Ruggles KV, Fang Y, Tate J, Mentor SM, Bryant KJ, Fiellin DA, Justice AC, Braithwaite RS. What are the patterns between depression, smoking, unhealthy alcohol use, and other substance use among individuals receiving medical care? A longitudinal study of 5479 participants. AIDS Behav. 2017;21:2014–22.
Article
Google Scholar
Helleberg M, May MT, Ingle SM, Dabis F, Reiss P, Fatkenheuer G, Costagliola D, d’Arminio A, Cavassini M, Smith C, et al. Smoking and life expectancy among HIV-infected individuals on antiretroviral therapy in Europe and North America. AIDS. 2015;29:221–9.
Article
CAS
Google Scholar
Reddy KP, Parker RA, Losina E, Baggett TP, Paltiel AD, Rigotti NA, Weinstein MC, Freedberg KA, Walensky RP. Impact of cigarette smoking and smoking cessation on life expectancy among people with HIV: a US-based modeling study. J Infect Dis. 2016;214:1672–81.
Article
Google Scholar
Gao X, Jia M, Zhang Y, Breitling LP, Brenner H. DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies. Clin Epigenetics. 2015;7:113.
Article
Google Scholar
Zhang Y, Florath I, Saum KU, Brenner H. Self-reported smoking, serum cotinine, and blood DNA methylation. Environ Res. 2016;146:395–403.
Article
CAS
Google Scholar
Philibert R, Hollenbeck N, Andersen E, McElroy S, Wilson S, Vercande K, Beach SR, Osborn T, Gerrard M, Gibbons FX, Wang K. Reversion of AHRR demethylation is a quantitative biomarker of smoking cessation. Front Psychiatry. 2016;7:55.
Article
Google Scholar
Gao X, Gao X, Zhang Y, Breitling LP, Schottker B, Brenner H. Associations of self-reported smoking, cotinine levels and epigenetic smoking indicators with oxidative stress among older adults: a population-based study. Eur J Epidemiol. 2017;32:443–56.
Article
CAS
Google Scholar
Fasanelli F, Baglietto L, Ponzi E, Guida F, Campanella G, Johansson M, Grankvist K, Johansson M, Assumma MB, Naccarati A, et al. Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts. Nat Commun. 2015;6:10192.
Article
CAS
Google Scholar
Marabita F, Almgren M, Sjoholm LK, Kular L, Liu Y, James T, Kiss NB, Feinberg AP, Olsson T, Kockum I, et al. Smoking induces DNA methylation changes in multiple sclerosis patients with exposure-response relationship. Sci Rep. 2017;7:14589.
Article
Google Scholar
Zhang Y, Elgizouli M, Schottker B, Holleczek B, Nieters A, Brenner H. Smoking-associated DNA methylation markers predict lung cancer incidence. Clin Epigenetics. 2016;8:127.
Article
Google Scholar
Teschendorff AE, Yang Z, Wong A, Pipinikas CP, Jiao Y, Jones A, Anjum S, Hardy R, Salvesen HB, Thirlwell C, et al. Correlation of smoking-associated DNA methylation changes in buccal cells with DNA methylation changes in epithelial cancer. JAMA Oncol. 2015;1:476–85.
Article
Google Scholar
Gao X, Zhang Y, Saum KU, Schottker B, Breitling LP, Brenner H. Tobacco smoking and smoking-related DNA methylation are associated with the development of frailty among older adults. Epigenetics. 2017;12:149–56.
Article
Google Scholar
Zhang Y, Wilson R, Heiss J, Breitling LP, Saum KU, Schottker B, Holleczek B, Waldenberger M, Peters A, Brenner H. DNA methylation signatures in peripheral blood strongly predict all-cause mortality. Nat Commun. 2017;8:14617.
Article
CAS
Google Scholar
Zhang Y, Schottker B, Ordonez-Mena J, Holleczek B, Yang R, Burwinkel B, Butterbach K, Brenner H. F2RL3 methylation, lung cancer incidence and mortality. Int J Cancer. 2015;137:1739–48.
Article
CAS
Google Scholar
Zhang Y, Schottker B, Florath I, Stock C, Butterbach K, Holleczek B, Mons U, Brenner H. Smoking-associated DNA methylation biomarkers and their predictive value for all-cause and cardiovascular mortality. Environ Health Perspect. 2016;124:67–74.
Article
CAS
Google Scholar
Nelson KN, Hui Q, Rimland D, Xu K, Freiberg MS, Justice AC, Marconi VC, Sun YV. Identification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans. AIDS. 2017;31:571–5.
Article
CAS
Google Scholar
Horvath S, Levine AJ. HIV-1 infection accelerates age according to the epigenetic clock. J Infect Dis. 2015;212:1563–73.
Article
Google Scholar
Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nat Commun. 2017;8:2243.
Article
Google Scholar
Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics. 2016:11(10):750–60.
Corley MJ, Dye C, D’Antoni ML, Byron MM, Yo KL, Lum-Jones A, Nakamoto B, Valcour V, SahBandar I, Shikuma CM, et al. Comparative DNA methylation profiling reveals an immunoepigenetic signature of HIV-related cognitive impairment. Sci Rep. 2016;6:33310.
