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Interaction between the microbiome and TP53 in human lung cancer.

Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC.

Genome Biol. 2018 Aug 24;19(1):123. doi: 10.1186/s13059-018-1501-6.


A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A.

Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA.

Genetics. 2018 Sep;210(1):203-218. doi: 10.1534/genetics.118.301305. Epub 2018 Jul 16.


Progenitor B-1 B-cell acute lymphoblastic leukemia is associated with collaborative mutations in 3 critical pathways.

Gough SM, Goldberg L, Pineda M, Walker RL, Zhu YJ, Bilke S, Chung YJ, Dufraine J, Kundu S, Jacoby E, Fry TJ, Fischer S, Panzer-Grümayer R, Meltzer PS, Aplan PD.

Blood Adv. 2017 Sep 8;1(20):1749-1759. doi: 10.1182/bloodadvances.2017009837. eCollection 2017 Sep 12.


Somatic mutations in murine models of leukemia and lymphoma: Disease specificity and clinical relevance.

Goldberg L, Gough SM, Lee F, Dang C, Walker RL, Zhu YJ, Bilke S, Pineda M, Onozawa M, Jo Chung Y, Meltzer PS, Aplan PD.

Genes Chromosomes Cancer. 2017 Jun;56(6):472-483. doi: 10.1002/gcc.22451. Epub 2017 Mar 31.


SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma.

Tang SW, Bilke S, Cao L, Murai J, Sousa FG, Yamade M, Rajapakse V, Varma S, Helman LJ, Khan J, Meltzer PS, Pommier Y.

Clin Cancer Res. 2015 Sep 15;21(18):4184-93. doi: 10.1158/1078-0432.CCR-14-2112. Epub 2015 Mar 16.


The CDX1-microRNA-215 axis regulates colorectal cancer stem cell differentiation.

Jones MF, Hara T, Francis P, Li XL, Bilke S, Zhu Y, Pineda M, Subramanian M, Bodmer WF, Lal A.

Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):E1550-8. doi: 10.1073/pnas.1503370112. Epub 2015 Mar 16.


EWS-FLI1 employs an E2F switch to drive target gene expression.

Schwentner R, Papamarkou T, Kauer MO, Stathopoulos V, Yang F, Bilke S, Meltzer PS, Girolami M, Kovar H.

Nucleic Acids Res. 2015 Mar 11;43(5):2780-9. doi: 10.1093/nar/gkv123. Epub 2015 Feb 20.


Identification of RECQ1-regulated transcriptome uncovers a role of RECQ1 in regulation of cancer cell migration and invasion.

Li XL, Lu X, Parvathaneni S, Bilke S, Zhang H, Thangavel S, Vindigni A, Hara T, Zhu Y, Meltzer PS, Lal A, Sharma S.

Cell Cycle. 2014;13(15):2431-45. doi: 10.4161/cc.29419.


Replicon: a software to accurately predict DNA replication timing in metazoan cells.

Gindin Y, Meltzer PS, Bilke S.

Front Genet. 2014 Nov 3;5:378. doi: 10.3389/fgene.2014.00378. eCollection 2014.


A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors.

Petrini I, Meltzer PS, Kim IK, Lucchi M, Park KS, Fontanini G, Gao J, Zucali PA, Calabrese F, Favaretto A, Rea F, Rodriguez-Canales J, Walker RL, Pineda M, Zhu YJ, Lau C, Killian KJ, Bilke S, Voeller D, Dakshanamurthy S, Wang Y, Giaccone G.

Nat Genet. 2014 Aug;46(8):844-9. doi: 10.1038/ng.3016. Epub 2014 Jun 29.


A chromatin structure-based model accurately predicts DNA replication timing in human cells.

Gindin Y, Valenzuela MS, Aladjem MI, Meltzer PS, Bilke S.

Mol Syst Biol. 2014 Mar 28;10:722. doi: 10.1002/msb.134859.


A mutant p53/let-7i-axis-regulated gene network drives cell migration, invasion and metastasis.

Subramanian M, Francis P, Bilke S, Li XL, Hara T, Lu X, Jones MF, Walker RL, Zhu Y, Pineda M, Lee C, Varanasi L, Yang Y, Martinez LA, Luo J, Ambs S, Sharma S, Wakefield LM, Meltzer PS, Lal A.

