Joseph Costello, PhD
Professor
Neurological Surgery
School of Medicine

Websites

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• Profile at UCSF Cancer Center (cancer.ucsf.edu)

Grants and Projects

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• Training Program in Translational Brain Tumor Research, NIH, 2010-2025
• 3-D spatial approach to discover genomic effectors of immunosuppression during malignant transformation, NIH, 2020-2025
• Noninvasive Metabolic Signatures to Improve Management of Molecular Subtypes of Glioma, NIH, 2005-2024
• Global Analyses of the Placental Epigenome in Preeclampsia, NIH, 2017-2022
• Center Core Grant for Vision Research, NIH, 1985-2021
• Imaging Guided Genomics of Malignant Transformation, NIH, 2013-2019
• Antigens for Molecularly Targeted Vaccines for Progressive Glioma, NIH, 2015-2018
• Integrated Epigenetic Maps of Human Embryonic and Adult Cells, NIH, 2008-2014
• General Clinical Research Center, NIH, 1983-2009
• Convergent Mechanisms Contributing to Cancer, NIH, 2002-2007

Publications (187)

Top publication keywords:
Epigenesis, GeneticGenetic HeterogeneityGliomaBrain NeoplasmsEpigenomicsGA-Binding Protein Transcription FactorIsocitrate DehydrogenaseAntineoplastic Agents, AlkylatingGene Expression Regulation, NeoplasticDNA MethylationCpG IslandsOligodendrogliomaPromoter Regions, GeneticTelomeraseGlioblastoma

• Longitudinal multimodal profiling of IDH-wildtype glioblastoma reveals the molecular evolution and cellular phenotypes underlying prognostically different treatment responses.
  Neuro-oncology 2024 Lucas CG, Al-Adli NN, Young JS, Gupta R, Morshed RA, Wu J, Ravindranathan A, Shai A, Oberheim Bush NA, Taylor JW, de Groot J, Villanueva-Meyer JE, Pekmezci M, Perry A, Bollen AW, Theodosopoulos PV, …
• Activating the dark genome to illuminate cancer vaccine targets.
  Nature genetics 2024 Kwok DW, Okada H, Costello JF
• Functional Electrical Stimulation and Brain-Machine Interfaces for Simultaneous Control of Wrist and Finger Flexion.
  bioRxiv : the preprint server for biology 2024 Mender MJ, Ward AL, Cubillos LH, Kelberman MM, Costello JT, Temmar H, Wallace DM, Lin ET, Lam JLW, Willsey MS, Ganesh Kumar N, Kung TA, Patil PG, Chestek CA
• Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections.
  Cancers 2024 Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC
• Telomeres in glioma: Maintenance mechanisms to therapeutic potential.
  Neuro-oncology 2024 Stevers NO, Costello JF

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• Quantitative Assessment of Preanalytic Variables on Clinical Evaluation of PI3/AKT/mTOR Signaling Activity in Diffuse Glioma.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2024 Beccari S, Mohamed E, Voong V, Hilz S, Lafontaine M, Shai A, Lim Y, Martinez J, Switzman B, Yu RL, Lupo JM, Chang EF, Hervey-Jumper SL, Berger MS, Costello JF, Phillips JJ
• Whole tumor analysis reveals early origin of the TERT promoter mutation and intercellular heterogeneity in TERT expression.
  Neuro-oncology 2024 Appin CL, Hong C, Suwala AK, Hilz S, Mathur R, Solomon DA, Smirnov IV, Stevers NO, Shai A, Wang A, Berger MS, Chang SM, Phillips JJ, Costello JF
• Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections.
  bioRxiv : the preprint server for biology 2024 Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC
• Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma.
  Scientific reports 2024 Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker PB, Naik A, Shai A, Phillips JJ, Chang …
• Artificial neural network for brain-machine interface consistently produces more naturalistic finger movements than linear methods.
  bioRxiv : the preprint server for biology 2024 Temmar H, Willsey MS, Costello JT, Mender MJ, Cubillos LH, Lam JL, Wallace DM, Kelberman MM, Patil PG, Chestek CA
• Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.
  Cell 2024 Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, …
• "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade.
  Acta neuropathologica 2023 Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, …
• Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs.
