization of the proneural gene regulatory network during mouse telencephalon development. BMC biology. 2008;6:15. PMCID: PMC2330019.

52. Grilley-Olson JE, Hayes DN, Moore DT, Leslie KO, Wilkerson MD, Qaqish BF, Hayward MC, Cabanski CR, Yin X, Socinski MA, Stinchcombe TE, Thorne LB, Allen TC, Banks PM, Beasley MB, Borczuk AC, Cagle PT, Christensen R, Colby TV, Deblois GG, Elmberger G, Graziano P, Hart CF, Jones KD, Maia DM, Miller CR, Nance KV, Travis WD, Funkhouser WK. Validation of interobserver agreement in lung cancer assessment: hematoxylin-eosin diagnostic reproducibility for non-small cell lung cancer: the 2004 World Health Organization classification and therapeutically relevant subsets. Archives of pathology & laboratory medicine. 2013;137(1):32-40.

53. Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, TakedaS, Voss MH, Tickoo SK, Reuter VE, Russo P, Cheng EH, Sander C, Motzer RJ, HsiehJJ; ccRCC Cancer Genome Atlas (KIRC TCGA) Research Network investigators. Adverseoutcomes in clear cell renal cell carcinoma with mutations of 3p21 epigeneticregulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res. 2013 Jun 15;19(12):3259-67. doi: 10.1158/1078-0432.CCR-12-3886. Epub 2013 Apr 25. PubMed PMID: 23620406; PubMed Central PMCID: PMC3708609.

54. Harrell JC, Pfefferle AD, Zalles N, Prat A, Fan C, Khramtsov A, Olopade OI, Troester MA, Dudley AC, Perou CM. Endothelial-like properties of claudin-low breast cancer cells promote tumor vascular permeability and metastasis. Clin Exp Metastasis. 2014;31(1):33-45. PMCID: 3892109.

55. Harrell JC, Prat A, Parker JS, Fan C, He X, Carey L, Anders C, Ewend M, Perou CM. Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse. Breast Cancer Res Treat. 2012;132(2):523-35. PMCID: 3303043.

56. Haugen AC, Di Prospero NA, Parker JS, Fannin RD, Chou J, Meyer JN, Halweg C, Collins JB, Durr A, Fischbeck K, Van Houten B. Altered gene expression and DNA damage in peripheral blood cells from Friedreich’s ataxia patients: cellular model of pathology. PLoS Genet. 2010;6(1):e1000812. PMCID: PMC2799513.

57. Hennessy BT, Gonzalez-Angulo AM, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, Lee JS, Fridlyand J, Sahin A, Agarwal R, Joy C, Liu W, Stivers D, Baggerly K, Carey M, Lluch A, Monteagudo C, He X, Weigman V, Fan C, Palazzo J, Hortobagyi GN, Nolden LK, Wang NJ, Valero V, Gray JW, Perou CM, Mills GB. Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res. 2009;69(10):4116-24. PMCID: 2737191.

58. Herschkowitz JI, He X, Fan C, Perou CM. The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas. Breast Cancer Res. 2008;10(5):R75. PMCID: 2614508.

59. Hester SD, Reid L, Nowak N, Jones WD, Parker JS, Knudtson K, Ward W, Tiesman J, Denslow ND. Comparison of comparative genomic hybridization technologies across microarray platforms. Journal of biomolecular techniques : JBT. 2009;20(2):135-51. PMCID: PMC2685605.

60. Holbrook JD, Parker JS, Gallagher KT, Halsey WS, Hughes AM, Weigman VJ, Lebowitz PF, Kumar R. Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine. Journal of translational medicine. 2011;9:119. PMCID: PMC3152520.

61. Hu Z, Fan C, Livasy C, He X, Oh DS, Ewend MG, Carey LA, Subramanian S, West R, Ikpatt F, Olopade OI, van de Rijn M, Perou CM. A compact VEGF signature associated with distant metastases and poor outcomes. BMC Med. 2009;7:9. PMCID: 2671523.

