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Joseph Costello, PhD

Title(s)Professor, Neurological Surgery
SchoolSchool of Medicine
Address1450 3rd Street
San Francisco CA 94158
Phone415-514-1183
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Research 
    Collapse Research Activities and Funding
    3-D spatial approach to discover genomic effectors of immunosuppression during malignant transformation
    NIH/NCI R01CA244838Jul 1, 2020 - Jun 30, 2025
    Role: Principal Investigator
    Global Analyses of the Placental Epigenome in Preeclampsia
    NIH/NICHD R01HD092419Sep 1, 2017 - May 31, 2022
    Role: Principal Investigator
    Antigens for Molecularly Targeted Vaccines for Progressive Glioma
    NIH/NINDS R21NS093654Jul 1, 2015 - Jun 30, 2017
    Role: Co-Principal Investigator
    Imaging Guided Genomics of Malignant Transformation
    NIH/NCI R01CA169316Apr 8, 2013 - Mar 31, 2018
    Role: Principal Investigator
    Training Program in Translational Brain Tumor Research
    NIH/NCI T32CA151022Sep 1, 2010 - Aug 31, 2020
    Role: Principal Investigator
    Integrated Epigenetic Maps of Human Embryonic and Adult Cells
    NIH/NIEHS U01ES017154Sep 30, 2008 - Jun 30, 2014
    Role: Principal Investigator
    Noninvasive Metabolic Signatures to Improve Management of Molecular Subtypes of Glioma
    NIH/NCI P01CA118816Jul 1, 2007 - Jun 30, 2013
    Role: Co-Investigator
    CONVERGENT MECHANISMS CONTRIBUTING TO CANCER
    NIH/NCI R01CA094971Apr 1, 2002 - Sep 30, 2007
    Role: Principal Investigator
    Center Core Grant for Vision Research
    NIH P30EY005722Mar 1, 1985 - Aug 31, 2021
    Role: Co-Investigator
    General Clinical Research Center
    NIH M01RR002172Jan 1, 1983 - Mar 31, 2009
    Role: Co-Investigator

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma. Nat Commun. 2020 09 23; 11(1):4803. Magill ST, Vasudevan HN, Seo K, Villanueva-Meyer JE, Choudhury A, John Liu S, Pekmezci M, Findakly S, Hilz S, Lastella S, Demaree B, Braunstein SE, Bush NAO, Aghi MK, Theodosopoulos PV, Sneed PK, Abate AR, Berger MS, McDermott MW, Lim DA, Ullian EM, Costello JF, Raleigh DR. PMID: 32968068.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Glutamate is a non-invasive metabolic biomarker of IDH1 mutant glioma response to temozolomide treatment. Cancer Res. 2020 Sep 21. Subramani E, Radoul M, Najac C, Batsios G, Molloy AR, Hong D, Gillespie AM, Delos Santos R, Viswanath P, Costello JF, Pieper RO, Ronen SM. PMID: 32958546.
      View in: PubMed   Mentions:    Fields:    
    3. Epigenomic programming in early fetal brain development. Epigenomics. 2020 Jun; 12(12):1053-1070. Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJ, Marra MA, Ligon KL, Costello JF, Hirst M. PMID: 32677466.
      View in: PubMed   Mentions:    Fields:    
    4. Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma. Neurooncol Adv. 2020 Jan-Dec; 2(1):vdaa088. Jones LE, Hilz S, Grimmer MR, Mazor T, Najac C, Mukherjee J, McKinney A, Chow T, Pieper RO, Ronen SM, Chang SM, Phillips JJ, Costello JF. PMID: 32904945.
      View in: PubMed   Mentions:
    5. The DNA methylation landscape of advanced prostate cancer. Nat Genet. 2020 08; 52(8):778-789. Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. PMID: 32661416.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. MGMT promoter methylation level in newly diagnosed low-grade glioma is a predictor of hypermutation at recurrence. Neuro Oncol. 2020 Mar 13. Mathur R, Zhang Y, Grimmer MR, Hong C, Zhang M, Bollam S, Petrecca K, Clarke J, Berger MS, Phillips JJ, Oberheim-Bush NA, Molinaro AM, Chang SM, Costello JF. PMID: 32166314.