  Neuro-oncology 2023 Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, …
• Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma.
  bioRxiv : the preprint server for biology 2023 Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker P, Naik A, Shai A, Phillips JJ, Chang …
• Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens.
  bioRxiv : the preprint server for biology 2023 Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, …
• Molecular biomarkers for assessing the heat-adapted phenotype: a narrative scoping review.
  The journal of physiological sciences : JPS 2023 Corbett J, Young JS, Tipton MJ, Costello JT, Williams TB, Walker EF, Lee BJ, Stevens CE
• Balancing Memorization and Generalization in RNNs for High Performance Brain-Machine Interfaces.
  bioRxiv : the preprint server for biology 2023 Costello JT, Temmar H, Cubillos LH, Mender MJ, Wallace DM, Willsey MS, Patil PG, Chestek CA
• Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2023 Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T,…
• Hyperpolarized δ-[1- 13C]gluconolactone imaging visualizes response to TERT or GABPB1 targeting therapy for glioblastoma.
  Scientific reports 2023 Minami N, Hong D, Taglang C, Batsios G, Gillespie AM, Viswanath P, Stevers N, Barger CJ, Costello JF, Ronen SM
• Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects.
  The Journal of clinical investigation 2023 Jain S, Rick JW, Joshi RS, Beniwal A, Spatz J, Gill S, Chang AC, Choudhary N, Nguyen AT, Sudhir S, Chalif EJ, Chen JS, Chandra A, Haddad AF, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, …
• Isocitrate dehydrogenase (IDH) mutant gliomas: A Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions.
  Neuro-oncology 2023 Miller JJ, Gonzalez Castro LN, McBrayer S, Weller M, Cloughesy T, Portnow J, Andronesi O, Barnholtz-Sloan JS, Baumert BG, Berger MS, Bi WL, Bindra R, Cahill DP, Chang SM, Costello JF, Horbinski C, …
• TERT promoter C228T mutation in neural progenitors confers growth advantage following telomere shortening in vivo.
  Neuro-oncology 2022 Miki S, Koga T, Mckinney AM, Parisian AD, Tadokoro T, Vadla R, Marsala M, Hevner RF, Costello JF, Furnari F
• Real-time brain-machine interface in non-human primates achieves high-velocity prosthetic finger movements using a shallow feedforward neural network decoder.
  Nature communications 2022 Willsey MS, Nason-Tomaszewski SR, Ensel SR, Temmar H, Mender MJ, Costello JT, Patil PG, Chestek CA
• Imaging biomarkers of TERT or GABPB1 silencing in TERT-positive glioblastoma.
  Neuro-oncology 2022 Minami N, Hong D, Stevers N, Barger CJ, Radoul M, Hong C, Chen L, Kim Y, Batsios G, Gillespie AM, Pieper RO, Costello JF, Viswanath P, Ronen SM
• GABP couples oncogene signaling to telomere regulation in TERT promoter mutant cancer.
  Cell reports 2022 McKinney AM, Mathur R, Stevers NO, Molinaro AM, Chang SM, Phillips JJ, Costello JF
• Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer.
  Nature communications 2022 Barger CJ, Suwala AK, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF
• PI3K/AKT/mTOR signaling pathway activity in IDH-mutant diffuse glioma and clinical implications.
  Neuro-oncology 2022 Mohamed E, Kumar A, Zhang Y, Wang AS, Chen K, Lim Y, Shai A, Taylor JW, Clarke J, Hilz S, Berger MS, Solomon DA, Costello JF, Molinaro AM, Phillips JJ
• Deuterium Metabolic Imaging Reports on TERT Expression and Early Response to Therapy in Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2022 Batsios G, Taglang C, Tran M, Stevers N, Barger C, Gillespie AM, Ronen SM, Costello JF, Viswanath P
• Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1.
  Acta neuropathologica 2022 Lucas CG, Sloan EA, Gupta R, Wu J, Pratt D, Vasudevan HN, Ravindranathan A, Barreto J, Williams EA, Shai A, Whipple NS, Bruggers CS, Maher O, Nabors B, Rodriguez M, Samuel D, Brown M, Carmichael J, Lu…
• Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
  Nature genetics 2022 Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW,…
• Spatial concordance of DNA methylation classification in diffuse glioma.