Oncogene. 2015 Feb 26;34(9):1094-104. doi: 10.1038/onc.2014.46. Epub 2014 Mar 24.


Evidence for a Functional Link between Chromosomal Breakpoints and Aberrant DNA Methylation in Cancer.

Bilke S, Gindin Y.

Front Oncol. 2014 Mar 11;4:46. doi: 10.3389/fonc.2014.00046. eCollection 2014. No abstract available.


NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function.

Gough SM, Lee F, Yang F, Walker RL, Zhu YJ, Pineda M, Onozawa M, Chung YJ, Bilke S, Wagner EK, Denu JM, Ning Y, Xu B, Wang GG, Meltzer PS, Aplan PD.

Cancer Discov. 2014 May;4(5):564-77. doi: 10.1158/2159-8290.CD-13-0419. Epub 2014 Feb 17.


104th American Association For Cancer Research (AACR) annual meeting; breakthroughs in science and technology changing cancer care.

Abaan OD, Bilke S.

ACS Chem Biol. 2013;8(6):1097-100. doi: 10.1021/cb400366r. No abstract available.


A p21-ZEB1 complex inhibits epithelial-mesenchymal transition through the microRNA 183-96-182 cluster.

Li XL, Hara T, Choi Y, Subramanian M, Francis P, Bilke S, Walker RL, Pineda M, Zhu Y, Yang Y, Luo J, Wakefield LM, Brabletz T, Park BH, Sharma S, Chowdhury D, Meltzer PS, Lal A.

Mol Cell Biol. 2014 Feb;34(3):533-50. doi: 10.1128/MCB.01043-13. Epub 2013 Nov 25.


Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer.

Bilke S, Schwentner R, Yang F, Kauer M, Jug G, Walker RL, Davis S, Zhu YJ, Pineda M, Meltzer PS, Kovar H.

Genome Res. 2013 Nov;23(11):1797-809. doi: 10.1101/gr.151340.112. Epub 2013 Aug 12.


The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.

Abaan OD, Polley EC, Davis SR, Zhu YJ, Bilke S, Walker RL, Pineda M, Gindin Y, Jiang Y, Reinhold WC, Holbeck SL, Simon RM, Doroshow JH, Pommier Y, Meltzer PS.

Cancer Res. 2013 Jul 15;73(14):4372-82. doi: 10.1158/0008-5472.CAN-12-3342. Epub 2013 Jul 15.


Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer.

Di LJ, Byun JS, Wong MM, Wakano C, Taylor T, Bilke S, Baek S, Hunter K, Yang H, Lee M, Zvosec C, Khramtsova G, Cheng F, Perou CM, Miller CR, Raab R, Olopade OI, Gardner K.

Nat Commun. 2013;4:1449. doi: 10.1038/ncomms2438.


Analyzing the association of SCNA boundaries with replication timing.

Bilke S, Gindin Y.

Nat Biotechnol. 2012 Nov;30(11):1043-5; author reply 1045-6. doi: 10.1038/nbt.2415. No abstract available.


Enforced expression of Lin28b leads to impaired T-cell development, release of inflammatory cytokines, and peripheral T-cell lymphoma.

Beachy SH, Onozawa M, Chung YJ, Slape C, Bilke S, Francis P, Pineda M, Walker RL, Meltzer P, Aplan PD.

Blood. 2012 Aug 2;120(5):1048-59. doi: 10.1182/blood-2012-01-401760. Epub 2012 Jun 21.


Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples.

Killian JK, Walker RL, Bilke S, Chen Y, Davis S, Cornelison R, Smith WI, Meltzer PS.

Methods Mol Biol. 2012;823:107-18. doi: 10.1007/978-1-60327-216-2_8.


Genome-wide depletion of replication initiation events in highly transcribed regions.

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI.

Genome Res. 2011 Nov;21(11):1822-32. doi: 10.1101/gr.124644.111. Epub 2011 Aug 3.


A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology.

Killian JK, Bilke S, Davis S, Walker RL, Jaeger E, Killian MS, Waterfall JJ, Bibikova M, Fan JB, Smith WI Jr, Meltzer PS.