      View in: PubMed   Mentions: 5     Fields:    
    7. Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features. Acta Neuropathol. 2020 05; 139(5):953-957. Sloan EA, Hilz S, Gupta R, Cadwell C, Ramani B, Hofmann J, Kline CN, Banerjee A, Reddy A, Oberheim Bush NA, Chang S, Braunstein S, Chang EF, Raffel C, Gupta N, Sun PP, Kim JYH, Moes G, Alva E, Li R, Bruggers CS, Alashari M, Wetmore C, Garg S, Dishop M, Van Ziffle J, Onodera C, Devine P, Grenert JP, Lee JC, Phillips JJ, Pekmezci M, Tihan T, Bollen AW, Berger MS, Costello JF, Perry A, Solomon DA. PMID: 32157385.
      View in: PubMed   Mentions:    Fields:    
    8. Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Rep. 2020 02 04; 30(5):1300-1309.e5. Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR. PMID: 32023450.
      View in: PubMed   Mentions:    Fields:    
    9. Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019 12; 576(7785):112-120. Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. PMID: 31748746.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    10. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun. 2019 08 08; 10(1):3583. Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N. PMID: 31395865.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    11. Recurrent KBTBD4 small in-frame insertions and absence of DROSHA deletion or DICER1 mutation differentiate pineal parenchymal tumor of intermediate differentiation (PPTID) from pineoblastoma. Acta Neuropathol. 2019 05; 137(5):851-854. Lee JC, Mazor T, Lao R, Wan E, Diallo AB, Hill NS, Thangaraj N, Wendelsdorf K, Samuel D, Kline CN, Banerjee A, Auguste K, Raffel C, Gupta N, Berger M, Raleigh DR, Shai A, Phillips JJ, Bollen AW, Tihan T, Perry A, Costello J, Solomon DA. PMID: 30877433.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    12. Corrigendum to "Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis" Neurosci. Biobehav. Rev. 74 (2017) 225-232. Neurosci Biobehav Rev. 2019 03; 98:333. McMorris T, Hale BJ, Barwood M, Costello J, Corbett J. PMID: 30686523.
      View in: PubMed   Mentions:    Fields:    
    13. Genomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts. Toxicol Sci. 2019 01 01; 167(1):211-226. Robinson JF, Kapidzic M, Hamilton EG, Chen H, Puckett KW, Zhou Y, Ona K, Parry E, Wang Y, Park JS, Costello JF, Fisher SJ. PMID: 30202865.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    14. Disruption of the ß1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell. 2018 09 10; 34(3):513-528.e8. Mancini A, Xavier-Magalhães A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF. PMID: 30205050.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    15. Temozolomide-associated hypermutation in gliomas. Neuro Oncol. 2018 09 03; 20(10):1300-1309. Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello JF. PMID: 29452419.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    16. To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. Front Genet. 2018; 9:298. Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS. PMID: 30154825.
      View in: PubMed   Mentions:
    17. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol. 2018 04 09; 20(5):632-641. Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi MK, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon DA, Costello JF. PMID: 29077933.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    18. The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma. Oncotarget. 2018 Mar 20; 9(21):15740-15756. Xavier-Magalhães A, Gonçalves CS, Fogli A, Lourenço T, Pojo M, Pereira B, Rocha M, Lopes MC, Crespo I, Rebelo O, Tão H, Lima J, Moreira R, Pinto AA, Jones C, Reis RM, Costello JF, Arnaud P, Sousa N, Costa BM. PMID: 29644006.
      View in: PubMed   Mentions: 4     Fields:    
    19. Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia. Nat Commun. 2017 12 19; 8(1):2127. Stieglitz E, Mazor T, Olshen AB, Geng H, Gelston LC, Akutagawa J, Lipka DB, Plass C, Flotho C, Chehab FF, Braun BS, Costello JF, Loh ML. PMID: 29259179.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsCTClinical Trials
    20. Antigenic expression and spontaneous immune responses support the use of a selected peptide set from the IMA950 glioblastoma vaccine for immunotherapy of grade II and III glioma. Oncoimmunology. 2018; 7(2):e1391972. Dutoit V, Migliorini D, Ranzanici G, Marinari E, Widmer V, Lobrinus JA, Momjian S, Costello J, Walker PR, Okada H, Weinschenk T, Herold-Mende C, Dietrich PY. PMID: 29308320.
