Loading...

Joseph Costello, PhD

TitleProfessor
InstitutionUniversity of California San Francisco
DepartmentNeurological Surgery
Address1450 3rd Street
San Francisco CA 94158
Phone415-514-1183
vCardDownload vCard

    Collapse Research 
    Collapse Research Activities and Funding
    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
    Imaging and Tissue Correlates to Optimize Management of Glioblastoma
    NIH/NCI P01CA118816Dec 1, 2005 - Jul 31, 2018
    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

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    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.
    List All   |   Timeline
    1. 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 J. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol. 2018 Apr 09; 20(5):632-641. PMID: 29077933.
      View in: PubMed
    2. 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 J, Arnaud P, Sousa N, Costa BM. 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. PMID: 29644006.
      View in: PubMed
    3. Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello J. Temozolomide-associated Hypermutation in Gliomas. Neuro Oncol. 2018 Feb 14. PMID: 29452419.
      View in: PubMed
    4. Stieglitz E, Mazor T, Olshen AB, Geng H, Gelston LC, Akutagawa J, Lipka DB, Plass C, Flotho C, Chehab FF, Braun BS, Costello J, Loh ML. Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia. Nat Commun. 2017 Dec 19; 8(1):2127. PMID: 29259179.
      View in: PubMed
    5. 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. 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. PMID: 29308320.
      View in: PubMed
    6. 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 J, Meyn MS, Pursell ZF, Malkin D, Tabori U, Shlien A. Comprehensive Analysis of Hypermutation in Human Cancer. Cell. 2017 Nov 16; 171(5):1042-1056.e10. PMID: 29056344.
      View in: PubMed
    7. 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 J. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. Proc Natl Acad Sci U S A. 2017 Oct 03; 114(40):10743-10748. PMID: 28916733.
      View in: PubMed
    8. Venkatesan S, Swanton C, Taylor BS, Costello J. Treatment-Induced Mutagenesis and Selective Pressures Sculpt Cancer Evolution. Cold Spring Harb Perspect Med. 2017 Aug 01; 7(8). PMID: 28289245.
      View in: PubMed
    9. Wahl M, Chang SM, Phillips JJ, Molinaro AM, Costello J, Mazor T, Alexandrescu S, Lupo JM, Nelson SJ, Berger M, Prados M, Taylor JW, Butowski N, Clarke JL, Haas-Kogan D. 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. PMID: 28759109.
      View in: PubMed
    10. Kim M, Costello J. DNA methylation: an epigenetic mark of cellular memory. Exp Mol Med. 2017 04 28; 49(4):e322. PMID: 28450738.
      View in: PubMed
    11. 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 J, Okada H. Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas. J Clin Invest. 2017 Apr 03; 127(4):1425-1437. PMID: 28319047.
      View in: PubMed
    12. Wahl M, Phillips JJ, Molinaro AM, Lin Y, Perry A, Haas-Kogan DA, Costello J, Dayal M, Butowski N, Clarke JL, Prados M, Nelson S, Berger MS, Chang SM. 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. PMID: 27571885.
      View in: PubMed
    13. McMorris T, Hale BJ, Barwood M, Costello J, Corbett J. Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis. Neurosci Biobehav Rev. 2017 03; 74(Pt A):225-232. PMID: 28111267.
      View in: PubMed
    14. 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 J, Ronen SM, Pieper RO. Mutant IDH1 Expression Drives TERT Promoter Reactivation as Part of the Cellular Transformation Process. Cancer Res. 2016 11 15; 76(22):6680-6689. PMID: 27758882.
      View in: PubMed
    15. 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 J, Nakamura AO, Shannon KM, Bhatia S, Nakamura JL. Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors. Clin Cancer Res. 2017 Apr 01; 23(7):1852-1861. PMID: 27683180.
      View in: PubMed
    16. Viswanath P, Najac C, Izquierdo-Garcia JL, Pankov A, Hong C, Eriksson P, Costello J, Pieper RO, Ronen SM. Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters. Oncotarget. 2016 Jun 07; 7(23):34942-55. PMID: 27144334.
      View in: PubMed
    17. Mazor T, Pankov A, Song JS, Costello J. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 2016 Apr 11; 29(4):440-451. PMID: 27070699; PMCID: PMC4852161 [Available on 04/11/17].
    18. Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello J, Wang T. 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. PMID: 26888867; PMCID: PMC4825665.
    19. Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello J. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res. 2016 Apr; 14(4):315-23. PMID: 26941407; PMCID: PMC4852159 [Available on 04/01/17].
    20. 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 J, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber TA, Golub TR, Stegmaier K, Loh ML. Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia. Nat Genet. 2016 Jan; 48(1):101. PMID: 26711114.