62. Jarinova O, Stewart AF, Roberts R, Wells G, Lau P, Naing T, Buerki C, McLean BW, Cook RC, Parker JS, McPherson R. Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus. Arteriosclerosis, thrombosis, and vascular biology. 2009;29(10):1671-7.

63. Jeck WR, Parker J, Carson CC, Shields JM, Sambade MJ, Peters EC, Burd CE, Thomas NE, Chiang DY, Liu W, Eberhard DA, Ollila D, Grilley-Olson J, Moschos S, Hayes DN, Sharpless NE. Targeted Next Generation Sequencing Identifies Clinically Actionable Mutations in Patients with Melanoma. Pigment cell & melanoma research. 2014.

64. Kim Y, Hammerman PS, Kim J, Yoon JA, Lee Y, Sun JM, Wilkerson MD, Pedamallu CS, Cibulskis K, Yoo YK, Lawrence MS, Stojanov P, Carter SL, McKenna A, Stewart C, Sivachenko AY, Oh IJ, Kim HK, Choi YS, Kim K, Shim YM, Kim KS, Song SY, Na KJ, Choi YL, Hayes DN, Kim J, Cho S, Kim YC, Ahn JS, Ahn MJ, Getz G, Meyerson M, Park K. Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients. J Clin Oncol. 2014;32(2):121-8.

65. King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ. Topoisomerases facilitate transcription of long genes linked to autism. Nature. 2013;501(7465):58-62. PMCID: PMC3767287.

66. Korde LA, Lusa L, McShane L, Lebowitz PF, Lukes L, Camphausen K, Parker JS, Swain SM, Hunter K, Zujewski JA. Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer. Breast Cancer Res Treat. 2010;119(3):685-99.

67. Lambrechts D, Despierre E, Barrowdale D, McGuffog L, Healey S, Easton DF,

68. Larman TC, DePalma SR, Hadjipanayis AG; Cancer Genome Atlas Research Network,Protopopov A, Zhang J, Gabriel SB, Chin L, Seidman CE, Kucherlapati R, SeidmanJG. Spectrum of somatic mitochondrial mutations in five cancers. Proc Natl AcadSci U S A. 2012 Aug 28;109(35):14087-91. Epub 2012 Aug 13. PubMed PMID: 22891333;PubMed Central PMCID: PMC3435197.

69. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ 3rd, Lohr JG,Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C,Kharchenko PV, Park PJ; Cancer Genome Atlas Research Network. Landscape ofsomatic retrotransposition in human cancers. Science. 2012 Aug24;337(6097):967-71. doi: 10.1126/science.1222077. Epub 2012 Jun 28. PubMed PMID:PubMed Central PMCID: PMC3656569.

70. Liao RG, Jung J, Tchaicha J, Wilkerson MD, Sivachenko A, Beauchamp EM, Liu Q, Pugh TJ, Pedamallu CS, Hayes DN, Gray NS, Getz G, Wong KK, Haddad RI, Meyerson M, Hammerman PS. Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma. Cancer Res. 2013;73(16):5195-205. PMCID: PMC3749739.

71. Makowski L, Zhou C, Zhong Y, Kuan PF, Fan C, Sampey BP, Difurio M, Bae-Jump VL. Obesity increases tumor aggressiveness in a genetically engineered mouse model of serous ovarian cancer. Gynecol Oncol. 2014;133(1):90-7.

72. Mavrakis KJ, Wolfe AL, Oricchio E, Palomero T, de Keersmaecker K, McJunkin K, Zuber J, James T, Khan AA, Leslie CS, Parker JS, Paddison PJ, Tam W, Ferrando A, Wendel HG. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nature cell biology. 2010;12(4):372-9. PMCID: PMC2989719.

73. Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res. 2010;16(21):5222-32. PMCID: 2970720.

74. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, PanF, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM,Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P,Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K; Cancer Genome AtlasResearch Network. Identification of a CpG island methylator phenotype thatdefines a distinct subgroup of glioma. Cancer Cell. 2010 May 18;17(5):510-22.doi: 10.1016/j.ccr.2010.03.017. Epub 2010 Apr 15. PubMed PMID: 20399149; PubMedCentral PMCID: PMC2872684.

