TY - JOUR AU - You, J. S. AU - Kelly, T. K. AU - De Carvalho, D. D. AU - Taberlay, P. C. AU - Liang, G. AU - Jones, P. A. PY - 2011 DA - 2011// TI - OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1111309108 DO - 10.1073/pnas.1111309108 ID - You2011 ER - TY - JOUR AU - Bocker, M. T. AU - Hellwig, I. AU - Breiling, A. AU - Eckstein, V. AU - Ho, A. D. AU - Lyko, F. PY - 2011 DA - 2011// TI - Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging JO - Blood VL - 117 UR - https://doi.org/10.1182/blood-2011-01-331926 DO - 10.1182/blood-2011-01-331926 ID - Bocker2011 ER - TY - JOUR AU - Calvanese, V. AU - Fernández, A. F. AU - Urdinguio, R. G. AU - Suárez-Alvarez, B. AU - Mangas, C. AU - Pérez-García, V. AU - Bueno, C. AU - Montes, R. AU - Ramos-Mejía, V. AU - Martínez-Camblor, P. PY - 2012 DA - 2012// TI - A promoter DNA demethylation landscape of human hematopoietic differentiation JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr685 DO - 10.1093/nar/gkr685 ID - Calvanese2012 ER - TY - JOUR AU - Smith, Z. D. AU - Meissner, A. PY - 2013 DA - 2013// TI - DNA methylation: roles in mammalian development JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3354 DO - 10.1038/nrg3354 ID - Smith2013 ER - TY - JOUR AU - Augui, S. AU - Nora, E. P. AU - Heard, E. PY - 2011 DA - 2011// TI - Regulation of X-chromosome inactivation by the X-inactivation Centre JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg2987 DO - 10.1038/nrg2987 ID - Augui2011 ER - TY - JOUR AU - Ben-Avraham, D. AU - Muzumdar, R. H. AU - Atzmon, G. PY - 2012 DA - 2012// TI - Epigenetic genome-wide association methylation in aging and longevity JO - Epigenomics VL - 4 UR - https://doi.org/10.2217/epi.12.41 DO - 10.2217/epi.12.41 ID - Ben-Avraham2012 ER - TY - JOUR AU - Ciccarone, F. AU - Tagliatesta, S. AU - Caiafa, P. AU - Zampieri, M. PY - 2018 DA - 2018// TI - DNA methylation dynamics in aging: how far are we from understanding the mechanisms? JO - Mech Ageing Dev VL - 174 UR - https://doi.org/10.1016/j.mad.2017.12.002 DO - 10.1016/j.mad.2017.12.002 ID - Ciccarone2018 ER - TY - JOUR AU - Morgan, A. E. AU - Davies, T. J. AU - Mc Auley, M. T. PY - 2018 DA - 2018// TI - The role of DNA methylation in ageing and cancer JO - Proc Nutr Soc VL - 77 UR - https://doi.org/10.1017/S0029665118000150 DO - 10.1017/S0029665118000150 ID - Morgan2018 ER - TY - JOUR AU - Meier, K. AU - Recillas-Targa, F. PY - 2017 DA - 2017// TI - New insights on the role of DNA methylation from a global view JO - Front Biosci (Landmark Ed) VL - 22 UR - https://doi.org/10.2741/4508 DO - 10.2741/4508 ID - Meier2017 ER - TY - STD TI - Baylin SB, Jones PA. Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol. 2016;8:a019505. ID - ref10 ER - TY - JOUR AU - Fernandez-Sanles, A. AU - Sayols-Baixeras, S. AU - Subirana, I. AU - Degano, I. R. AU - Elosua, R. PY - 2017 DA - 2017// TI - Association between DNA methylation and coronary heart disease or other atherosclerotic events: a systematic review JO - Atherosclerosis VL - 263 UR - https://doi.org/10.1016/j.atherosclerosis.2017.05.022 DO - 10.1016/j.atherosclerosis.2017.05.022 ID - Fernandez-Sanles2017 ER - TY - JOUR AU - De Jager, P. L. AU - Srivastava, G. AU - Lunnon, K. AU - Burgess, J. AU - Schalkwyk, L. C. AU - Yu, L. AU - Eaton, M. L. AU - Keenan, B. T. AU - Ernst, J. AU - McCabe, C. PY - 2014 DA - 2014// TI - Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci JO - Nat Neurosci