      View in: PubMed
    21. Grimmer MR, Costello J. Cancer: Oncogene brought into the loop. Nature. 2016 Jan 07; 529(7584):34-5. PMID: 26700812; PMCID: PMC4920076.
    22. 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 J, Olshen AB, Stewart C, Li Y, Ma J, Gerbing RB, Alonzo TA, Getz G, Gruber T, Golub T, Stegmaier K, Loh ML. The genomic landscape of juvenile myelomonocytic leukemia. Nat Genet. 2015 Nov; 47(11):1326-1333. PMID: 26457647; PMCID: PMC4626387.
    23. 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 J. 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. PMID: 26373278; PMCID: PMC4573399.
    24. 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 J. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science. 2015 May 29; 348(6238):1036-9. PMID: 25977370; PMCID: PMC4456397.
    25. Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello J, Wang T. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol. 2015 Apr; 33(4):345-6. PMID: 25690851; PMCID: PMC4467764.
    26. 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 J. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathol. 2015 Apr; 129(4):597-607. PMID: 25724300; PMCID: PMC4482618.
    27. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
    28. 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 J. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. PMID: 25691127; PMCID: PMC4333717.
    29. Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello J, Hirst M. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18; 6:6351. PMID: 25690954; PMCID: PMC4346612.
    30. Ameri K, Jahangiri A, Rajah AM, Tormos KV, Nagarajan R, Pekmezci M, Nguyen V, Wheeler ML, Murphy MP, Sanders TA, Jeffrey SS, Yeghiazarians Y, Rinaudo PF, Costello J, Aghi MK, Maltepe E. HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth. Cell Rep. 2015 Feb 12. PMID: 25683712.
      View in: PubMed
    31. Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello J, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. The genetics of splicing in neuroblastoma. Cancer Discov. 2015 Apr; 5(4):380-95. PMID: 25637275; PMCID: PMC4390477.
    32. Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello J, Wang T, Cheng JB. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat Commun. 2014 Nov 25; 5:5442. PMID: 25421844; PMCID: PMC4385735.
    33. Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello J, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep. 2014 Nov 20; 9(4):1228-34. PMID: 25456125; PMCID: PMC4254608.
    34. Clarke JL, Molinaro AM, Phillips JJ, Butowski NA, Chang SM, Perry A, Costello J, DeSilva AA, Rabbitt JE, Prados MD. A single-institution phase II trial of radiation, temozolomide, erlotinib, and bevacizumab for initial treatment of glioblastoma. Neuro Oncol. 2014 Jul; 16(7):984-90. PMID: 24637230; PMCID: PMC4057142.
    35. Zhou X, Li D, Lowdon RF, Costello J, Wang T. methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. Bioinformatics. 2014 Aug 01; 30(15):2206-7. PMID: 24728854; PMCID: PMC4103599.
    36. Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello J. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res. 2014 May; 24(5):761-74. PMID: 24709822; PMCID: PMC4009606.
    37. Bleakley CM, Bieuzen F, Davison GW, Costello J. Whole-body cryotherapy: empirical evidence and theoretical perspectives. Open Access J Sports Med. 2014; 5:25-36. PMID: 24648779; PMCID: PMC3956737.
    38. Sturm D, Bender S, Jones DT, Lichter P, Grill J, Becher O, Hawkins C, Majewski J, Jones C, Costello J, Iavarone A, Aldape K, Brennan CW, Jabado N, Pfister SM. Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge. Nat Rev Cancer. 2014 Feb; 14(2):92-107. PMID: 24457416; PMCID: PMC4003223.
    39. Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello J, Lorincz MC, Karimi MM, Jones SJ. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014 04 15; 30(8):1172-1174. PMID: 24371156.
      View in: PubMed
    40. Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJM, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello J. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science. 2014 Jan 10; 343(6167):189-193. PMID: 24336570; PMCID: PMC3998672.
    41. Fouse SD, Nakamura JL, James CD, Chang S, Costello J. Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype. Neuro Oncol. 2014 Mar; 16(3):361-71. PMID: 24311636; PMCID: PMC3922516.
    42. Huse JT, Wallace M, Aldape KD, Berger MS, Bettegowda C, Brat DJ, Cahill DP, Cloughesy T, Haas-Kogan DA, Marra M, Miller CR, Nelson SJ, Salama SR, Soffietti R, Wen PY, Yip S, Yen K, Costello J, Chang S. Where are we now? And where are we going? A report from the Accelerate Brain Cancer Cure (ABC2) low-grade glioma research workshop. Neuro Oncol. 2014 Jan; 16(2):173-8. PMID: 24305708; PMCID: PMC3895389.
    43. Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello J, Wilkinson MF, Joung JK. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol. 2013 Dec; 31(12):1137-42. PMID: 24108092; PMCID: PMC3858462.