      View in: PubMed   Mentions:
    21. Comprehensive Analysis of Hypermutation in Human Cancer. Cell. 2017 Nov 16; 171(5):1042-1056.e10. Campbell BB, Light N, Fabrizio D, Zatzman M, Fuligni F, de Borja R, Davidson S, Edwards M, Elvin JA, Hodel KP, Zahurancik WJ, Suo Z, Lipman T, Wimmer K, Kratz CP, Bowers DC, Laetsch TW, Dunn GP, Johanns TM, Grimmer MR, Smirnov IV, Larouche V, Samuel D, Bronsema A, Osborn M, Stearns D, Raman P, Cole KA, Storm PB, Yalon M, Opocher E, Mason G, Thomas GA, Sabel M, George B, Ziegler DS, Lindhorst S, Issai VM, Constantini S, Toledano H, Elhasid R, Farah R, Dvir R, Dirks P, Huang A, Galati MA, Chung J, Ramaswamy V, Irwin MS, Aronson M, Durno C, Taylor MD, Rechavi G, Maris JM, Bouffet E, Hawkins C, Costello JF, Meyn MS, Pursell ZF, Malkin D, Tabori U, Shlien A. PMID: 29056344.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCells
    22. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. Proc Natl Acad Sci U S A. 2017 10 03; 114(40):10743-10748. Mazor T, Chesnelong C, Pankov A, Jalbert LE, Hong C, Hayes J, Smirnov IV, Marshall R, Souza CF, Shen Y, Viswanath P, Noushmehr H, Ronen SM, Jones SJM, Marra MA, Cairncross JG, Perry A, Nelson SJ, Chang SM, Bollen AW, Molinaro AM, Bengtsson H, Olshen AB, Weiss S, Phillips JJ, Luchman HA, Costello JF. PMID: 28916733.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    23. Treatment-Induced Mutagenesis and Selective Pressures Sculpt Cancer Evolution. Cold Spring Harb Perspect Med. 2017 Aug 01; 7(8). Venkatesan S, Swanton C, Taylor BS, Costello JF. PMID: 28289245.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    24. Probing the phosphatidylinositol 3-kinase/mammalian target of rapamycin pathway in gliomas: A phase 2 study of everolimus for recurrent adult low-grade gliomas. Cancer. 2017 Dec 01; 123(23):4631-4639. Wahl M, Chang SM, Phillips JJ, Molinaro AM, Costello JF, Mazor T, Alexandrescu S, Lupo JM, Nelson SJ, Berger M, Prados M, Taylor JW, Butowski N, Clarke JL, Haas-Kogan D. PMID: 28759109.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCTClinical Trials
    25. DNA methylation: an epigenetic mark of cellular memory. Exp Mol Med. 2017 04 28; 49(4):e322. Kim M, Costello J. PMID: 28450738.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    26. Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas. J Clin Invest. 2017 Apr 03; 127(4):1425-1437. Kohanbash G, Carrera DA, Shrivastav S, Ahn BJ, Jahan N, Mazor T, Chheda ZS, Downey KM, Watchmaker PB, Beppler C, Warta R, Amankulor NA, Herold-Mende C, Costello JF, Okada H. PMID: 28319047.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    27. Chemotherapy for adult low-grade gliomas: clinical outcomes by molecular subtype in a phase II study of adjuvant temozolomide. Neuro Oncol. 2017 02 01; 19(2):242-251. Wahl M, Phillips JJ, Molinaro AM, Lin Y, Perry A, Haas-Kogan DA, Costello JF, Dayal M, Butowski N, Clarke JL, Prados M, Nelson S, Berger MS, Chang SM. PMID: 27571885.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCTClinical Trials
    28. Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis. Neurosci Biobehav Rev. 2017 Mar; 74(Pt A):225-232. McMorris T, Hale BJ, Barwood M, Costello J, Corbett J. PMID: 28111267.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    29. Mutant IDH1 Expression Drives TERT Promoter Reactivation as Part of the Cellular Transformation Process. Cancer Res. 2016 11 15; 76(22):6680-6689. Ohba S, Mukherjee J, Johannessen TC, Mancini A, Chow TT, Wood M, Jones L, Mazor T, Marshall RE, Viswanath P, Walsh KM, Perry A, Bell RJ, Phillips JJ, Costello JF, Ronen SM, Pieper RO. PMID: 27758882.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    30. Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors. Clin Cancer Res. 2017 Apr 01; 23(7):1852-1861. Sherborne AL, Lavergne V, Yu K, Lee L, Davidson PR, Mazor T, Smirnoff IV, Horvai AE, Loh M, DuBois SG, Goldsby RE, Neglia JP, Hammond S, Robison LL, Wustrack R, Costello JF, Nakamura AO, Shannon KM, Bhatia S, Nakamura JL. PMID: 27683180.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    31. Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters. Oncotarget. 2016 Jun 07; 7(23):34942-55. Viswanath P, Najac C, Izquierdo-Garcia JL, Pankov A, Hong C, Eriksson P, Costello JF, Pieper RO, Ronen SM. PMID: 27144334.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    32. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 2016 Apr 11; 29(4):440-451. Mazor T, Pankov A, Song JS, Costello JF. PMID: 27070699.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    33. Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. G3 (Bethesda). 2016 04 07; 6(4):973-86. Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T. PMID: 26888867.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    34. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res. 2016 Apr; 14(4):315-23. Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. PMID: 26941407.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    35. Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia. Nat Genet. 2016 Jan; 48(1):101. Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen SR, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T, Dahl GV, Emanuel PD, Fluchel MN, Goyal RK, Hayashi RJ, Hitzler J, Hugge C, Liu YL, Messinger YH, Mahoney DH, Monteleone P, Nemecek ER, Roehrs PA, Schore RJ, Stine KC, Takemoto CM, Toretsky JA, Costello JF, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber TA, Golub TR, Stegmaier K, Loh ML. PMID: 26711114.