VL - 17 UR - https://doi.org/10.1038/nn.3786 DO - 10.1038/nn.3786 ID - De Jager2014 ER - TY - JOUR AU - Lunnon, K. AU - Smith, R. AU - Hannon, E. AU - De Jager, P. L. AU - Srivastava, G. AU - Volta, M. AU - Troakes, C. AU - Al-Sarraj, S. AU - Burrage, J. AU - Macdonald, R. PY - 2014 DA - 2014// TI - Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease JO - Nat Neurosci VL - 17 UR - https://doi.org/10.1038/nn.3782 DO - 10.1038/nn.3782 ID - Lunnon2014 ER - TY - JOUR AU - Cashen, A. F. AU - Schiller, G. J. AU - O'Donnell, M. R. AU - DiPersio, J. F. PY - 2010 DA - 2010// TI - Multicenter, phase II study of decitabine for the first-line treatment of older patients with acute myeloid leukemia JO - J Clin Oncol VL - 28 UR - https://doi.org/10.1200/JCO.2009.23.9178 DO - 10.1200/JCO.2009.23.9178 ID - Cashen2010 ER - TY - JOUR AU - Estey, E. H. PY - 2013 DA - 2013// TI - Epigenetics in clinical practice: the examples of azacitidine and decitabine in myelodysplasia and acute myeloid leukemia JO - Leukemia VL - 27 UR - https://doi.org/10.1038/leu.2013.173 DO - 10.1038/leu.2013.173 ID - Estey2013 ER - TY - JOUR AU - Santini, V. AU - Allione, B. AU - Zini, G. AU - Gioia, D. AU - Lunghi, M. AU - Poloni, A. AU - Cilloni, D. AU - Sanna, A. AU - Masiera, E. AU - Ceccarelli, M. PY - 2018 DA - 2018// TI - A phase II, multicentre trial of decitabine in higher-risk chronic myelomonocytic leukemia JO - Leukemia VL - 32 UR - https://doi.org/10.1038/leu.2017.186 DO - 10.1038/leu.2017.186 ID - Santini2018 ER - TY - JOUR AU - Rivera, C. M. AU - Ren, B. PY - 2013 DA - 2013// TI - Mapping human epigenomes JO - Cell VL - 155 UR - https://doi.org/10.1016/j.cell.2013.09.011 DO - 10.1016/j.cell.2013.09.011 ID - Rivera2013 ER - TY - JOUR AU - Horvath, S. AU - Ritz, B. R. PY - 2015 DA - 2015// TI - Increased epigenetic age and granulocyte counts in the blood of Parkinson's disease patients JO - Aging (Albany NY) VL - 7 UR - https://doi.org/10.18632/aging.100859 DO - 10.18632/aging.100859 ID - Horvath2015 ER - TY - JOUR AU - Yang, I. V. AU - Pedersen, B. S. AU - Liu, A. AU - O'Connor, G. T. AU - Teach, S. J. AU - Kattan, M. AU - Misiak, R. T. AU - Gruchalla, R. AU - Steinbach, S. F. AU - Szefler, S. J. PY - 2015 DA - 2015// TI - DNA methylation and childhood asthma in the inner city JO - J Allergy Clin Immunol VL - 136 UR - https://doi.org/10.1016/j.jaci.2015.01.025 DO - 10.1016/j.jaci.2015.01.025 ID - Yang2015 ER - TY - JOUR AU - Nones, K. AU - Waddell, N. AU - Song, S. AU - Patch, A. M. AU - Miller, D. AU - Johns, A. AU - Wu, J. AU - Kassahn, K. S. AU - Wood, D. AU - Bailey, P. PY - 2014 DA - 2014// TI - Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling JO - Int J Cancer VL - 135 UR - https://doi.org/10.1002/ijc.28765 DO - 10.1002/ijc.28765 ID - Nones2014 ER - TY - JOUR AU - Guo, X. AU - Chen, X. AU - Wang, J. AU - Liu, Z. AU - Gaile, D. AU - Wu, H. AU - Yu, G. AU - Mao, G. AU - Yang, Z. AU - Di, Z. PY - 2018 DA - 2018// TI - Multi-generational impacts of arsenic exposure on genome-wide DNA methylation and the implications for arsenic-induced skin lesions JO - Environ Int VL - 119 UR - https://doi.org/10.1016/j.envint.2018.06.024 DO - 10.1016/j.envint.2018.06.024 ID - Guo2018 ER - TY - JOUR AU - Liu, D. AU - Zhao, L. AU - Wang, Z. AU - Zhou, X. AU - Fan, X. AU - Li, Y. AU - Xu, J. AU - Hu, S. AU - Niu, M. AU - Song, X. PY - 2019 DA - 2019// TI - EWASdb: epigenome-wide association study database JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky942 DO - 10.1093/nar/gky942 ID - Liu2019 ER - TY - JOUR AU - Zhao, L. AU - Liu, D. AU - Xu, J. AU - Wang, Z. AU - Chen, Y. AU - Lei, C. AU - Li, Y. AU - Liu, G. AU - Jiang, Y. PY - 2018 DA - 2018// TI - The framework for population epigenetic study JO - Brief Bioinform VL - 19 UR - https://doi.org/10.1093/bib/bbx012 DO - 10.1093/bib/bbx012 ID - Zhao2018 ER - TY - JOUR AU - Bonferroni, C. E. PY - 1936 DA - 1936// TI - Teoria statistica delle classi e calcolo delle probabilità JO - Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze VL - 8 ID - Bonferroni1936 ER - TY - JOUR AU - Tan, Q. AU - Heijmans, B. T. AU - Hjelmborg, J. V. AU - Soerensen, M. AU - Christensen, K. AU - Christiansen, L. PY - 2016 DA - 2016// TI - Epigenetic drift in the aging genome: a ten-year follow-up in an elderly twin cohort JO - Int J Epidemiol VL - 45 ID - Tan2016 ER - TY - JOUR AU - Nordlund, J. AU - Backlin, C. L. AU - Wahlberg, P. AU - Busche, S. AU - Berglund, E. C. AU - Eloranta, M. L. AU - Flaegstad, T. AU - Forestier, E. AU - Frost, B. M. AU - Harila-Saari, A. PY - 2013 DA - 2013// TI - Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-9-r105 DO - 10.1186/gb-2013-14-9-r105 ID - Nordlund2013 ER - TY - JOUR AU - Butcher, D. T. AU - Cytrynbaum, C. AU - Turinsky, A. L. AU - Siu, M. T. AU - Inbar-Feigenberg, M. AU - Mendoza-Londono, R. AU - Chitayat, D. PY - 2017 DA - 2017// TI - CHARGE and kabuki syndromes: gene-specific DNA methylation signatures identify epigenetic mechanisms linking these clinically overlapping conditions JO - Am J Hum Genet VL - 100 UR - https://doi.org/10.1016/j.ajhg.2017.04.004 DO - 10.1016/j.ajhg.2017.04.004 ID - Butcher2017 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc Ser B VL - 57 ID - Benjamini1995 ER - TY - JOUR PY - 2002 DA - 2002// TI - A direct approach to false discovery rates JO - J R Stat Soc Ser B VL - 64 UR - https://doi.org/10.1111/1467-9868.00346 DO - 10.1111/1467-9868.00346 ID - ref29 ER - TY - JOUR AU - Liu, Y. AU - Duong, W. AU - Krawczyk, C. AU - Bretschneider, N. AU - Borbely, G. AU - Varshney, M. AU - Zinser, C. AU - Schar, P. AU - Ruegg, J. PY - 2016 DA - 2016// TI - Oestrogen receptor beta regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase JO - Epigenetics Chromatin VL - 9 UR - https://doi.org/10.1186/s13072-016-0055-7 DO - 10.1186/s13072-016-0055-7 ID - Liu2016 ER - TY - JOUR AU - Declerck, K. AU - Remy, S. AU - Wohlfahrt-Veje, C. AU - Main, K. M. AU - Van Camp, G. AU - Schoeters, G. AU - Vanden Berghe, W. AU - Andersen, H. R. PY - 2017 DA - 2017// TI - Interaction between prenatal pesticide exposure and a common polymorphism in the PON1 gene on DNA methylation in genes associated with cardio-metabolic disease risk-an exploratory study JO - Clin Epigenetics VL - 9 UR - https://doi.org/10.1186/s13148-017-0336-4 DO - 10.1186/s13148-017-0336-4 ID - Declerck2017 ER - TY - JOUR AU - Zhang, Y. AU - Fukui, N. AU - Yahata, M. AU - Katsuragawa, Y. AU - Tashiro, T. AU - Ikegawa, S. AU - Lee, M. T. PY - 2016 DA - 2016// TI - Identification of DNA methylation changes associated with disease progression in subchondral bone with site-matched cartilage in knee osteoarthritis JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep34460 DO - 10.1038/srep34460 ID - Zhang2016 ER - TY - JOUR AU - Li, Y. AU - Chen, J. A. AU - Sears, R. L. AU - Gao, F. AU - Klein, E. D. AU - Karydas, A. AU - Geschwind, M. D. AU - Rosen, H. J. AU - Boxer, A. L. AU - Guo, W. PY - 2014 DA - 2014// TI - An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004211 DO - 10.1371/journal.pgen.1004211 ID - Li2014 ER - TY - JOUR AU - Karlsson, L. AU - Barbaro, M. AU - Ewing, E. AU - Gomez-Cabrero, D. AU - Lajic, S. PY - 2019 DA - 2019// TI - Epigenetic alterations associated with early prenatal dexamethasone treatment JO - J Endocr Soc VL - 3 UR - https://doi.org/10.1210/js.2018-00377 DO - 10.1210/js.2018-00377 ID - Karlsson2019 ER - TY - JOUR AU - Chen, J. AU - Just, A. C. AU - Schwartz, J. AU - Hou, L. AU - Jafari, N. AU - Sun, Z. AU - Kocher, J. P. AU - Baccarelli, A. AU - Lin, X. PY - 2016 DA - 2016// TI - CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btv577 DO - 10.1093/bioinformatics/btv577 ID - Chen2016 ER - TY - JOUR AU - Bose, M. AU - Wu, C. AU - Pankow, J. S. AU - Demerath, E. W. AU - Bressler, J. AU - Fornage, M. AU - Grove, M. L. AU - Mosley, T. H. AU - Hicks, C. AU - North, K. PY - 2014 DA - 2014// TI - Evaluation of microarray-based DNA methylation measurement using technical replicates: the atherosclerosis risk in communities (ARIC) study JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/1471-2105-15-312 DO - 10.1186/1471-2105-15-312 ID - Bose2014 ER - TY - JOUR AU - Roeder, K. AU - Wasserman, L. PY - 2009 DA - 2009// TI - Genome-wide significance levels and weighted hypothesis testing JO - Stat Sci VL - 24 UR - https://doi.org/10.1214/09-STS289 DO - 10.1214/09-STS289 ID - Roeder2009 ER - TY - JOUR AU - Cai, T. T. AU - Sun, W. PY - 2009 DA - 2009// TI - Simultaneous testing of grouped hypotheses: finding needles in multiple haystacks JO - J Am Stat Assoc VL - 104 UR - https://doi.org/10.1198/jasa.2009.tm08415 DO - 10.1198/jasa.2009.tm08415 ID - Cai2009 ER - TY - JOUR AU - Scott, J. G. AU - Kelly, R. C. AU - Smith, M. A. AU - Zhou, P. AU - Kass, R. E. PY - 2015 DA - 2015// TI - False discovery rate regression: an application to neural synchrony detection in primary visual cortex JO - J Am Stat Assoc VL - 110 UR - https://doi.org/10.1080/01621459.2014.990973 DO - 10.1080/01621459.2014.990973 ID - Scott2015 ER - TY - JOUR AU - Ignatiadis, N. AU - Klaus, B. AU - Zaugg, J. B. AU - Huber, W. PY - 2016 DA - 2016// TI - Data-driven hypothesis weighting increases detection power in genome-scale multiple testing JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3885 DO - 10.1038/nmeth.3885 ID - Ignatiadis2016 ER - TY - JOUR AU - Stephens, M. PY - 2017 DA - 2017// TI - False discovery rates: a new deal JO - Biostatistics VL - 18 ID - Stephens2017 ER - TY - JOUR AU - Boca, S. M. AU - Leek, J. T. PY - 2018 DA - 2018// TI - A direct approach to estimating false discovery rates conditional on covariates JO - PeerJ VL - 6 UR - https://doi.org/10.7717/peerj.6035 DO - 10.7717/peerj.6035 ID - Boca2018 ER - TY - JOUR PY - 2018 DA - 2018// TI - AdaPT: an interactive procedure for multiple testing with side information JO - J R Stat Soc Ser B VL - 80 UR - https://doi.org/10.1111/rssb.12274 DO - 10.1111/rssb.12274 ID - ref43 ER - TY - STD TI - Zhang X, Chen J. Covariate adaptive false discovery rate control with applications to Omics-wide multiple testing. arXiv e-prints. arXiv. 