  Neuro-oncology 2021 Verburg N, Barthel FP, Anderson KJ, Johnson KC, Koopman T, Yaqub MM, Hoekstra OS, Lammertsma AA, Barkhof F, Pouwels PJW, Reijneveld JC, Rozemuller AJM, Beliën JAM, Boellaard R, Taylor MD, Das S, …
• Temozolomide-induced hypermutation is associated with distant recurrence and reduced survival after high-grade transformation of low-grade IDH-mutant gliomas.
  Neuro-oncology 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, Butowski N, Clarke JL, Berger MS, …
• Publisher Correction: Epigenomic contributions to tumor cell heterogeneity and plasticity.
  Nature genetics 2021 Mathur R, Costello JF
• Epigenomic contributions to tumor cell heterogeneity and plasticity.
  Nature genetics 2021 Mathur R, Costello JF
• Metabolic imaging detects elevated glucose flux through the pentose phosphate pathway associated with TERT expression in low-grade gliomas.
  Neuro-oncology 2021 Viswanath P, Batsios G, Ayyappan V, Taglang C, Gillespie AM, Larson PEZ, Luchman HA, Costello JF, Pieper RO, Ronen SM
• The Placenta - Fast, Loose, and in Control.
  The New England journal of medicine 2021 Costello JF, Fisher SJ
• Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.
  Developmental cell 2021 Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M…
• Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors.
  Neuro-oncology 2021 Manjunath M, Yan J, Youn Y, Drucker KL, Kollmeyer TM, McKinney AM, Zazubovich V, Zhang Y, Costello JF, Eckel-Passow J, Selvin PR, Jenkins RB, Song JS
• Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Amen AM, Fellmann C, Soczek KM, Ren SM, Lew RJ, Knott GJ, Park JE, McKinney AM, Mancini A, Doudna JA, Costello JF
• miRNA-independent function of long noncoding pri-miRNA loci.
  Proceedings of the National Academy of Sciences of the United States of America 2021 He D, Wu D, Muller S, Wang L, Saha P, Ahanger SH, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello JF, Diaz A, Lim DA
• Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank.
  Neuro-oncology 2021 Chuntova P, Chow F, Watchmaker PB, Galvez M, Heimberger AB, Newell EW, Diaz A, DePinho RA, Li MO, Wherry EJ, Mitchell D, Terabe M, Wainwright DA, Berzofsky JA, Herold-Mende C, Heath JR, Lim M, …
• Early Noninvasive Metabolic Biomarkers of Mutant IDH Inhibition in Glioma.
  Metabolites 2021 Radoul M, Hong D, Gillespie AM, Najac C, Viswanath P, Pieper RO, Costello JF, Luchman HA, Ronen SM
• Non-invasive assessment of telomere maintenance mechanisms in brain tumors.
  Nature communications 2021 Viswanath P, Batsios G, Mukherjee J, Gillespie AM, Larson PEZ, Luchman HA, Phillips JJ, Costello JF, Pieper RO, Ronen SM
• Prostate Cancer Progression and the Epigenome.
  The New England journal of medicine 2020 Arap W, Pasqualini R, Costello JF
• MGMT promoter methylation level in newly diagnosed low-grade glioma is a predictor of hypermutation at recurrence.
  Neuro-oncology 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
• Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma.
  Nature communications 2020 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, …
• Glutamate Is a Noninvasive Metabolic Biomarker of IDH1-Mutant Glioma Response to Temozolomide Treatment.
  Cancer research 2020 Subramani E, Radoul M, Najac C, Batsios G, Molloy AR, Hong D, Gillespie AM, Santos RD, Viswanath P, Costello JF, Pieper RO, Ronen SM
• Epigenomic programming in early fetal brain development.
  Epigenomics 2020 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, …
• Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma.
  Neuro-oncology advances 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
• The DNA methylation landscape of advanced prostate cancer.
  Nature genetics 2020 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, …
• Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features.
  Acta neuropathologica 2020 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, …
• Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma.
  Cell reports 2020 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, …
• Proceedings of the Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) Oligodendroglioma Workshop.
