Joseph Costello, Ph.D. - Publications

Affiliations: 
Neurological Surgery University of California, San Francisco, San Francisco, CA 
Area:
Restriction Landmark Genomic Scanning (RLGS), CpG islands
Website:
http://neurosurgery.ucsf.edu/index.php/about_us_faculty_costello.html

99 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Yu Y, Villanueva-Meyer J, Grimmer MR, Hilz S, Solomon DA, Choi S, Wahl M, Mazor T, Hong C, Shai A, Phillips JJ, Wainer BH, McDermott M, Haas-Kogan D, Taylor JW, ... ... Costello JF, et al. Temozolomide-induced hypermutation is associated with distant recurrence and reduced survival after high-grade transformation of low-grade IDH-mutant gliomas. Neuro-Oncology. PMID 33823014 DOI: 10.1093/neuonc/noab081  0.92
2020 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. Patient-derived cells from recurrent tumors that model the evolution of -mutant glioma. Neuro-Oncology Advances. 2: vdaa088. PMID 32904945 DOI: 10.1093/noajnl/vdaa088  0.92
2020 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. MGMT promoter methylation level in newly diagnosed low-grade glioma is a predictor of hypermutation at recurrence. Neuro-Oncology. PMID 32166314 DOI: 10.1093/Neuonc/Noaa059  0.92
2019 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, ... ... Costello JF, et al. Longitudinal molecular trajectories of diffuse glioma in adults. Nature. PMID 31748746 DOI: 10.1038/S41586-019-1775-1  0.92
2018 Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello JF. Temozolomide-associated Hypermutation in Gliomas. Neuro-Oncology. PMID 29452419 DOI: 10.1093/Neuonc/Noy016  0.92
2017 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, ... ... Costello JF, et al. Comprehensive Analysis of Hypermutation in Human Cancer. Cell. PMID 29056344 DOI: 10.1016/J.Cell.2017.09.048  0.92
2016 Viswanath P, Najac C, Izquierdo-Garcia JL, Pankov A, Hong C, Eriksson P, Costello JF, Pieper RO, Ronen SM. Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters. Oncotarget. PMID 27144334 DOI: 10.18632/Oncotarget.9006  0.92
2016 Mazor T, Pankov A, Song JS, Costello JF. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 29: 440-51. PMID 27070699 DOI: 10.1016/J.Ccell.2016.03.009  0.92
2016 Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. Understanding TERT Promoter Mutations: a Common Path to Immortality. Molecular Cancer Research : McR. PMID 26941407 DOI: 10.1158/1541-7786.Mcr-16-0003  0.92
2016 Gu J, Stevens M, Xing X, Li D, Zhang B, Payton J, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T. Mapping of Variable DNA Methylation across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. G3 (Bethesda, Md.). PMID 26888867 DOI: 10.1534/g3.115.025437  0.92
2015 Grimmer MR, Costello JF. Cancer: Oncogene brought into the loop. Nature. PMID 26700812 DOI: 10.1038/Nature16330  0.92
2015 Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJ, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers ML, Bollen AW, ... ... Costello JF, et al. DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. Cancer Cell. 28: 307-17. PMID 26373278 DOI: 10.1016/J.Ccell.2015.07.012  0.92
2015 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, ... ... Costello JF, et al. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathologica. 129: 597-607. PMID 25724300 DOI: 10.1007/S00401-015-1403-6  0.92
2015 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, ... ... Costello JF, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications. 6: 6363. PMID 25691127 DOI: 10.1038/Ncomms7363  0.92
2015 Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nature Biotechnology. 33: 345-6. PMID 25690851 DOI: 10.1038/nbt.3158  0.92
2014 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, ... ... Costello JF, et al. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Reports. 9: 1228-34. PMID 25456125 DOI: 10.1016/J.Celrep.2014.10.031  0.92
2014 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 JF, Wang T, Cheng JB. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nature Communications. 5: 5442. PMID 25421844 DOI: 10.1038/Ncomms6442  0.92
2014 Zhou X, Li D, Lowdon RF, Costello JF, Wang T. methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. Bioinformatics (Oxford, England). 30: 2206-7. PMID 24728854 DOI: 10.1093/bioinformatics/btu191  0.92
2014 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 JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Research. 24: 761-74. PMID 24709822 DOI: 10.1101/Gr.164707.113  0.92
