 Joseph Costello, PhD
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| Title | Professor in Residence |
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| School | UCSF School of Medicine |
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| Department | Neurological Surgery |
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| Address | 1450 3rd Street
San Francisco CA 94158
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| Phone | 415-514-1183 |
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| Email | jcostello@cc.ucsf.edu |
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 Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods. 2013 May; 10(5):375-6.
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Nagarajan RP, Fouse SD, Bell RJ, Costello JF. Methods for cancer epigenome analysis. Adv Exp Med Biol. 2013; 754:313-38.
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Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24.
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Moniz S, Martinho O, Pinto F, Sousa B, Loureiro C, Oliveira MJ, Moita LF, Honavar M, Pinheiro C, Pires M, Lopes JM, Jones C, Costello JF, Paredes J, Reis RM, Jordan P. Loss of WNK2 expression by promoter gene methylation occurs in adult gliomas and triggers Rac1-mediated tumour cell invasiveness. Hum Mol Genet. 2013 Jan 1; 22(1):84-95.
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Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: A navigational paradigm for genomic data exploration. Genome Res. 2012 Nov; 22(11):2262-9.
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Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Jun 21; 486(7403):395-9.
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Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM. Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3. Pharmacogenomics J. 2013 Apr; 13(2):110-20.
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Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T. The Human Epigenome Browser at Washington University. Nat Methods. 2011 Dec; 8(12):989-90.
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Butowski N, Chang SM, Lamborn KR, Polley MY, Pieper R, Costello JF, Vandenberg S, Parvataneni R, Nicole A, Sneed PK, Clarke J, Hsieh E, Costa BM, Reis RM, Hristova-Kazmierski M, Nicol SJ, Thornton DE, Prados MD. Phase II and pharmacogenomics study of enzastaurin plus temozolomide during and following radiation therapy in patients with newly diagnosed glioblastoma multiforme and gliosarcoma. Neuro Oncol. 2011 Dec; 13(12):1331-8.
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Wong KY, Liang R, So CC, Jin DY, Costello JF, Chim CS. Epigenetic silencing of MIR203 in multiple myeloma. Br J Haematol. 2011 Sep; 154(5):569-78.
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Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May; 13(5):541-9.
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Leng S, Bernauer AM, Hong C, Do KC, Yingling CM, Flores KG, Tessema M, Tellez CS, Willink RP, Burki EA, Picchi MA, Stidley CA, Prados MD, Costello JF, Gilliland FD, Crowell RE, Belinsky SA. The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas. Clin Cancer Res. 2011 Apr 1; 17(7):2014-23.
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Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011; 6(2):e17121.
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Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8.
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Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105.
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Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8; 466(7303):253-7.
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Chen R, Nishimura MC, Bumbaca SM, Kharbanda S, Forrest WF, Kasman IM, Greve JM, Soriano RH, Gilmour LL, Rivers CS, Modrusan Z, Nacu S, Guerrero S, Edgar KA, Wallin JJ, Lamszus K, Westphal M, Heim S, James CD, VandenBerg SR, Costello JF, Moorefield S, Cowdrey CJ, Prados M, Phillips HS. A hierarchy of self-renewing tumor-initiating cell types in glioblastoma. Cancer Cell. 2010 Apr 13; 17(4):362-75.
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Fouse SD, Nagarajan RO, Costello JF. Genome-scale DNA methylation analysis. Epigenomics. 2010 Feb; 2(1):105-17.
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Chim CS, Wong KY, Qi Y, Loong F, Lam WL, Wong LG, Jin DY, Costello JF, Liang R. Epigenetic inactivation of the miR-34a in hematological malignancies. Carcinogenesis. 2010 Apr; 31(4):745-50.
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Costa BM, Smith JS, Chen Y, Chen J, Phillips HS, Aldape KD, Zardo G, Nigro J, James CD, Fridlyand J, Reis RM, Costello JF. Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res. 2010 Jan 15; 70(2):453-62.
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Fouse SD, Costello JF. Epigenetics of neurological cancers. Future Oncol. 2009 Dec; 5(10):1615-29.
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Costello JF, Krzywinski M, Marra MA. A first look at entire human methylomes. Nat Biotechnol. 2009 Dec; 27(12):1130-2.
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Costello JF, Moore AR, Wieczorek PM, Macarthur AJ, Balki M, Carvalho JC. The transversus abdominis plane block, when used as part of a multimodal regimen inclusive of intrathecal morphine, does not improve analgesia after cesarean delivery. Reg Anesth Pain Med. 2009 Nov-Dec; 34(6):586-9.
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Nagarajan RP, Costello JF. Molecular epigenetics and genetics in neuro-oncology. Neurotherapeutics. 2009 Jul; 6(3):436-46.
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Nagarajan RP, Costello JF. Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol. 2009 Jun; 19(3):188-97.