      View in: PubMed   Mentions: 2     Fields:    
    36. Cancer: Oncogene brought into the loop. Nature. 2016 Jan 07; 529(7584):34-5. Grimmer MR, Costello JF. PMID: 26700812.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    37. The genomic landscape of juvenile myelomonocytic leukemia. Nat Genet. 2015 Nov; 47(11):1326-1333. Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen S, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T, Dahl GV, Emanuel PD, Fluchel MN, Goyal RK, Hayashi RJ, Hitzler J, Hugge C, Liu YL, Messinger YH, Mahoney DH, Monteleone P, Nemecek ER, Roehrs PA, Schore RJ, Stine KC, Takemoto CM, Toretsky JA, Costello JF, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber T, Golub T, Stegmaier K, Loh ML. PMID: 26457647.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    38. DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. Cancer Cell. 2015 Sep 14; 28(3):307-317. Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJA, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers MLM, Bollen AW, Taylor BS, Molinaro AM, Olshen AB, Chang SM, Song JS, Costello JF. PMID: 26373278.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansCells
    39. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science. 2015 May 29; 348(6238):1036-9. Bell RJ, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song JS, Costello JF. PMID: 25977370.
      View in: PubMed   Mentions: 137     Fields:    Translation:HumansCells
    40. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol. 2015 Apr; 33(4):345-6. Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T. PMID: 25690851.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    41. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathol. 2015 Apr; 129(4):597-607. van Thuijl HF, Mazor T, Johnson BE, Fouse SD, Aihara K, Hong C, Malmström A, Hallbeck M, Heimans JJ, Kloezeman JJ, Stenmark-Askmalm M, Lamfers ML, Saito N, Aburatani H, Mukasa A, Berger MS, Söderkvist P, Taylor BS, Molinaro AM, Wesseling P, Reijneveld JC, Chang SM, Ylstra B, Costello JF. PMID: 25724300.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    42. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. PMID: 25693563.
      View in: PubMed   Mentions: 1521     Fields:    Translation:HumansCells
    43. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. PMID: 25691127.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
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    105. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Res. 2006 Sep 01; 66(17):8469-76. Cadieux B, Ching TT, VandenBerg SR, Costello JF. PMID: 16951158.
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    106. Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. J Biol Chem. 2006 Aug 25; 281(34):24790-802. Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD. PMID: 16766534.
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    107. A broad band of silence. Nat Genet. 2006 May; 38(5):504-6. Smith JS, Costello JF. PMID: 16642011.
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    108. DNA motifs associated with aberrant CpG island methylation. Genomics. 2006 May; 87(5):572-9. Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. PMID: 16487676.
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    109. Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer. Genet Test. 2006; 10(4):281-4. Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello JF, Ziegler JL. PMID: 17253935.
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    110. Meningioma transcript profiles reveal deregulated Notch signaling pathway. Cancer Res. 2005 Jun 15; 65(12):5070-5. Cuevas IC, Slocum AL, Jun P, Costello JF, Bollen AW, Riggins GJ, McDermott MW, Lal A. PMID: 15958550.
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    111. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005 Jun; 37(6):645-51. Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K, Weiss WA, Costello JF. PMID: 15895082.
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    112. Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8. Cancer Res. 2005 May 01; 65(9):3617-23. Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, Weiss WA, Costello JF. PMID: 15867356.
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    113. Comparative epigenomics of leukemia. Nat Genet. 2005 Mar; 37(3):211-2. Costello JF. PMID: 15731751.
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    114. Phosphatase and tensin homologue growth suppression without phosphatase. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2677-8. Stokoe D, Costello JF. PMID: 15710873.
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    115. The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas. Cancer Res. 2003 Nov 15; 63(22):7600-5. Hong C, Bollen AW, Costello JF. PMID: 14633674.