2019:1909.04811. Available from: https://ui.adsabs.harvard.edu/abs/2019arXiv190904811Z. R package available at https://github.com/jchen1981/CAMT. Accessed 17 Sept 2019. UR - https://github.com/jchen1981/CAMT ID - ref44 ER - TY - JOUR AU - Korthauer, K. AU - Kimes, P. K. AU - Duvallet, C. AU - Reyes, A. AU - Subramanian, A. AU - Teng, M. AU - Shukla, C. AU - Alm, E. J. AU - Hicks, S. C. PY - 2019 DA - 2019// TI - A practical guide to methods controlling false discoveries in computational biology JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1716-1 DO - 10.1186/s13059-019-1716-1 ID - Korthauer2019 ER - TY - JOUR AU - Chen, J. AU - Behnam, E. AU - Huang, J. AU - Moffatt, M. F. AU - Schaid, D. J. AU - Liang, L. AU - Lin, X. PY - 2017 DA - 2017// TI - Fast and robust adjustment of cell mixtures in epigenome-wide association studies with SmartSVA JO - BMC Genomics VL - 18 UR - https://doi.org/10.1186/s12864-017-3808-1 DO - 10.1186/s12864-017-3808-1 ID - Chen2017 ER - TY - JOUR AU - McGregor, K. AU - Bernatsky, S. AU - Colmegna, I. AU - Hudson, M. AU - Pastinen, T. AU - Labbe, A. AU - Greenwood, C. M. PY - 2016 DA - 2016// TI - An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0935-y DO - 10.1186/s13059-016-0935-y ID - McGregor2016 ER - TY - JOUR AU - Leek, J. T. AU - Scharpf, R. B. AU - Bravo, H. C. AU - Simcha, D. AU - Langmead, B. AU - Johnson, W. E. AU - Geman, D. AU - Baggerly, K. AU - Irizarry, R. A. PY - 2010 DA - 2010// TI - Tackling the widespread and critical impact of batch effects in high-throughput data JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2825 DO - 10.1038/nrg2825 ID - Leek2010 ER - TY - JOUR AU - Wang, X. AU - Laird, P. W. AU - Hinoue, T. AU - Groshen, S. AU - Siegmund, K. D. PY - 2014 DA - 2014// TI - Non-specific filtering of beta-distributed data JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/1471-2105-15-199 DO - 10.1186/1471-2105-15-199 ID - Wang2014 ER - TY - JOUR AU - Wijnands, K. P. AU - Chen, J. AU - Liang, L. AU - Verbiest, M. M. AU - Lin, X. AU - Helbing, W. A. AU - Gittenberger-de Groot, A. C. AU - van der Spek, P. J. AU - Uitterlinden, A. G. AU - Steegers-Theunissen, R. P. PY - 2017 DA - 2017// TI - Genome-wide methylation analysis identifies novel CpG loci for perimembranous ventricular septal defects in human JO - Epigenomics VL - 9 UR - https://doi.org/10.2217/epi-2016-0093 DO - 10.2217/epi-2016-0093 ID - Wijnands2017 ER - TY - STD TI - Zhang X, Chen J. Covariate Adaptive False Discovery Rate Control with Applications to Omics-Wide Multiple Testing. arXiv preprint arXiv:1909.04811. 2019. ID - ref51 ER - TY - JOUR AU - Portales-Casamar, E. AU - Lussier, A. A. AU - Jones, M. J. AU - MacIsaac, J. L. AU - Edgar, R. D. AU - Mah, S. M. AU - Barhdadi, A. AU - Provost, S. AU - Lemieux-Perreault, L. P. AU - Cynader, M. S. PY - 2016 DA - 2016// TI - DNA methylation signature of human fetal alcohol spectrum disorder JO - Epigenetics Chromatin VL - 9 UR - https://doi.org/10.1186/s13072-016-0074-4 DO - 10.1186/s13072-016-0074-4 ID - Portales-Casamar2016 ER - TY - JOUR AU - Tserel, L. AU - Kolde, R. AU - Limbach, M. AU - Tretyakov, K. AU - Kasela, S. AU - Kisand, K. AU - Saare, M. AU - Vilo, J. AU - Metspalu, A. AU - Milani, L. AU - Peterson, P. PY - 2015 DA - 2015// TI - Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep13107 DO - 10.1038/srep13107 ID - Tserel2015 ER - TY - JOUR AU - Lee, K. W. AU - Pausova, Z. PY - 2013 DA - 2013// TI - Cigarette smoking and DNA methylation JO - Front Genet VL - 4 ID - Lee2013 ER - TY - JOUR AU - Prince, C. AU - Hammerton, G. AU - Taylor, A. E. AU - Anderson, E. L. AU - Timpson, N. J. AU - Davey