75. Oh DS, Cheang MC, Fan C, Perou CM. Radiation-induced gene signature predicts pathologic complete response to neoadjuvant chemotherapy in breast cancer patients. Radiat Res. 2014;181(2):193-207.

76. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009;27(8):1160-7. PMCID: 2667820.

77. Pei XH, Bai F, Smith MD, Usary J, Fan C, Pai SY, Ho IC, Perou CM, Xiong Y. CDK inhibitor p18(INK4c) is a downstream target of GATA3 and restrains mammary luminal progenitor cell proliferation and tumorigenesis. Cancer Cell. 2009;15(5):389-401. PMCID: 2699569.

78. Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS. Clinical implementation of the intrinsic subtypes of breast cancer. Lancet Oncol. 2010;11(8):718-9; author reply 20-1.

79. Polkinghorn WR, Parker JS, Lee MX, Kass EM, Spratt DE, Iaquinta PJ, Arora VK, Yen WF, Cai L, Zheng D, Carver BS, Chen Y, Watson PA, Shah NP, Fujisawa S, Goglia AG, Gopalan A, Hieronymus H, Wongvipat J, Scardino PT, Zelefsky MJ, Jasin M, Chaudhuri J, Powell SN, Sawyers CL. Androgen receptor signaling regulates DNA repair in prostate cancers. Cancer Discov. 2013;3(11):1245-53. PMCID: PMC3888815.

80. Prat A, Adamo B, Fan C, Peg V, Vidal M, Galvan P, Vivancos A, Nuciforo P, Palmer HG, Dawood S, Rodon J, Cajal SR, Del Campo JM, Felip E, Tabernero J, Cortes J. Genomic analyses across six cancer types identify basal-like breast cancer as a unique molecular entity. Sci Rep. 2013;3:3544.

81. Prat A, Cheang MC, Martin M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. J Clin Oncol. 2013;31(2):203-9. PMCID: 3532392.

82. Prat A, Karginova O, Parker JS, Fan C, He X, Bixby L, Harrell JC, Roman E, Adamo B, Troester M, Perou CM. Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes. Breast Cancer Res Treat. 2013;142(2):237-55. PMCID: 3832776.

83. Prat A, Parker JS, Fan C, Cheang MC, Miller LD, Bergh J, Chia SK, Bernard PS, Nielsen TO, Ellis MJ, Carey LA, Perou CM. Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen. Ann Oncol. 2012;23(11):2866-73. PMCID: 3477878.

84. Prat A, Parker JS, Fan C, Perou CM. PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer. Breast Cancer Res Treat. 2012;135(1):301-6. PMCID: 3413822.

85. Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res. 2010;12(5):R68. PMCID: 3096954.

86. Rager JE, Bailey KA, Smeester L, Miller SK, Parker JS, Laine JE, Drobna Z, Currier J, Douillet C, Olshan AF, Rubio-Andrade M, Styblo M, Garcia-Vargas G, Fry RC. Prenatal arsenic exposure and the epigenome: Altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. Environmental and molecular mutagenesis. 2014;55(3):196-208.

87. Richards KL, Motsinger-Reif AA, Chen HW, Fedoriw Y, Fan C, Nielsen DM, Small GW, Thomas R, Smith C, Dave SS, Perou CM, Breen M, Borst LB, Suter SE. Gene profiling of canine B-cell lymphoma reveals germinal center and postgerminal center subtypes with different survival times, modeling human DLBCL. Cancer Res. 2013;73(16):5029-39. PMCID: 3755352.

88. Roll JD, Rivenbark AG, Sandhu R, Parker JS, Jones WD, Carey LA, Livasy CA, Coleman WB. Dysregulation of the epigenome in triple-negative breast cancers: basal-like and claudin-low breast cancers express aberrant DNA hypermethylation. Experimental and molecular pathology. 2013;95(3):276-87.

89. Schisler JC, Charles PC, Parker JS, Hilliard EG, Mapara S, Meredith D, Lineberger RE, Wu SS, Alder BD, Stouffer GA, Patterson C. Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry. PLoS One. 2009;4(12):e8183. PMCID: PMC2790609. 90. Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB. Merging two gene-expression studies via cross-platform normalization. Bioinformatics. 2008;24(9):1154-60.

91. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Jr., Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010;28(8):827-38. PMCID: PMC3315840.

92. Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science. 2008;319(5863):617-20. PMCID: PMC2981861.

93. Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome research. 2014;24(2):241-50. PMCID: PMC3912414.

94. Sinilnikova O, Benítez J, García MJ, Neuhausen S, Gail MH, Hartge P, Peock S, 95. Stratford JK, Bentrem DJ, Anderson JM, Fan C, Volmar KA, Marron JS, Routh ED, Caskey LS, Samuel JC, Der CJ, Thorne LB, Calvo BF, Kim HJ, Talamonti MS, Iacobuzio-Donahue CA, Hollingsworth MA, Perou CM, Yeh JJ. A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma. PLoS Med. 2010;7(7):e1000307. PMCID: 2903589.

96. Thorner AR, Hoadley KA, Parker JS, Winkel S, Millikan RC, Perou CM. In vitro and in vivo analysis of B-Myb in basal-like breast cancer. Oncogene. 2009;28(5):742-51. PMCID: 2636852.

97. Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One. 2010;5(10):e13073. PMCID: 2951337.

98. Troester MA, Lee MH, Carter M, Fan C, Cowan DW, Perez ER, Pirone JR, Perou CM, Jerry DJ, Schneider SS. Activation of host wound responses in breast cancer microenvironment. Clin Cancer Res. 2009;15(22):7020-8. PMCID: 2783932.

99. Tsuchiya M, Parker JS, Kono H, Matsuda M, Fujii H, Rusyn I. Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma. Mol Cancer. 2010;9:74. PMCID: PMC2856554.

100. Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T. Vimentin DNA methylation predicts survival in breast cancer. Breast Cancer Res Treat. 2013;137(2):383-96. PMCID: 3838916.

101. Uziel T, Karginov FV, Xie S, Parker JS, Wang YD, Gajjar A, He L, Ellison D, Gilbertson RJ, Hannon G, Roussel MF. The miR-17~92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proc Natl Acad Sci U S A. 2009;106(8):2812-7. PMCID: PMC2636735.

102. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O’Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98-110. PMCID: 2818769.

103. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, DingL, Golub T, Mesirov JP, Alexe G, Lawrence M, O’Kelly M, Tamayo P, Weir BA,Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD,Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW,Meyerson M, Getz G, Perou CM, Hayes DN; Cancer Genome Atlas Research Network.Integrated genomic analysis identifies clinically relevant subtypes ofglioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.Cancer Cell. 2010 Jan 19;17(1):98-110. doi: 10.1016/j.ccr.2009.12.020. PubMedPMID: 20129251; PubMed Central PMCID: PMC2818769.

104. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S,Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G,Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A,Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN,Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M; Cancer GenomeAtlas Research Network. Prognostically relevant gene signatures of high-gradeserous ovarian carcinoma. J Clin Invest. 2013 Jan 2;123(1):517-25. doi:10.1172/JCI65833. Epub 2012 Dec 21. PubMed PMID: 23257362; PubMed Central PMCID: PMC3533304.

105. Wakamatsu N, Collins JB, Parker JS, Tessema M, Clayton NP, Ton TV, Hong HH, Belinsky S, Devereux TR, Sills RC, Lahousse SA. Gene expression studies demonstrate that the K-ras/Erk MAP kinase signal transduction pathway and other novel pathways contribute to the pathogenesis of cumene-induced lung tumors. Toxicologic pathology. 2008;36(5):743-52.

106. Walter V, Yin X, Wilkerson MD, Cabanski CR, Zhao N, Du Y, Ang MK, Hayward MC, Salazar AH, Hoadley KA, Fritchie K, Sailey CJ, Weissler MC, Shockley WW, Zanation AM, Hackman T, Thorne LB, Funkhouser WD, Muldrew KL, Olshan AF, Randell SH, Wright FA, Shores CG, Hayes DN. Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes. PLoS One. 2013;8(2):e56823. PMCID: PMC3579892.