  Neuro-oncology advances 2019 Penas-Prado M, Wu J, Cahill DP, Brat DJ, Costello JF, Kluetz PG, Cairncross JG, van den Bent M, Verhaak RGW, Aboud O, Burger P, Chang SM, Cordova C, Huang RY, Rowe LS, Taphoorn MJB, Gilbert MR, …
• Longitudinal molecular trajectories of diffuse glioma in adults.
  Nature 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, Beroukhim R, Bock C, …
• Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
  Nature communications 2019 Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N
• 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 neuropathologica 2019 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…
• Corrigendum to "Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis" Neurosci. Biobehav. Rev. 74 (2017) 225-232.
  Neuroscience and biobehavioral reviews 2019 McMorris T, Hale BJ, Barwood M, Costello J, Corbett J
• Genomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts.
  Toxicological sciences : an official journal of the Society of Toxicology 2019 Robinson JF, Kapidzic M, Hamilton EG, Chen H, Puckett KW, Zhou Y, Ona K, Parry E, Wang Y, Park JS, Costello JF, Fisher SJ
• Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner.
  Cancer cell 2018 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…
• Temozolomide-associated hypermutation in gliomas.
  Neuro-oncology 2018 Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello JF
• To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes.
  Frontiers in genetics 2018 Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS
• Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas.
  Neuro-oncology 2018 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,…
• The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma.
  Oncotarget 2018 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, …
• Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia.
  Nature communications 2017 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
• 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 2017 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
• Comprehensive Analysis of Hypermutation in Human Cancer.
  Cell 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, Bowers DC, Laetsch TW, Dunn GP, …
• Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1.
  Proceedings of the National Academy of Sciences of the United States of America 2017 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, …
• Treatment-Induced Mutagenesis and Selective Pressures Sculpt Cancer Evolution.
  Cold Spring Harbor perspectives in medicine 2017 Venkatesan S, Swanton C, Taylor BS, Costello JF
• 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 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
• DNA methylation: an epigenetic mark of cellular memory.
  Experimental & molecular medicine 2017 Kim M, Costello J
• Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas.
  The Journal of clinical investigation 2017 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
• Chemotherapy for adult low-grade gliomas: clinical outcomes by molecular subtype in a phase II study of adjuvant temozolomide.
  Neuro-oncology 2017 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
• Effect of acute hypoxia on cognition: A systematic review and meta-regression analysis.
  Neuroscience and biobehavioral reviews 2017 McMorris T, Hale BJ, Barwood M, Costello J, Corbett J
• Mutant IDH1 Expression Drives TERT Promoter Reactivation as Part of the Cellular Transformation Process.
  Cancer research 2016 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
• Somatic and Germline TP53 Alterations in Second Malignant Neoplasms from Pediatric Cancer Survivors.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2016 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, …
• Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters.
  Oncotarget 2016 Viswanath P, Najac C, Izquierdo-Garcia JL, Pankov A, Hong C, Eriksson P, Costello JF, Pieper RO, Ronen SM
• Intratumoral Heterogeneity of the Epigenome.
  Cancer cell 2016 Mazor T, Pankov A, Song JS, Costello JF
• Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome.
  G3 (Bethesda, Md.) 2016 Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T
• Understanding TERT Promoter Mutations: A Common Path to Immortality.
  Molecular cancer research : MCR 2016 Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF
• Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia.
  Nature genetics 2016 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,…
• Cancer: Oncogene brought into the loop.
  Nature 2015 Grimmer MR, Costello JF
• The genomic landscape of juvenile myelomonocytic leukemia.
  Nature genetics 2015 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, …
• DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors.
  Cancer cell 2015 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…
• Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer.
  Science (New York, N.Y.) 2015 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
• Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.
  Nature biotechnology 2015 Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T
• Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.
  Acta neuropathologica 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, Berger MS, Söderkvist…
• Integrative analysis of 111 reference human epigenomes.
  Nature 2015 Roadmap Epigenomics Consortium, 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 …
• Epigenetic and transcriptional determinants of the human breast.
  Nature communications 2015 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, …
• Intermediate DNA methylation is a conserved signature of genome regulation.
  Nature communications 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, Mill J, Farnham PJ, Kellis M, Marra MA, …
• HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth.
  Cell reports 2015 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 JF, Aghi MK, Maltepe E
• The genetics of splicing in neuroblastoma.