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    116. 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. He B, You L, Uematsu K, Zang K, Xu Z, Lee AY, Costello JF, McCormick F, Jablons DM. PMID: 14617776.
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    117. Predicting aberrant CpG island methylation. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12253-8. Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. PMID: 14519846.
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    118. DNA methylation in brain development and gliomagenesis. Front Biosci. 2003 Jan 01; 8:s175-84. Costello JF. PMID: 12456310.
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    119. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet. 2002 Nov; 32(3):453-8. Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D, Albertson DG, Costello JF. PMID: 12355068.
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    120. Restriction landmark genome scanning. Methods. 2002 Jun; 27(2):144-9. Costello JF, Smiraglia DJ, Plass C. PMID: 12095273.
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    121. Methylation matters: a new spin on maspin. Nat Genet. 2002 Jun; 31(2):123-4. Costello JF, Vertino PM. PMID: 12040372.
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    122. Restriction landmark genome scanning. Methods Mol Biol. 2002; 200:53-70. Costello JF, Plass C, Cavenee WK. PMID: 11951655.
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    123. Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum Mol Genet. 2001 Jun 15; 10(13):1413-9. Smiraglia DJ, Rush LJ, Frühwald MC, Dai Z, Held WA, Costello JF, Lang JC, Eng C, Li B, Wright FA, Caligiuri MA, Plass C. PMID: 11440994.
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    124. Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci. Blood. 2001 May 15; 97(10):3226-33. 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. PMID: 11342453.
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    125. Methylation matters. J Med Genet. 2001 May; 38(5):285-303. Costello JF, Plass C. PMID: 11333864.
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    126. Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon. J Med Genet. 2000 Jul; 37(7):501-9. Frühwald MC, O'Dorisio MS, Rush LJ, Reiter JL, Smiraglia DJ, Wenger G, Costello JF, White PS, Krahe R, Brodeur GM, Plass C. PMID: 10882752.
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    127. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet. 2000 Feb; 24(2):132-8. 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. PMID: 10655057.
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    128. Aberrant methylation of genes in low-grade astrocytomas. Brain Tumor Pathol. 2000; 17(2):49-56. Costello JF, Plass C, Cavenee WK. PMID: 11210171.
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    129. 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. Smiraglia DJ, Frühwald MC, Costello JF, McCormick SP, Dai Z, Peltomäki P, O'Dorisio MS, Cavenee WK, Plass C. PMID: 10373323.
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    130. 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. Bachman KE, Herman JG, Corn PG, Merlo A, Costello JF, Cavenee WK, Baylin SB, Graff JR. PMID: 10029065.
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    131. 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. Watts GS, Pieper RO, Costello JF, Peng YM, Dalton WS, Futscher BW. PMID: 9271436.
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    132. An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res. 1997 Jun 30; 4(3):253-5. Plass C, Weichenhan D, Catanese J, Costello JF, Yu F, Yu L, Smiraglia D, Cavenee WK, Caligiuri MA, deJong P, Held WA. PMID: 9330914.
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    133. Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res. 1997 Apr 01; 57(7):1250-4. Costello JF, Plass C, Arap W, Chapman VM, Held WA, Berger MS, Su Huang HJ, Cavenee WK. PMID: 9102208.
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    134. Methylation of CpG island transcription factor binding sites is unnecessary for aberrant silencing of the human MGMT gene. J Biol Chem. 1996 Jun 07; 271(23):13916-24. Pieper RO, Patel S, Ting SA, Futscher BW, Costello JF. PMID: 8662860.
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    135. Silencing of p16/CDKN2 expression in human gliomas by methylation and chromatin condensation. Cancer Res. 1996 May 15; 56(10):2405-10. Costello JF, Berger MS, Huang HS, Cavenee WK. PMID: 8625319.
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    136. O6-methylguanine-DNA methyltransferase in tumors and cells of the oligodendrocyte lineage. Can J Neurol Sci. 1995 May; 22(2):111-5. Nutt CL, Costello JF, Bambrick LL, Yarosh DB, Swinnen LJ, Chambers AF, Cairncross JG. PMID: 7627911.
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    137. 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. Costello JF, Futscher BW, Kroes RA, Pieper RO. PMID: 7523853.
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    138. 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. Costello JF, Futscher BW, Tano K, Graunke DM, Pieper RO. PMID: 8006031.
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    139. Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene. Cancer Commun. 1991 Aug; 3(8):241-53. Pieper RO, Costello JF, Kroes RA, Futscher BW, Marathi U, Erickson LC. PMID: 1716139.
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