2014 Clarke JL, Molinaro AM, Phillips JJ, Butowski NA, Chang SM, Perry A, Costello JF, DeSilva AA, Rabbitt JE, Prados MD. A single-institution phase II trial of radiation, temozolomide, erlotinib, and bevacizumab for initial treatment of glioblastoma. Neuro-Oncology. 16: 984-90. PMID 24637230 DOI: 10.1093/Neuonc/Nou029  0.92
2014 Sturm D, Bender S, Jones DT, Lichter P, Grill J, Becher O, Hawkins C, Majewski J, Jones C, Costello JF, Iavarone A, Aldape K, Brennan CW, Jabado N, Pfister SM. Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge. Nature Reviews. Cancer. 14: 92-107. PMID 24457416 DOI: 10.1038/Nrc3655  0.92
2014 Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics (Oxford, England). PMID 24371156 DOI: 10.1093/Bioinformatics/Btt744  0.92
2014 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, ... ... Costello JF, et al. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science (New York, N.Y.). 343: 189-93. PMID 24336570 DOI: 10.1126/Science.1239947  0.92
2014 Fouse SD, Nakamura JL, James CD, Chang S, Costello JF. Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype. Neuro-Oncology. 16: 361-71. PMID 24311636 DOI: 10.1093/Neuonc/Not223  0.92
2014 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, ... ... Costello JF, et al. Where are we now? And where are we going? A report from the Accelerate Brain Cancer Cure (ABC2) low-grade glioma research workshop. Neuro-Oncology. 16: 173-8. PMID 24305708 DOI: 10.1093/Neuonc/Not229  0.92
2014 Dutruel C, Bergmann F, Rooman I, Zucknick M, Weichenhan D, Geiselhart L, Kaffenberger T, Rachakonda PS, Bauer A, Giese N, Hong C, Xie H, Costello JF, Hoheisel J, Kumar R, et al. Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development. Oncogene. 33: 3401-10. PMID 23912455 DOI: 10.1038/Onc.2013.312  0.92
2013 Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnology. 31: 1137-42. PMID 24108092 DOI: 10.1038/Nbt.2726  0.92
2013 Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Research. 23: 1541-53. PMID 23804401 DOI: 10.1101/Gr.152231.112  0.92
2013 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, ... ... Costello JF, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Research. 23: 1522-40. PMID 23804400 DOI: 10.1101/Gr.156539.113  0.92
2013 Fouse SD, Costello JF. Cancer Stem Cells Activate STAT3 the EZ Way. Cancer Cell. 23: 711-3. PMID 23763996 DOI: 10.1016/J.Ccr.2013.05.016  0.92
2013 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, ... ... Costello JF, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genetics. 45: 836-41. PMID 23708189 DOI: 10.1038/Ng.2649  0.92
2013 Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nature Methods. 10: 375-6. PMID 23629413 DOI: 10.1038/nmeth.2440  0.92
2013 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, et al. Loss of WNK2 expression by promoter gene methylation occurs in adult gliomas and triggers Rac1-mediated tumour cell invasiveness. Human Molecular Genetics. 22: 84-95. PMID 23035050 DOI: 10.1093/hmg/dds405  0.92
2013 Nagarajan RP, Fouse SD, Bell RJ, Costello JF. Methods for cancer epigenome analysis. Advances in Experimental Medicine and Biology. 754: 313-38. PMID 22956508 DOI: 10.1007/978-1-4419-9967-2_15  0.92
2013 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 Journal. 13: 110-120. PMID 22231567 DOI: 10.1038/Tpj.2011.60  0.92
2013 Stevens M, Cheng JB, Xie M, Costello JF, Wang T. MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 266-268. DOI: 10.1007/978-3-642-37195-0_23  0.92
2012 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 Research. 72: 6319-24. PMID 23188507 DOI: 10.1158/0008-5472.Can-12-3658  0.92
2012 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 Research. 22: 2262-9. PMID 22960372 DOI: 10.1101/Gr.140665.112  0.92
2012 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, ... ... Costello JF, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 486: 395-9. PMID 22495314 DOI: 10.1038/Nature10933  0.92
2011 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, ... ... Costello JF, et al. The Human Epigenome Browser at Washington University. Nature Methods. 8: 989-90. PMID 22127213 DOI: 10.1038/Nmeth.1772  0.92
2011 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, et al. Phase II and pharmacogenomics study of enzastaurin plus temozolomide during and following radiation therapy in patients with newly diagnosed glioblastoma multiforme and gliosarcoma. Neuro-Oncology. 13: 1331-8. PMID 21896554 DOI: 10.1093/Neuonc/Nor130  0.92
2011 Wong KY, Liang R, So CC, Jin DY, Costello JF, Chim CS. Epigenetic silencing of MIR203 in multiple myeloma. British Journal of Haematology. 154: 569-78. PMID 21707582 DOI: 10.1111/j.1365-2141.2011.08782.x  0.92
2011 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, et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nature Cell Biology. 13: 541-9. PMID 21499256 DOI: 10.1038/Ncb2239  0.92