  Cancer discovery 2015 Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA
• Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
  Nature communications 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
• Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.
  Cell reports 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, Mihm FG, Cunningham BB, Neuhaus IM, …
• A single-institution phase II trial of radiation, temozolomide, erlotinib, and bevacizumab for initial treatment of glioblastoma.
  Neuro-oncology 2014 Clarke JL, Molinaro AM, Phillips JJ, Butowski NA, Chang SM, Perry A, Costello JF, DeSilva AA, Rabbitt JE, Prados MD
• methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser.
  Bioinformatics (Oxford, England) 2014 Zhou X, Li D, Lowdon RF, Costello JF, Wang T
• Recurrent epimutations activate gene body promoters in primary glioblastoma.
  Genome research 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
• Whole-body cryotherapy: empirical evidence and theoretical perspectives.
  Open access journal of sports medicine 2014 Bleakley CM, Bieuzen F, Davison GW, Costello JT
• Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge.
  Nature reviews. Cancer 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
• ALEA: a toolbox for allele-specific epigenomics analysis.
  Bioinformatics (Oxford, England) 2013 Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ
• Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
  Science (New York, N.Y.) 2013 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…
• Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype.
  Neuro-oncology 2013 Fouse SD, Nakamura JL, James CD, Chang S, Costello JF
• 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 2013 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 JF, Chang …
• Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.
  Nature biotechnology 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
• Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development.
  Oncogene 2013 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, Rehli M, Schirmacher P, …
• Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
  Genome research 2013 Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T
• Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.
  Genome research 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, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A…
• Cancer Stem Cells Activate STAT3 the EZ Way.
  Cancer cell 2013 Fouse SD, Costello JF
• DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.
  Nature genetics 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, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh…
• Exploring long-range genome interactions using the WashU Epigenome Browser.
  Nature methods 2013 Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T
• Methods for cancer epigenome analysis.
  Advances in experimental medicine and biology 2013 Nagarajan RP, Fouse SD, Bell RJ, Costello JF
• A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.
  Cancer research 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, AACR Cancer Epigenome Task Force
• Loss of WNK2 expression by promoter gene methylation occurs in adult gliomas and triggers Rac1-mediated tumour cell invasiveness.
  Human molecular genetics 2012 Moniz S, Martinho O, Pinto F, Sousa B, Loureiro C, Oliveira MJ, Moita LF, Honavar M, Pinheiro C, Pires M, Lopes JM, Jones C, Costello JF, Paredes J, Reis RM, Jordan P
• Spark: a navigational paradigm for genomic data exploration.
  Genome research 2012 Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ
• The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
  Nature 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, Bernard V, McPherson A, Shumansky K, Crisan A, …
• Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.
  The pharmacogenomics journal 2012 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
• The Human Epigenome Browser at Washington University.
  Nature methods 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, Madden PA, Costello JF, Wang T
• 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 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, Nicol SJ, Thornton DE,…
• Epigenetic silencing of MIR203 in multiple myeloma.
  British journal of haematology 2011 Wong KY, Liang R, So CC, Jin DY, Costello JF, Chim CS
• Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.
  Nature cell biology 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, Ramalho-Santos M
• 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 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, Crowell RE, Belinsky SA
• Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.
  PloS one 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
• The NIH Roadmap Epigenomics Mapping Consortium.
  Nature biotechnology 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
• Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
  Nature biotechnology 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, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi…
• Conserved role of intragenic DNA methylation in regulating alternative promoters.
  Nature 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, Heine VM, Rowitch DH, Xing X, …
• A hierarchy of self-renewing tumor-initiating cell types in glioblastoma.
  Cancer cell 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, Lamszus K, Westphal M, Heim S, …
• Genome-scale DNA methylation analysis.
  Epigenomics 2010 Fouse SD, Nagarajan RO, Costello JF
• Epigenetic inactivation of the miR-34a in hematological malignancies.
  Carcinogenesis 2010 Chim CS, Wong KY, Qi Y, Loong F, Lam WL, Wong LG, Jin DY, Costello JF, Liang R
• Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma.
  Cancer research 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
• A first look at entire human methylomes.
  Nature biotechnology 2009 Costello JF, Krzywinski M, Marra MA
• Epigenetics of neurological cancers.