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Costello JF, Hong C, Plass C, Smiraglia DJ. Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis. Methods Mol Biol. 2009; 507:131-48.
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Jun P, Hong C, Lal A, Wong JM, McDermott MW, Bollen AW, Plass C, Held WA, Smiraglia DJ, Costello JF. Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific. Neuro Oncol. 2009 Aug; 11(4):414-22.
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Yi JM, Tsai HC, Glöckner SC, Lin S, Ohm JE, Easwaran H, James CD, Costello JF, Riggins G, Eberhart CG, Laterra J, Vescovi AL, Ahuja N, Herman JG, Schuebel KE, Baylin SB. Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors. Cancer Res. 2008 Oct 1; 68(19):8094-103.
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Costello JF, Balki M. Cesarean delivery under ultrasound-guided spinal anesthesia [corrected] in a parturient with poliomyelitis and Harrington instrumentation. Can J Anaesth. 2008 Sep; 55(9):606-11.
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Costello JF. Stem cells: Tips for priming potency. Nature. 2008 Jul 3; 454(7200):45-6.
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Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, Yu M, Vandenberg SR, Ginzinger DG, James CD, Costello JF, Bergers G, Weiss WA, Alvarez-Buylla A, Hodgson JG. miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med. 2008; 6:14.
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Randall IM, Costello J, Carvalho JC. Transversus abdominis plane block in a patient with debilitating pain from an abdominal wall hematoma following cesarean delivery. Anesth Analg. 2008 Jun; 106(6):1928.
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Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008; 9(3):R59.
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Smiraglia DJ, Kazhiyur-Mannar R, Oakes CC, Wu YZ, Liang P, Ansari T, Su J, Rush LJ, Smith LT, Yu L, Liu C, Dai Z, Chen SS, Wang SH, Costello J, Ioshikhes I, Dawson DW, Hong JS, Teitell MA, Szafranek A, Camoriano M, Song F, Elliott R, Held W, Trasler JM, Plass C, Wenger R. Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations. BMC Genomics. 2007; 8:446.
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Carvalho LH, Smirnov I, Baia GS, Modrusan Z, Smith JS, Jun P, Costello JF, McDermott MW, Vandenberg SR, Lal A. Molecular signatures define two main classes of meningiomas. Mol Cancer. 2007; 6:64.
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Smith JF, Mahmood S, Song F, Morrow A, Smiraglia D, Zhang X, Rajput A, Higgins MJ, Krumm A, Petrelli NJ, Costello JF, Nagase H, Plass C, Held WA. Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer. Epigenetics. 2007 Sep; 2(3):161-72.
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Hong C, Moorefield KS, Jun P, Aldape KD, Kharbanda S, Phillips HS, Costello JF. Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth. Proc Natl Acad Sci U S A. 2007 Jun 26; 104(26):10974-9.
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Brena RM, Costello JF. Genome-epigenome interactions in cancer. Hum Mol Genet. 2007 Apr 15; 16 Spec No 1:R96-105.
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Brena RM, Plass C, Costello JF. Mining methylation for early detection of common cancers. PLoS Med. 2006 Dec; 3(12):e479.
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Cadieux B, Ching TT, VandenBerg SR, Costello JF. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Res. 2006 Sep 1; 66(17):8469-76.
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Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD. Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. J Biol Chem. 2006 Aug 25; 281(34):24790-802.
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Smith JS, Costello JF. A broad band of silence. Nat Genet. 2006 May; 38(5):504-6.
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Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. DNA motifs associated with aberrant CpG island methylation. Genomics. 2006 May; 87(5):572-9.
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Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello JF, Ziegler JL. Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer. Genet Test. 2006; 10(4):281-4.
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Cuevas IC, Slocum AL, Jun P, Costello JF, Bollen AW, Riggins GJ, McDermott MW, Lal A. Meningioma transcript profiles reveal deregulated Notch signaling pathway. Cancer Res. 2005 Jun 15; 65(12):5070-5.
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Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K, Weiss WA, Costello JF. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005 Jun; 37(6):645-51.
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Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, Weiss WA, Costello JF. Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8. Cancer Res. 2005 May 1; 65(9):3617-23.
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Costello JF. Comparative epigenomics of leukemia. Nat Genet. 2005 Mar; 37(3):211-2.
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Stokoe D, Costello JF. Phosphatase and tensin homologue growth suppression without phosphatase. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2677-8.
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Hong C, Bollen AW, Costello JF. The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas. Cancer Res. 2003 Nov 15; 63(22):7600-5.
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He B, You L, Uematsu K, Zang K, Xu Z, Lee AY, Costello JF, McCormick F, Jablons DM. SOCS-3 is frequently silenced by hypermethylation and suppresses cell growth in human lung cancer. Proc Natl Acad Sci U S A. 2003 Nov 25; 100(24):14133-8.
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Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. Predicting aberrant CpG island methylation. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12253-8.