    44. Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello J, Wang T. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013 Sep; 23(9):1522-40. PMID: 23804400; PMCID: PMC3759728.
    45. Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello J, Wang T. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 2013 Sep; 23(9):1541-53. PMID: 23804401; PMCID: PMC3759729.
    46. Fouse SD, Costello J. Cancer Stem Cells Activate STAT3 the EZ Way. Cancer Cell. 2013 Jun 10; 23(6):711-3. PMID: 23763996; PMCID: PMC3706087.
    47. Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello J, Wang T. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013 Jul; 45(7):836-41. PMID: 23708189; PMCID: PMC3695047.
    48. Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello J, Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods. 2013 May; 10(5):375-6. PMID: 23629413; PMCID: PMC3820286.
    49. Nagarajan RP, Fouse SD, Bell RJ, Costello J. Methods for cancer epigenome analysis. Adv Exp Med Biol. 2013; 754:313-38. PMID: 22956508; PMCID: PMC4090090.
    50. Beck S, Bernstein BE, Campbell RM, Costello J, 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. PMID: 23188507.
      View in: PubMed
    51. 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 J, 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 01; 22(1):84-95. PMID: 23035050.
      View in: PubMed
    52. Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello J, Hirst M, Farnham PJ, Jones SJ. Spark: a navigational paradigm for genomic data exploration. Genome Res. 2012 Nov; 22(11):2262-9. PMID: 22960372; PMCID: PMC3483555.
    53. 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 J, 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 Apr 04; 486(7403):395-9. PMID: 22495314; PMCID: PMC3863681.
    54. 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 J, Wang T. The Human Epigenome Browser at Washington University. Nat Methods. 2011 Nov 29; 8(12):989-90. PMID: 22127213; PMCID: PMC3552640.
    55. Butowski N, Chang SM, Lamborn KR, Polley MY, Pieper R, Costello J, 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. PMID: 21896554; PMCID: PMC3223090.
    56. Wong KY, Liang R, So CC, Jin DY, Costello J, Chim CS. Epigenetic silencing of MIR203 in multiple myeloma. Br J Haematol. 2011 Sep; 154(5):569-78. PMID: 21707582.
      View in: PubMed
    57. 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 J, 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. PMID: 21499256; PMCID: PMC3987913.
    58. 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 J, 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 01; 17(7):2014-23. PMID: 21355081; PMCID: PMC3070839.
    59. Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello J, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15; 6(2):e17121. PMID: 21347206.
      View in: PubMed
    60. Bernstein BE, Stamatoyannopoulos JA, Costello J, 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. PMID: 20944595; PMCID: PMC3607281.
    61. 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 J. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
    62. 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 J. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 08; 466(7303):253-7. PMID: 20613842; PMCID: PMC3998662.
    63. 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 J, 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. PMID: 20385361.
      View in: PubMed
    64. Fouse SD, Nagarajan RO, Costello J. Genome-scale DNA methylation analysis. Epigenomics. 2010 Feb; 2(1):105-17. PMID: 20657796.
      View in: PubMed
    65. Costa BM, Smith JS, Chen Y, Chen J, Phillips HS, Aldape KD, Zardo G, Nigro J, James CD, Fridlyand J, Reis RM, Costello J. Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res. 2010 Jan 15; 70(2):453-62. PMID: 20068170; PMCID: PMC2849935.
    66. Costello J, Krzywinski M, Marra MA. A first look at entire human methylomes. Nat Biotechnol. 2009 Dec; 27(12):1130-2. PMID: 20010593.
      View in: PubMed
    67. Fouse SD, Costello J. Epigenetics of neurological cancers. Future Oncol. 2009 Dec; 5(10):1615-29. PMID: 20001799; PMCID: PMC4018230.
    68. Costello J, 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. PMID: 19916252.
      View in: PubMed
    69. Nagarajan RP, Costello J. Molecular epigenetics and genetics in neuro-oncology. Neurotherapeutics. 2009 Jul; 6(3):436-46. PMID: 19560734; PMCID: PMC3981537.
    70. Nagarajan RP, Costello J. Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol. 2009 Jun; 19(3):188-97. PMID: 19429483.
      View in: PubMed
    71. Costello J, 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. PMID: 18987812.
      View in: PubMed
    72. Jun P, Hong C, Lal A, Wong JM, McDermott MW, Bollen AW, Plass C, Held WA, Smiraglia DJ, Costello J. Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific. Neuro Oncol. 2009 Aug; 11(4):414-22. PMID: 19001526; PMCID: PMC2743221.
    73. Yi JM, Tsai HC, Glöckner SC, Lin S, Ohm JE, Easwaran H, James CD, Costello J, 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 01; 68(19):8094-103. PMID: 18829568; PMCID: PMC2744404.