2011 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, et al. The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 17: 2014-23. PMID 21355081 DOI: 10.1158/1078-0432.Ccr-10-3026  0.92
2011 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. 6: e17121. PMID 21347206 DOI: 10.1371/Journal.Pone.0017121  0.92
2010 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. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/Nbt1010-1045  0.92
2010 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, ... ... Costello JF, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  0.92
2010 Fouse SD, Nagarajan RO, Costello JF. Genome-scale DNA methylation analysis. Epigenomics. 2: 105-17. PMID 20657796 DOI: 10.2217/Epi.09.35  0.92
2010 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, ... ... Costello JF, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 466: 253-7. PMID 20613842 DOI: 10.1038/Nature09165  0.92
2010 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, ... ... Costello JF, et al. A hierarchy of self-renewing tumor-initiating cell types in glioblastoma. Cancer Cell. 17: 362-75. PMID 20385361 DOI: 10.1016/J.Ccr.2009.12.049  0.92
2010 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. 31: 745-750. PMID 20118199 DOI: 10.1093/carcin/bgq033  0.92
2010 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 Research. 70: 453-62. PMID 20068170 DOI: 10.1158/0008-5472.Can-09-2189  0.92
2010 Brena RM, Costello JF. The role of the epigenome in human cancers Vogel and Motulsky's Human Genetics: Problems and Approaches (Fourth Edition). 471-486. DOI: 10.1007/978-3-540-37654-5_17  0.92
2009 Costello JF, Krzywinski M, Marra MA. A first look at entire human methylomes. Nature Biotechnology. 27: 1130-2. PMID 20010593 DOI: 10.1038/Nbt1209-1130  0.92
2009 Fouse SD, Costello JF. Epigenetics of neurological cancers. Future Oncology (London, England). 5: 1615-29. PMID 20001799 DOI: 10.2217/Fon.09.132  0.92
2009 Nagarajan RP, Costello JF. Molecular epigenetics and genetics in neuro-oncology. Neurotherapeutics : the Journal of the American Society For Experimental Neurotherapeutics. 6: 436-46. PMID 19560734 DOI: 10.1016/j.nurt.2009.04.002  0.92
2009 Nagarajan RP, Costello JF. Epigenetic mechanisms in glioblastoma multiforme. Seminars in Cancer Biology. 19: 188-97. PMID 19429483 DOI: 10.1016/j.semcancer.2009.02.005  0.92
2009 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-Oncology. 11: 414-22. PMID 19001526 DOI: 10.1215/15228517-2008-096  0.92
2009 Costello JF, Hong C, Plass C, Smiraglia DJ. Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis. Methods in Molecular Biology (Clifton, N.J.). 507: 131-48. PMID 18987812 DOI: 10.1007/978-1-59745-522-0_11  0.92
2008 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, et al. Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors. Cancer Research. 68: 8094-103. PMID 18829568 DOI: 10.1158/0008-5472.Can-07-6208  0.92
2008 Jones PA, Archer TK, Baylin SB, Beck S, Berger S, Bernstein BE, Carpten JD, Clark SJ, Costello JF, Doerge RW, Esteller M, Feinberg AP, Gingeras TR, Greally JM, Henikoff S, et al. Moving AHEAD with an international human epigenome project Nature. 454: 711-715. PMID 18685699 DOI: 10.1038/454711A  0.92
2008 Costello JF. Stem cells: Tips for priming potency. Nature. 454: 45-6. PMID 18596797 DOI: 10.1038/454045a  0.92
2008 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 Medicine. 6: 14. PMID 18577219 DOI: 10.1186/1741-7015-6-14  0.92
2008 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, et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biology. 9: R59. PMID 18364049 DOI: 10.1186/Gb-2008-9-3-R59  0.92
2008 Spellman PT, Costello JF, Gray JW. Cancer Genomics The Molecular Basis of Cancer. 267-282. DOI: 10.1016/B978-141603703-3.10020-2  0.92
2007 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, et al. Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations. Bmc Genomics. 8: 446. PMID 18053125 DOI: 10.1186/1471-2164-8-446  0.92
2007 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. 2: 161-72. PMID 17965620 DOI: 10.4161/Epi.2.3.4805  0.92
2007 Brena RM, Costello JF. Genome - Epigenome interactions in cancer Human Molecular Genetics. 16. PMID 17613554 DOI: 10.1093/hmg/ddm073  0.92
2007 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 10974-9. PMID 17578925 DOI: 10.1073/Pnas.0700683104  0.92
2006 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 Genetic Testing. 10: 281-284. PMID 17253935 DOI: 10.1089/Gte.2006.10.281  0.92