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Costello JF. DNA methylation in brain development and gliomagenesis. Front Biosci. 2003 Jan 1; 8:s175-84.
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Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D, Albertson DG, Costello JF. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet. 2002 Nov; 32(3):453-8.
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Costello JF, Smiraglia DJ, Plass C. Restriction landmark genome scanning. Methods. 2002 Jun; 27(2):144-9.
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Costello JF, Vertino PM. Methylation matters: a new spin on maspin. Nat Genet. 2002 Jun; 31(2):123-4.
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Costello JF, Plass C, Cavenee WK. Restriction landmark genome scanning. Methods Mol Biol. 2002; 200:53-70.
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Smiraglia DJ, Rush LJ, Frühwald MC, Dai Z, Held WA, Costello JF, Lang JC, Eng C, Li B, Wright FA, Caligiuri MA, Plass C. Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum Mol Genet. 2001 Jun 15; 10(13):1413-9.
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Rush LJ, Dai Z, Smiraglia DJ, Gao X, Wright FA, Frühwald M, Costello JF, Held WA, Yu L, Krahe R, Kolitz JE, Bloomfield CD, Caligiuri MA, Plass C. Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci. Blood. 2001 May 15; 97(10):3226-33.
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Costello JF, Plass C. Methylation matters. J Med Genet. 2001 May; 38(5):285-303.
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Frühwald MC, O'Dorisio MS, Rush LJ, Reiter JL, Smiraglia DJ, Wenger G, Costello JF, White PS, Krahe R, Brodeur GM, Plass C. Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon. J Med Genet. 2000 Jul; 37(7):501-9.
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Costello JF, Frühwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, Wright FA, Feramisco JD, Peltomäki P, Lang JC, Schuller DE, Yu L, Bloomfield CD, Caligiuri MA, Yates A, Nishikawa R, Su Huang H, Petrelli NJ, Zhang X, O'Dorisio MS, Held WA, Cavenee WK, Plass C. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet. 2000 Feb; 24(2):132-8.
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Costello JF, Plass C, Cavenee WK. Aberrant methylation of genes in low-grade astrocytomas. Brain Tumor Pathol. 2000; 17(2):49-56.
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Smiraglia DJ, Frühwald MC, Costello JF, McCormick SP, Dai Z, Peltomäki P, O'Dorisio MS, Cavenee WK, Plass C. A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels. Genomics. 1999 Jun 15; 58(3):254-62.
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Bachman KE, Herman JG, Corn PG, Merlo A, Costello JF, Cavenee WK, Baylin SB, Graff JR. Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggest a suppressor role in kidney, brain, and other human cancers. Cancer Res. 1999 Feb 15; 59(4):798-802.
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Watts GS, Pieper RO, Costello JF, Peng YM, Dalton WS, Futscher BW. Methylation of discrete regions of the O6-methylguanine DNA methyltransferase (MGMT) CpG island is associated with heterochromatinization of the MGMT transcription start site and silencing of the gene. Mol Cell Biol. 1997 Sep; 17(9):5612-9.
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Plass C, Weichenhan D, Catanese J, Costello JF, Yu F, Yu L, Smiraglia D, Cavenee WK, Caligiuri MA, deJong P, Held WA. An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res. 1997 Jun 30; 4(3):253-5.
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Costello JF, Plass C, Arap W, Chapman VM, Held WA, Berger MS, Su Huang HJ, Cavenee WK. Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res. 1997 Apr 1; 57(7):1250-4.
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Pieper RO, Patel S, Ting SA, Futscher BW, Costello JF. Methylation of CpG island transcription factor binding sites is unnecessary for aberrant silencing of the human MGMT gene. J Biol Chem. 1996 Jun 7; 271(23):13916-24.
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Costello JF, Berger MS, Huang HS, Cavenee WK. Silencing of p16/CDKN2 expression in human gliomas by methylation and chromatin condensation. Cancer Res. 1996 May 15; 56(10):2405-10.
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Nutt CL, Costello JF, Bambrick LL, Yarosh DB, Swinnen LJ, Chambers AF, Cairncross JG. O6-methylguanine-DNA methyltransferase in tumors and cells of the oligodendrocyte lineage. Can J Neurol Sci. 1995 May; 22(2):111-5.
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Costello JF, Futscher BW, Kroes RA, Pieper RO. Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines. Mol Cell Biol. 1994 Oct; 14(10):6515-21.
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Costello JF, Futscher BW, Tano K, Graunke DM, Pieper RO. Graded methylation in the promoter and body of the O6-methylguanine DNA methyltransferase (MGMT) gene correlates with MGMT expression in human glioma cells. J Biol Chem. 1994 Jun 24; 269(25):17228-37.
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Pieper RO, Costello JF, Kroes RA, Futscher BW, Marathi U, Erickson LC. Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene. Cancer Commun. 1991 Aug; 3(8):241-53.
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