    74. Costello J, 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. PMID: 18840590.
      View in: PubMed
    75. Costello J. Stem cells: Tips for priming potency. Nature. 2008 Jul 03; 454(7200):45-6. PMID: 18596797.
      View in: PubMed
    76. Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, Yu M, Vandenberg SR, Ginzinger DG, James CD, Costello J, 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 Jun 24; 6:14. PMID: 18577219; PMCID: PMC2443372.
    77. 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. PMID: 18499643.
      View in: PubMed
    78. 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. PMID: 18364049; PMCID: PMC2397511.
    79. 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 Nov 30; 8:446. PMID: 18053125; PMCID: PMC2235865.
    80. Carvalho LH, Smirnov I, Baia GS, Modrusan Z, Smith JS, Jun P, Costello J, McDermott MW, Vandenberg SR, Lal A. Molecular signatures define two main classes of meningiomas. Mol Cancer. 2007 Oct 15; 6:64. PMID: 17937814; PMCID: PMC2173907.
    81. Smith JF, Mahmood S, Song F, Morrow A, Smiraglia D, Zhang X, Rajput A, Higgins MJ, Krumm A, Petrelli NJ, Costello J, 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. PMID: 17965620.
      View in: PubMed
    82. Hong C, Moorefield KS, Jun P, Aldape KD, Kharbanda S, Phillips HS, Costello J. 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. PMID: 17578925; PMCID: PMC1904113.
    83. Brena RM, Costello J. Genome-epigenome interactions in cancer. Hum Mol Genet. 2007 Apr 15; 16 Spec No 1:R96-105. PMID: 17613554.
      View in: PubMed
    84. Brena RM, Plass C, Costello J. Mining methylation for early detection of common cancers. PLoS Med. 2006 Dec; 3(12):e479. PMID: 17194184; PMCID: PMC1762083.
    85. Cadieux B, Ching TT, VandenBerg SR, Costello J. 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. PMID: 16951158.
      View in: PubMed
    86. Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello J, 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. PMID: 16766534.
      View in: PubMed
    87. Smith JS, Costello J. A broad band of silence. Nat Genet. 2006 May; 38(5):504-6. PMID: 16642011.
      View in: PubMed
    88. Feltus FA, Lee EK, Costello J, Plass C, Vertino PM. DNA motifs associated with aberrant CpG island methylation. Genomics. 2006 May; 87(5):572-9. PMID: 16487676.
      View in: PubMed
    89. Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello J, Ziegler JL. Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer. Genet Test. 2006; 10(4):281-4. PMID: 17253935.
      View in: PubMed
    90. Cuevas IC, Slocum AL, Jun P, Costello J, 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. PMID: 15958550.
      View in: PubMed
    91. Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K, Weiss WA, Costello J. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005 Jun; 37(6):645-51. PMID: 15895082.
      View in: PubMed
    92. Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, Weiss WA, Costello J. Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8. Cancer Res. 2005 May 01; 65(9):3617-23. PMID: 15867356.
      View in: PubMed
    93. Costello J. Comparative epigenomics of leukemia. Nat Genet. 2005 Mar; 37(3):211-2. PMID: 15731751.
      View in: PubMed
    94. Stokoe D, Costello J. Phosphatase and tensin homologue growth suppression without phosphatase. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2677-8. PMID: 15710873; PMCID: PMC549471.
    95. Hong C, Bollen AW, Costello J. The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas. Cancer Res. 2003 Nov 15; 63(22):7600-5. PMID: 14633674.
      View in: PubMed
    96. He B, You L, Uematsu K, Zang K, Xu Z, Lee AY, Costello J, 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. PMID: 14617776; PMCID: PMC283558.
    97. Costello J. DNA methylation in brain development and gliomagenesis. Front Biosci. 2003 Jan 01; 8:s175-84. PMID: 12456310.
      View in: PubMed
    98. Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D, Albertson DG, Costello J. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet. 2002 Nov; 32(3):453-8. PMID: 12355068.
      View in: PubMed
    99. Costello J, Vertino PM. Methylation matters: a new spin on maspin. Nat Genet. 2002 Jun; 31(2):123-4. PMID: 12040372.
      View in: PubMed
    100. Costello J, Smiraglia DJ, Plass C. Restriction landmark genome scanning. Methods. 2002 Jun; 27(2):144-9. PMID: 12095273.
      View in: PubMed
    101. Costello J, Plass C, Cavenee WK. Restriction landmark genome scanning. Methods Mol Biol. 2002; 200:53-70. PMID: 11951655.
      View in: PubMed
    Joseph's Networks
    Concepts
    Derived automatically from this person's publications.
    _
    Co-Authors
    People in Profiles who have published with this person.
    _
    Related Authors
    People who share related concepts with this person.
    _