Am J Pathol. 2011 Jul;179(1):55-65. doi: 10.1016/j.ajpath.2011.03.022. Epub 2011 May 13.


Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences.

Valenzuela MS, Chen Y, Davis S, Yang F, Walker RL, Bilke S, Lueders J, Martin MM, Aladjem MI, Massion PP, Meltzer PS.

PLoS One. 2011;6(5):e17308. doi: 10.1371/journal.pone.0017308. Epub 2011 May 13.


Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.

Killian JK, Walker RL, Suuriniemi M, Jones L, Scurci S, Singh P, Cornelison R, Harmon S, Boisvert N, Zhu J, Wang Y, Bilke S, Davis S, Giaccone G, Smith WI Jr, Meltzer PS.

J Mol Diagn. 2010 Nov;12(6):739-45. doi: 10.2353/jmoldx.2010.090238.


Genome-wide identification of PAX3-FKHR binding sites in rhabdomyosarcoma reveals candidate target genes important for development and cancer.

Cao L, Yu Y, Bilke S, Walker RL, Mayeenuddin LH, Azorsa DO, Yang F, Pineda M, Helman LJ, Meltzer PS.

Cancer Res. 2010 Aug 15;70(16):6497-508. doi: 10.1158/0008-5472.CAN-10-0582. Epub 2010 Jul 27.


Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes.

Byun JS, Wong MM, Cui W, Idelman G, Li Q, De Siervi A, Bilke S, Haggerty CM, Player A, Wang YH, Thirman MJ, Kaberlein JJ, Petrovas C, Koup RA, Longo D, Ozato K, Gardner K.

Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19286-91. doi: 10.1073/pnas.0905469106. Epub 2009 Oct 30.


Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.

Killian JK, Bilke S, Davis S, Walker RL, Killian MS, Jaeger EB, Chen Y, Hipp J, Pittaluga S, Raffeld M, Cornelison R, Smith WI Jr, Bibikova M, Fan JB, Emmert-Buck MR, Jaffe ES, Meltzer PS.

Cancer Res. 2009 Feb 1;69(3):758-64. doi: 10.1158/0008-5472.CAN-08-2984. Epub 2009 Jan 20.


Whole chromosome alterations predict survival in high-risk neuroblastoma without MYCN amplification.

Bilke S, Chen QR, Wei JS, Khan J.

Clin Cancer Res. 2008 Sep 1;14(17):5540-7. doi: 10.1158/1078-0432.CCR-07-4461.


An integrated cross-platform prognosis study on neuroblastoma patients.

Chen QR, Song YK, Wei JS, Bilke S, Asgharzadeh S, Seeger RC, Khan J.

Genomics. 2008 Oct;92(4):195-203. doi: 10.1016/j.ygeno.2008.05.014. Epub 2008 Jul 30.


Transcriptional networks inferred from molecular signatures of breast cancer.

Tongbai R, Idelman G, Nordgard SH, Cui W, Jacobs JL, Haggerty CM, Chanock SJ, Børresen-Dale AL, Livingston G, Shaunessy P, Chiang CH, Kristensen VN, Bilke S, Gardner K.

Am J Pathol. 2008 Feb;172(2):495-509. doi: 10.2353/ajpath.2008.061079. Epub 2008 Jan 10.


Analysis of comparative genomic hybridization data on cDNA microarrays.

Bilke S, Khan J.

Methods Mol Biol. 2007;377:175-86. Review.


Functional profiling of uncommon VCAM1 promoter polymorphisms prevalent in African American populations.

Idelman G, Taylor JG, Tongbai R, Chen RA, Haggerty CM, Bilke S, Chanock SJ, Gardner K.

Hum Mutat. 2007 Aug;28(8):824-9.


Proteomic expression profiling of thyroid neoplasms.

Braunschweig T, Kaserer K, Chung JY, Bilke S, Krizman D, Knezevic V, Hewitt SM.

Proteomics Clin Appl. 2007 Mar;1(3):264-71. doi: 10.1002/prca.200600381.


Credentialing preclinical pediatric xenograft models using gene expression and tissue microarray analysis.