107. Wang SE, Xiang B, Guix M, Olivares MG, Parker J, Chung CH, Pandiella A, Arteaga CL. Transforming growth factor beta engages TACE and ErbB3 to activate phosphatidylinositol-3 kinase/Akt in ErbB2-overexpressing breast cancer and desensitizes cells to trastuzumab. Mol Cell Biol. 2008;28(18):5605-20. PMCID: PMC2546920.

108. Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Borresen-Dale AL, Olopade OI, Perou CM. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat. 2012;133(3):865-80. PMCID: 3387500.

109. Wilkerson LM, Iwata I, Wilkerson MD, Heflin MT. An Educational Intervention to Improve Internal Medicine Interns’ Awareness of Hazards of Hospitalization in Acutely Ill Older Adults. J Am Geriatr Soc. 2014.

110. Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572-3. PMCID: PMC2881355.

111. Wilkerson MD, Ru Y, Brendel VP. Common introns within orthologous genes: software and application to plants. Brief Bioinform. 2009;10(6):631-44.

112. Wilkerson MD, Schallheim JM, Hayes DN, Roberts PJ, Bastien RR, Mullins M, Yin X, Miller CR, Thorne LB, Geiersbach KB, Muldrew KL, Funkhouser WK, Fan C, Hayward MC, Bayer S, Perou CM, Bernard PS. Prediction of lung cancer histological types by RT-qPCR gene expression in FFPE specimens. J Mol Diagn. 2013;15(4):485-97. PMCID: 3699698.

113. Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR, Muldrew K, Miller CR, Randell SH, Socinski MA, Parsons AM, Funkhouser WK, Lee CB, Roberts PJ, Thorne L, Bernard PS, Perou CM, Hayes DN. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin Cancer Res. 2010;16(19):4864-75. PMCID: 2953768.

114. Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC, Miller CR, Socinski MA, Parsons AM, Thorne LB, Haithcock BE, Veeramachaneni NK, Funkhouser WK, Randell SH, Bernard PS, Perou CM, Hayes DN. Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation. PLoS One. 2012;7(5):e36530. PMCID: 3349715.

115. Wu D, Pang Y, Wilkerson MD, Wang D, Hammerman PS, Liu JS. Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity. Br J Cancer. 2013;109(6):1599-608. PMCID: 3776976.

116. Yang JY, Yoshihara K, Tanaka K, Hatae M, Masuzaki H, Itamochi H; CancerGenome Atlas (TCGA) Research Network, Takano M, Ushijima K, Tanyi JL, Coukos G,Lu Y, Mills GB, Verhaak RG. Predicting time to ovarian carcinoma recurrence usingprotein markers. J Clin Invest. 2013 Sep 3;123(9):3740-50. doi: 10.1172/JCI68509.Epub 2013 Aug 15. Erratum in: J Clin Invest. 2013 Dec 2;123(12):5410. PubMedPMID: 23945238; PubMed Central PMCID: PMC3754259.

117. Zawistowski JS, Nakamura K, Parker JS, Granger DA, Golitz BT, Johnson GL. MicroRNA 9-3p targets beta1 integrin to sensitize claudin-low breast cancer cells to MEK inhibition. Mol Cell Biol. 2013;33(11):2260-74. PMCID: PMC3648081.

118. Zhao N, Ang MK, Yin XY, Patel MR, Fritchie K, Thorne L, Muldrew KL, Hayward MC, Sun W, Wilkerson MD, Chera BS, Hackman T, Zanation AM, Grilley-Olson JE, Couch ME, Shockley WW, Weissler MC, Shores CG, Funkhouser WK, Olshan AF, Hayes DN. Different cellular p16(INK4a) localisation may signal different survival outcomes in head and neck cancer. Br J Cancer. 2012;107(3):482-90. PMCID: PMC3405208.

119. Zhou B, Damrauer JS, Bailey ST, Hadzic T, Jeong Y, Clark K, Fan C, Murphy L, Lee CY, Troester MA, Miller CR, Jin J, Darr D, Perou CM, Levine RL, Diehn M, Kim WY. Erythropoietin promotes breast tumorigenesis through tumor-initiating cell self-renewal. J Clin Invest. 2014;124(2):553-63. PMCID: 3904607.