Smith, G. AU - Munafo, M. R. AU - Relton, C. L. AU - Richmond, R. C. PY - 2019 DA - 2019// TI - Investigating the impact of cigarette smoking behaviours on DNA methylation patterns in adolescence JO - Hum Mol Genet VL - 28 UR - https://doi.org/10.1093/hmg/ddy316 DO - 10.1093/hmg/ddy316 ID - Prince2019 ER - TY - JOUR AU - Joehanes, R. AU - Just, A. C. AU - Marioni, R. E. AU - Pilling, L. C. AU - Reynolds, L. M. AU - Mandaviya, P. R. AU - Guan, W. AU - Xu, T. AU - Elks, C. E. AU - Aslibekyan, S. PY - 2016 DA - 2016// TI - Epigenetic signatures of cigarette smoking JO - Circ Cardiovasc Genet VL - 9 UR - https://doi.org/10.1161/CIRCGENETICS.116.001506 DO - 10.1161/CIRCGENETICS.116.001506 ID - Joehanes2016 ER - TY - JOUR AU - Tsaprouni, L. G. AU - Yang, T. P. AU - Bell, J. AU - Dick, K. J. AU - Kanoni, S. AU - Nisbet, J. AU - Vinuela, A. AU - Grundberg, E. AU - Nelson, C. P. AU - Meduri, E. PY - 2014 DA - 2014// TI - Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation JO - Epigenetics VL - 9 UR - https://doi.org/10.4161/15592294.2014.969637 DO - 10.4161/15592294.2014.969637 ID - Tsaprouni2014 ER - TY - JOUR AU - Zhu, X. AU - Li, J. AU - Deng, S. AU - Yu, K. AU - Liu, X. AU - Deng, Q. AU - Sun, H. AU - Zhang, X. AU - He, M. AU - Guo, H. PY - 2016 DA - 2016// TI - Genome-wide analysis of DNA methylation and cigarette smoking in a Chinese population JO - Environ Health Perspect VL - 124 UR - https://doi.org/10.1289/ehp.1509834 DO - 10.1289/ehp.1509834 ID - Zhu2016 ER - TY - JOUR AU - Gao, X. AU - Jia, M. AU - Zhang, Y. AU - Breitling, L. P. AU - Brenner, H. PY - 2015 DA - 2015// TI - DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies JO - Clin Epigenetics VL - 7 UR - https://doi.org/10.1186/s13148-015-0148-3 DO - 10.1186/s13148-015-0148-3 ID - Gao2015 ER - TY - JOUR AU - Bojesen, S. E. AU - Timpson, N. AU - Relton, C. AU - Davey Smith, G. AU - Nordestgaard, B. G. PY - 2017 DA - 2017// TI - AHRR (cg05575921) hypomethylation marks smoking behaviour, morbidity and mortality JO - Thorax VL - 72 UR - https://doi.org/10.1136/thoraxjnl-2016-208789 DO - 10.1136/thoraxjnl-2016-208789 ID - Bojesen2017 ER - TY - JOUR AU - Philibert, R. A. AU - Beach, S. R. AU - Brody, G. H. PY - 2012 DA - 2012// TI - Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers JO - Epigenetics VL - 7 UR - https://doi.org/10.4161/epi.22520 DO - 10.4161/epi.22520 ID - Philibert2012 ER - TY - JOUR AU - Joubert, B. R. AU - Haberg, S. E. AU - Nilsen, R. M. AU - Wang, X. AU - Vollset, S. E. AU - Murphy, S. K. AU - Huang, Z. AU - Hoyo, C. AU - Midttun, O. AU - Cupul-Uicab, L. A. PY - 2012 DA - 2012// TI - 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy JO - Environ Health Perspect VL - 120 UR - https://doi.org/10.1289/ehp.1205412 DO - 10.1289/ehp.1205412 ID - Joubert2012 ER - TY - JOUR AU - Markunas, C. A. AU - Xu, Z. AU - Harlid, S. AU - Wade, P. A. AU - Lie, R. T. AU - Taylor, J. A. AU - Wilcox, A. J. PY - 2014 DA - 2014// TI - Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy JO - Environ Health Perspect VL - 122 UR - https://doi.org/10.1289/ehp.1307892 DO - 10.1289/ehp.1307892 ID - Markunas2014 ER - TY - JOUR AU - Janssen, B. G. AU - Gyselaers, W. AU - Byun, H. M. AU - Roels, H. A. AU - Cuypers, A. AU - Baccarelli, A. A. AU - Nawrot, T. S. PY - 2017 DA - 2017// TI - Placental mitochondrial DNA and CYP1A1 gene methylation as molecular signatures for tobacco smoke exposure in pregnant women and