  Future oncology (London, England) 2009 Fouse SD, Costello JF
• The transversus abdominis plane block, when used as part of a multimodal regimen inclusive of intrathecal morphine, does not improve analgesia after cesarean delivery.
  Regional anesthesia and pain medicine 2009 Costello JF, Moore AR, Wieczorek PM, Macarthur AJ, Balki M, Carvalho JC
• Molecular epigenetics and genetics in neuro-oncology.
  Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics 2009 Nagarajan RP, Costello JF
• Epigenetic mechanisms in glioblastoma multiforme.
  Seminars in cancer biology 2009 Nagarajan RP, Costello JF
• Food allergy is associated with an increased risk of asthma.
  Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2009 Schroeder A, Kumar R, Pongracic JA, Sullivan CL, Caruso DM, Costello J, Meyer KE, Vucic Y, Gupta R, Kim JS, Fuleihan R, Wang X
• Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.
  Methods in molecular biology (Clifton, N.J.) 2009 Costello JF, Hong C, Plass C, Smiraglia DJ
• Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific.
  Neuro-oncology 2008 Jun P, Hong C, Lal A, Wong JM, McDermott MW, Bollen AW, Plass C, Held WA, Smiraglia DJ, Costello JF
• Familial aggregation of food allergy and sensitization to food allergens: a family-based study.
  Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2008 Tsai HJ, Kumar R, Pongracic J, Liu X, Story R, Yu Y, Caruso D, Costello J, Schroeder A, Fang Y, Demirtas H, Meyer KE, O'Gorman MR, Wang X
• Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors.
  Cancer research 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, Baylin SB
• Cesarean delivery under ultrasound-guided spinal anesthesia [corrected] in a parturient with poliomyelitis and Harrington instrumentation.
  Canadian journal of anaesthesia = Journal canadien d'anesthesie 2008 Costello JF, Balki M
• Stem cells: Tips for priming potency.
  Nature 2008 Costello JF
• miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells.
  BMC medicine 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
• Transversus abdominis plane block in a patient with debilitating pain from an abdominal wall hematoma following cesarean delivery.
  Anesthesia and analgesia 2008 Randall IM, Costello J, Carvalho JC
• A sequence-based survey of the complex structural organization of tumor genomes.
  Genome biology 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, Tao Q, Aerni SJ, Brown RP, Bashir A…
• Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
  BMC genomics 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, Ioshikhes I, Dawson DW, Hong JS, Teitell MA, Szafranek A…
• Molecular signatures define two main classes of meningiomas.
  Molecular cancer 2007 Carvalho LH, Smirnov I, Baia GS, Modrusan Z, Smith JS, Jun P, Costello JF, McDermott MW, Vandenberg SR, Lal A
• Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer.
  Epigenetics 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
• 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 2007 Hong C, Moorefield KS, Jun P, Aldape KD, Kharbanda S, Phillips HS, Costello JF
• Genome-epigenome interactions in cancer.
  Human molecular genetics 2007 Brena RM, Costello JF
• Mining methylation for early detection of common cancers.
  PLoS medicine 2006 Brena RM, Plass C, Costello JF
• Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation.
  Cancer research 2006 Cadieux B, Ching TT, VandenBerg SR, Costello JF
• Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells.
  The Journal of biological chemistry 2006 Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD
• A broad band of silence.
  Nature genetics 2006 Smith JS, Costello JF
• DNA motifs associated with aberrant CpG island methylation.
  Genomics 2006 Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM
• Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer.
  Genetic testing 2006 Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello JF, Ziegler JL
• Meningioma transcript profiles reveal deregulated Notch signaling pathway.
  Cancer research 2005 Cuevas IC, Slocum AL, Jun P, Costello JF, Bollen AW, Riggins GJ, McDermott MW, Lal A
• Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3.
  Nature genetics 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
• Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8.
  Cancer research 2005 Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, Weiss WA, Costello JF
• Comparative epigenomics of leukemia.
  Nature genetics 2005 Costello JF
• Phosphatase and tensin homologue growth suppression without phosphatase.
  Proceedings of the National Academy of Sciences of the United States of America 2005 Stokoe D, Costello JF
• The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas.