2006 Brena RM, Plass C, Costello JF. Mining methylation for early detection of common cancers Plos Medicine. 3: 2184-2185. PMID 17194184 DOI: 10.1371/Journal.Pmed.0030479  0.92
2006 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 Research. 66: 8469-76. PMID 16951158 DOI: 10.1158/0008-5472.Can-06-1547  0.92
2006 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. The Journal of Biological Chemistry. 281: 24790-802. PMID 16766534 DOI: 10.1074/Jbc.M604175200  0.92
2006 Smith JS, Costello JF. A broad band of silence Nature Genetics. 38: 504-506. PMID 16642011 DOI: 10.1038/ng0506-504  0.92
2006 Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. DNA motifs associated with aberrant CpG island methylation. Genomics. 87: 572-9. PMID 16487676 DOI: 10.1016/J.Ygeno.2005.12.016  0.92
2005 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 Research. 65: 5070-5. PMID 15958550 DOI: 10.1158/0008-5472.Can-05-0240  0.92
2005 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. Nature Genetics. 37: 645-51. PMID 15895082 DOI: 10.1038/Ng1563  0.92
2005 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 Research. 65: 3617-23. PMID 15867356 DOI: 10.1158/0008-5472.Can-05-0048  0.92
2005 Costello JF. Comparative epigenomics of leukemia Nature Genetics. 37: 211-212. PMID 15731751 DOI: 10.1038/ng0305-211  0.92
2005 Stokoe D, Costello JF. Phosphatase and tensin homologue growth suppression without phosphatase Proceedings of the National Academy of Sciences of the United States of America. 102: 2677-2678. PMID 15710873 DOI: 10.1073/pnas.0500089102  0.92
2005 Pieper RO, Costello JF. Molecular and cell biology Textbook of Neuro-Oncology. 8-12. DOI: 10.1016/B978-0-7216-8148-1.50005-X  0.92
2003 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. Proceedings of the National Academy of Sciences of the United States of America. 100: 14133-8. PMID 14617776 DOI: 10.1073/Pnas.2232790100  0.92
2003 Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. Predicting aberrant CpG island methylation Proceedings of the National Academy of Sciences of the United States of America. 100: 12253-12258. PMID 14519846 DOI: 10.1073/Pnas.2037852100  0.92
2003 Costello JF. DNA methylation in brain development and gliomagenesis Frontiers in Bioscience. 8. PMID 12456310 DOI: 10.2741/1027  0.92
2002 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 Nature Genetics. 32: 453-458. PMID 12355068 DOI: 10.1038/Ng1007  0.92
2002 Costello JF, Smiraglia DJ, Plass C. Restriction landmark genome scanning. Methods (San Diego, Calif.). 27: 144-9. PMID 12095273 DOI: 10.1016/S1046-2023(02)00067-1  0.92
2002 Costello JF, Vertino PM. Methylation matters: A new spin on maspin Nature Genetics. 31: 123-124. PMID 12040372 DOI: 10.1038/Ng0602-123  0.92
2002 Costello JF, Plass C, Cavenee WK. Restriction landmark genome scanning. Methods in Molecular Biology (Clifton, N.J.). 200: 53-70. PMID 11951655 DOI: 10.1385/1-59259-182-5:053  0.92
2001 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 Human Molecular Genetics. 10: 1413-1419. PMID 11440994 DOI: 10.1093/Hmg/10.13.1413  0.92
2001 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. 97: 3226-33. PMID 11342453 DOI: 10.1182/Blood.V97.10.3226  0.92
2000 Costello JF, Plass C, Cavenee WK. Aberrant methylation of genes in low-grade astrocytomas. Brain Tumor Pathology. 17: 49-56. PMID 11210171 DOI: 10.1007/Bf02482735  0.92
2000 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. Journal of Medical Genetics. 37: 501-9. PMID 10882752 DOI: 10.1136/jmg.37.7.501  0.92
2000 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, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genetics. 24: 132-8. PMID 10655057 DOI: 10.1038/72785  0.92
1999 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. 58: 254-62. PMID 10373323 DOI: 10.1006/Geno.1999.5840  0.92
1997 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. Molecular and Cellular Biology. 17: 5612-9. PMID 9271436 DOI: 10.1128/Mcb.17.9.5612  0.92
1996 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 Journal of Biological Chemistry. 271: 13916-13924. PMID 8662860 DOI: 10.1074/Jbc.271.23.13916  0.92
1995 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. The Canadian Journal of Neurological Sciences. Le Journal Canadien Des Sciences Neurologiques. 22: 111-5. PMID 7627911 DOI: 10.1017/s0317167100040178  0.92
1994 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 Molecular and Cellular Biology. 14: 6515-6521. PMID 7523853 DOI: 10.1128/Mcb.14.10.6515  0.92
1991 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 Communications. 3: 241-53. PMID 1716139 DOI: 10.3727/095535491820873092  0.92
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