Whiteford CC, Bilke S, Greer BT, Chen Q, Braunschweig TA, Cenacchi N, Wei JS, Smith MA, Houghton P, Morton C, Reynolds CP, Lock R, Gorlick R, Khanna C, Thiele CJ, Takikita M, Catchpoole D, Hewitt SM, Khan J.

Cancer Res. 2007 Jan 1;67(1):32-40.


Increased WSB1 copy number correlates with its over-expression which associates with increased survival in neuroblastoma.

Chen QR, Bilke S, Wei JS, Greer BT, Steinberg SM, Westermann F, Schwab M, Khan J.

Genes Chromosomes Cancer. 2006 Sep;45(9):856-62.


Inferring a tumor progression model for neuroblastoma from genomic data.

Bilke S, Chen QR, Westerman F, Schwab M, Catchpoole D, Khan J.

J Clin Oncol. 2005 Oct 10;23(29):7322-31. Epub 2005 Sep 6.


High-resolution cDNA microarray-based comparative genomic hybridization analysis in neuroblastoma.

Chen QR, Bilke S, Khan J.

Cancer Lett. 2005 Oct 18;228(1-2):71-81. Review.


Database of mRNA gene expression profiles of multiple human organs.

Son CG, Bilke S, Davis S, Greer BT, Wei JS, Whiteford CC, Chen QR, Cenacchi N, Khan J.

Genome Res. 2005 Mar;15(3):443-50.


Altered expression of cell cycle genes distinguishes aggressive neuroblastoma.

Krasnoselsky AL, Whiteford CC, Wei JS, Bilke S, Westermann F, Chen QR, Khan J.

Oncogene. 2005 Feb 24;24(9):1533-41.


Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays.

Bilke S, Chen QR, Whiteford CC, Khan J.

Bioinformatics. 2005 Apr 1;21(7):1138-45. Epub 2004 Nov 11.


Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma.

Wei JS, Greer BT, Westermann F, Steinberg SM, Son CG, Chen QR, Whiteford CC, Bilke S, Krasnoselsky AL, Cenacchi N, Catchpoole D, Berthold F, Schwab M, Khan J.

Cancer Res. 2004 Oct 1;64(19):6883-91. Erratum in: Cancer Res. 2005 Jan 1;65(1):374.


cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma.

Chen QR, Bilke S, Wei JS, Whiteford CC, Cenacchi N, Krasnoselsky AL, Greer BT, Son CG, Westermann F, Berthold F, Schwab M, Catchpoole D, Khan J.

BMC Genomics. 2004 Sep 20;5:70.


The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles.

Cunliffe HE, Ringnér M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS.

Cancer Res. 2003 Nov 1;63(21):7158-66.


Probabilistic estimation of microarray data reliability and underlying gene expression.

Bilke S, Breslin T, Sigvardsson M.

BMC Bioinformatics. 2003 Sep 10;4:40. Epub 2003 Sep 10.


Simultaneous enantioselective analysis of chiral urinary metabolites in patients with Zellweger syndrome.

Muth A, Jung J, Bilke S, Scharrer A, Mosandl A, Sewell AC, Böhles H.

J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 25;792(2):269-77.


RNA analysis of B cell lines arrested at defined stages of differentiation allows for an approximation of gene expression patterns during B cell development.

Tsapogas P, Breslin T, Bilke S, Lagergren A, Månsson R, Liberg D, Peterson C, Sigvardsson M.

J Leukoc Biol. 2003 Jul;74(1):102-10.


Early B-cell factor, E2A, and Pax-5 cooperate to activate the early B cell-specific mb-1 promoter.

Sigvardsson M, Clark DR, Fitzsimmons D, Doyle M, Akerblad P, Breslin T, Bilke S, Li R, Yeamans C, Zhang G, Hagman J.

Mol Cell Biol. 2002 Dec;22(24):8539-51.


CD44-stimulated human B cells express transcripts specifically involved in immunomodulation and inflammation as analyzed by DNA microarrays.

Högerkorp CM, Bilke S, Breslin T, Ingvarsson S, Borrebaeck CA.

Blood. 2003 Mar 15;101(6):2307-13. Epub 2002 Oct 31.

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