the relevance for birth weight JO - J Transl Med VL - 15 UR - https://doi.org/10.1186/s12967-016-1113-4 DO - 10.1186/s12967-016-1113-4 ID - Janssen2017 ER - TY - JOUR AU - Wohak, L. E. AU - Krais, A. M. AU - Kucab, J. E. AU - Stertmann, J. AU - Ovrebo, S. AU - Seidel, A. AU - Phillips, D. H. AU - Arlt, V. M. PY - 2016 DA - 2016// TI - Carcinogenic polycyclic aromatic hydrocarbons induce CYP1A1 in human cells via a p53-dependent mechanism JO - Arch Toxicol VL - 90 UR - https://doi.org/10.1007/s00204-014-1409-1 DO - 10.1007/s00204-014-1409-1 ID - Wohak2016 ER - TY - JOUR AU - Absher, D. M. AU - Li, X. AU - Waite, L. L. AU - Gibson, A. AU - Roberts, K. AU - Edberg, J. AU - Chatham, W. W. AU - Kimberly, R. P. PY - 2013 DA - 2013// TI - Genome-wide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003678 DO - 10.1371/journal.pgen.1003678 ID - Absher2013 ER - TY - JOUR AU - Lauwerys, B. R. AU - Ducreux, J. AU - Houssiau, F. A. PY - 2014 DA - 2014// TI - Type I interferon blockade in systemic lupus erythematosus: where do we stand? JO - Rheumatology (Oxford) VL - 53 UR - https://doi.org/10.1093/rheumatology/ket403 DO - 10.1093/rheumatology/ket403 ID - Lauwerys2014 ER - TY - JOUR AU - Hackstadt, A. J. AU - Hess, A. M. PY - 2009 DA - 2009// TI - Filtering for increased power for microarray data analysis JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-11 DO - 10.1186/1471-2105-10-11 ID - Hackstadt2009 ER - TY - JOUR AU - Chen, Y. A. AU - Lemire, M. AU - Choufani, S. AU - Butcher, D. T. AU - Grafodatskaya, D. AU - Zanke, B. W. AU - Gallinger, S. AU - Hudson, T. J. AU - Weksberg, R. PY - 2013 DA - 2013// TI - Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray JO - Epigenetics VL - 8 UR - https://doi.org/10.4161/epi.23470 DO - 10.4161/epi.23470 ID - Chen2013 ER - TY - JOUR AU - Forest, M. AU - O'Donnell, K. J. AU - Voisin, G. AU - Gaudreau, H. AU - MacIsaac, J. L. AU - McEwen, L. M. AU - Silveira, P. P. AU - Steiner, M. AU - Kobor, M. S. AU - Meaney, M. J. AU - Greenwood, C. M. T. PY - 2018 DA - 2018// TI - Agreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time JO - Epigenetics VL - 13 UR - https://doi.org/10.1080/15592294.2017.1411443 DO - 10.1080/15592294.2017.1411443 ID - Forest2018 ER - TY - JOUR AU - Consortium, E. P. PY - 2012 DA - 2012// TI - An integrated encyclopedia of DNA elements in the human genome JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11247 DO - 10.1038/nature11247 ID - Consortium2012 ER - TY - JOUR AU - Aryee, M. J. AU - Jaffe, A. E. AU - Corrada-Bravo, H. AU - Ladd-Acosta, C. AU - Feinberg, A. P. AU - Hansen, K. D. AU - Irizarry, R. A. PY - 2014 DA - 2014// TI - Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays JO - Bioinformatics (Oxford, England) VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu049 DO - 10.1093/bioinformatics/btu049 ID - Aryee2014 ER - TY - JOUR AU - Davis, S. AU - Meltzer, P. S. PY - 2007 DA - 2007// TI - GEOquery: a bridge between the gene expression omnibus (GEO) and BioConductor JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/btm254 DO - 10.1093/bioinformatics/btm254 ID - Davis2007 ER - TY - BOOK AU - Hansen, K. D. PY - 2016 DA - 2016// TI - IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450k methylation arrays ID - Hansen2016 ER - TY - JOUR AU - Touleimat, N. AU - Tost, J. PY - 2012 DA - 2012// TI - Complete pipeline for Infinium((R)) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation JO - Epigenomics VL - 4 UR - https://doi.org/10.2217/epi.12.21 DO - 10.2217/epi.12.21 ID - Touleimat2012 ER - TY - BOOK AU - Teschendorff, A. E. PY - 2017 DA - 2017// TI - isva: Independent Surrogate Variable Analysis ID - Teschendorff2017 ER - TY - BOOK AU - Barfield, R. AU - Conneely, K. AU - Kilaru, V. PY - 2017 DA - 2017// TI - CpGassoc: Association Between Methylation and a Phenotype of Interest ID - Barfield2017 ER - TY - JOUR AU - Du, P. AU - Zhang, X. AU - Huang, C. C. AU - Jafari, N. AU - Kibbe, W. A. AU - Hou, L. AU - Lin, S. M. PY - 2010 DA - 2010// TI - Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-587 DO - 10.1186/1471-2105-11-587 ID - Du2010 ER - TY - BOOK AU - Team, R. C. PY - 2018 DA - 2018// TI - R: a language and environment for statistical computing ID - Team2018 ER - TY - BOOK AU - Storey, J. D. AU - Bass, A. J. AU - Dabney, A. AU - Robinson, D. PY - 2015 DA - 2015// TI - qvalue: Q-value estimation for false discovery rate control ID - Storey2015 ER - TY - JOUR AU - Sasieni, P. D. PY - 1997 DA - 1997// TI - From genotypes to genes: doubling the sample size JO - Biometrics VL - 53 UR - https://doi.org/10.2307/2533494 DO - 10.2307/2533494 ID - Sasieni1997 ER - TY - JOUR AU - Phipson, B. AU - Maksimovic, J. AU - Oshlack, A. PY - 2016 DA - 2016// TI - missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform JO - Bioinformatics VL - 32 ID - Phipson2016 ER - TY - BOOK AU - Wickham, H. PY - 2017 DA - 2017// TI - tidyverse: Easily Install and Load the 'Tidyverse' ID - Wickham2017 ER - TY - BOOK AU - Wickham, H. PY - 2016 DA - 2016// TI - ggplot2: Elegant Graphics for Data Analysis PB - Springer-Verlag CY - New York UR - https://doi.org/10.1007/978-3-319-24277-4 DO - 10.1007/978-3-319-24277-4 ID - Wickham2016 ER - TY - BOOK AU - Pedersen, T. L. PY - 2019 DA - 2019// TI - ggforce: Accelerating 'ggplot2' ID - Pedersen2019 ER - TY - JOUR AU - Gu, Z. AU - Eils, R. AU - Schlesner, M. PY - 2016 DA - 2016// TI - Complex heatmaps reveal patterns and correlations in multidimensional genomic data JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btw313 DO - 10.1093/bioinformatics/btw313 ID - Gu2016 ER - TY - BOOK AU - Gehlenborg, N. PY - 2017 DA - 2017// TI - UpSetR: a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets ID - Gehlenborg2017 ER - TY - BOOK AU - Kassambara, A. PY - 2018 DA - 2018// TI - ggpubr: 'ggplot2' based publication ready plots ID - Kassambara2018 ER - TY - BOOK AU - Wilke, C. O. PY - 2019 DA - 2019// TI - cowplot: streamlined plot theme and plot annotations for 'ggplot2' ID - Wilke2019 ER - TY - JOUR AU - Barrett, T. AU - Wilhite, S. E. AU - Ledoux, P. AU - Evangelista, C. AU - Kim, I. F. AU - Tomashevsky, M. AU - Marshall, K. A. AU - Phillippy, K. H. AU - Sherman, P. M. AU - Holko, M. PY - 2013 DA - 2013// TI - NCBI GEO: archive for functional genomics data sets--update JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1193 DO - 10.1093/nar/gks1193 ID - Barrett2013 ER - TY - STD TI - Huang J, Bai L, Cui B, Wu L, Wang L, An Z, Ruan S, Yue Y, Zhang X, Chen J. Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. GitHub. 2019; https://github.com/JhuangLab/EWASpaper. . UR - https://github.com/JhuangLab/EWASpaper ID - ref91 ER - TY - STD TI - Huang J, Bai L, Cui B, Wu L, Wang L, An Z, Ruan S, Yue Y, Zhang X, Chen J. Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. Zenodo. https://doi.org/10.5281/zenodo.3692126. ID - ref92 ER -