  Cancer research 2003 Hong C, Bollen AW, Costello JF
• 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 2003 He B, You L, Uematsu K, Zang K, Xu Z, Lee AY, Costello JF, McCormick F, Jablons DM
• Predicting aberrant CpG island methylation.
  Proceedings of the National Academy of Sciences of the United States of America 2003 Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM
• DNA methylation in brain development and gliomagenesis.
  Frontiers in bioscience : a journal and virtual library 2003 Costello JF
• Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors.
  Nature genetics 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
• Methylation matters: a new spin on maspin.
  Nature genetics 2002 Costello JF, Vertino PM
• Restriction landmark genome scanning.
  Methods (San Diego, Calif.) 2002 Costello JF, Smiraglia DJ, Plass C
• Restriction landmark genome scanning.
  Methods in molecular biology (Clifton, N.J.) 2002 Costello JF, Plass C, Cavenee WK
• Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies.
  Human molecular genetics 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
• Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci.
  Blood 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
• Methylation matters.
  Journal of medical genetics 2001 Costello JF, Plass C
• Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon.
  Journal of medical genetics 2000 Frühwald MC, O'Dorisio MS, Rush LJ, Reiter JL, Smiraglia DJ, Wenger G, Costello JF, White PS, Krahe R, Brodeur GM, Plass C
• Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.
  Nature genetics 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, Nishikawa R, Su Huang H, …
• Aberrant methylation of genes in low-grade astrocytomas.
  Brain tumor pathology 2000 Costello JF, Plass C, Cavenee WK
• A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels.
  Genomics 1999 Smiraglia DJ, Frühwald MC, Costello JF, McCormick SP, Dai Z, Peltomäki P, O'Dorisio MS, Cavenee WK, Plass C
• Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggest a suppressor role in kidney, brain, and other human cancers.
  Cancer research 1999 Bachman KE, Herman JG, Corn PG, Merlo A, Costello JF, Cavenee WK, Baylin SB, Graff JR
• 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 1997 Watts GS, Pieper RO, Costello JF, Peng YM, Dalton WS, Futscher BW
• An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis.
  DNA research : an international journal for rapid publication of reports on genes and genomes 1997 Plass C, Weichenhan D, Catanese J, Costello JF, Yu F, Yu L, Smiraglia D, Cavenee WK, Caligiuri MA, deJong P, Held WA
• Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA.
  Cancer research 1997 Costello JF, Plass C, Arap W, Chapman VM, Held WA, Berger MS, Su Huang HJ, Cavenee WK
• Methylation of CpG island transcription factor binding sites is unnecessary for aberrant silencing of the human MGMT gene.
  The Journal of biological chemistry 1996 Pieper RO, Patel S, Ting SA, Futscher BW, Costello JF
• Silencing of p16/CDKN2 expression in human gliomas by methylation and chromatin condensation.
  Cancer research 1996 Costello JF, Berger MS, Huang HS, Cavenee WK
• O6-methylguanine-DNA methyltransferase in tumors and cells of the oligodendrocyte lineage.
  The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques 1995 Nutt CL, Costello JF, Bambrick LL, Yarosh DB, Swinnen LJ, Chambers AF, Cairncross JG
• 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 1994 Costello JF, Futscher BW, Kroes RA, Pieper RO
• Graded methylation in the promoter and body of the O6-methylguanine DNA methyltransferase (MGMT) gene correlates with MGMT expression in human glioma cells.
  The Journal of biological chemistry 1994 Costello JF, Futscher BW, Tano K, Graunke DM, Pieper RO
• Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene.
  Cancer communications 1991 Pieper RO, Costello JF, Kroes RA, Futscher BW, Marathi U, Erickson LC
• Bombesin immunoreactive neurons in the hypothalamic paraventricular nucleus innervate the dorsal vagal complex in the rat.
  Brain research 1991 Costello JF, Brown MR, Gray TS
• Metropolitan forensic anthropology team (MFAT) case studies in identification: 3. Identification of John J. Sullivan, the missing journalist.
  Journal of forensic sciences 1985 Zugibe FT, Taylor J, Weg N, DiBennerdo R, Costello JT, DeForest P
• Glucose utilization and production by the dog kidney in vivo in metabolic acidosis and alkalosis.
  The Journal of clinical investigation 1973 Costello J, Scott JM, Wilson P, Bourke E