Article
CAS
Google Scholar
Holder LB, Haque MM, Skinner MK. Machine learning for epigenetics and future medical applications. Epigenetics. 2017;12:505–14.
Article
Google Scholar
Adorjan P, Distler J, Lipscher E, Model F, Muller J, Pelet C, Braun A, Florl AR, Gutig D, Grabs G, et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 2002;30:e21.
Article
Google Scholar
Zhu B, Song N, Shen R, Arora A, Machiela MJ, Song L, Landi MT, Ghosh D, Chatterjee N, Baladandayuthapani V, Zhao H. Integrating clinical and multiple omics data for prognostic assessment across human cancers. Sci Rep. 2017;7:16954.
Article
Google Scholar
Hao X, Luo H, Krawczyk M, Wei W, Wang W, Wang J, Flagg K, Hou J, Zhang H, Yi S, et al. DNA methylation markers for diagnosis and prognosis of common cancers. Proc Natl Acad Sci U S A. 2017;114:7414–9.
Article
CAS
Google Scholar
Jeschke J, Bizet M, Desmedt C, Calonne E, Dedeurwaerder S, Garaud S, Koch A, Larsimont D, Salgado R, Van den Eynden G, et al. DNA methylation-based immune response signature improves patient diagnosis in multiple cancers. J Clin Invest. 2017;127:3090–102.
Article
Google Scholar
Castellanos-Garzon JA, Ramos J, Lopez-Sanchez D, de Paz JF, Corchado JM. An ensemble framework coping with instability in the gene selection process. Interdiscip Sci. 2018;10:12–23.
Article
CAS
Google Scholar
Chen L, Jin P, Qin ZS. DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. Genome Biol. 2016;17:252.
Article
CAS
Google Scholar
Su D, Wang X, Campbell MR, Porter DK, Pittman GS, Bennett BD, Wan M, Englert NA, Crowl CL, Gimple RN, et al. Distinct epigenetic effects of tobacco smoking in whole blood and among leukocyte subtypes. PLoS One. 2016;11:e0166486.
Article
Google Scholar
Baselmans BM, van Dongen J, Nivard MG, Lin BD, Consortium B, Zilhao NR, Boomsma DI, Bartels M. Epigenome-wide association study of wellbeing. Twin Res Hum Genet. 2015;18:710–9.
Article
Google Scholar
Wilson R, Wahl S, Pfeiffer L, Ward-Caviness CK, Kunze S, Kretschmer A, Reischl E, Peters A, Gieger C, Waldenberger M. The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers. BMC Genomics. 2017;18:805.
Article
Google Scholar
Jhun MA, Smith JA, Ware EB, Kardia SLR, Mosley TH Jr, Turner ST, Peyser PA, Park SK. Modeling the causal role of DNA methylation in the association between cigarette smoking and inflammation in African Americans: a 2-step epigenetic Mendelian randomization study. Am J Epidemiol. 2017;186:1149–58.
Article
Google Scholar
Reynolds LM, Lohman K, Pittman GS, Barr RG, Chi GC, Kaufman J, Wan M, Bell DA, Blaha MJ, Rodriguez CJ, Liu Y. Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the multi-ethnic study of atherosclerosis (MESA). Epigenetics. 2017;12:1092–100.
Article
Google Scholar
Fa S, Larsen TV, Bilde K, Daugaard TF, Ernst EH, Olesen RH, Mamsen LS, Ernst E, Larsen A, Nielsen AL. Assessment of global DNA methylation in the first trimester fetal tissues exposed to maternal cigarette smoking. Clin Epigenetics. 2016;8:128.
Article
Google Scholar
Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, et al. Estimating and testing high-dimensional mediation effects in epigenetic studies. Bioinformatics. 2016;32:3150–4.
Article
CAS
Google Scholar
Joehanes R, Just AC, Marioni RE, Pilling LC, Reynolds LM, Mandaviya PR, Guan W, Xu T, Elks CE, Aslibekyan S, et al. Epigenetic signatures of cigarette smoking. Circ Cardiovasc Genet. 2016;9:436–47.
Article
CAS
Google Scholar
Justice AC, Freiberg MS, Tracy R, Kuller L, Tate JP, Goetz MB, Fiellin DA, Vanasse GJ, Butt AA, Rodriguez-Barradas MC, et al. Does an index composed of clinical data reflect effects of inflammation, coagulation, and monocyte activation on mortality among those aging with HIV? Clin Infect Dis. 2012;54:984–94.
Article
CAS
Google Scholar
Patil P, Parmigiani G. Training replicable predictors in multiple studies. Proc Natl Acad Sci U S A. 2018;115:2578–83.
Article
CAS
Google Scholar
Vogel CFA, Haarmann-Stemmann T. The aryl hydrocarbon receptor repressor - more than a simple feedback inhibitor of AhR signaling: clues for its role in inflammation and cancer. Curr Opin Toxicol. 2017;2:109–19.
Article
Google Scholar
Leenen FA, Muller CP, Turner JD. DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics. 2016;8:92.
Article
Google Scholar
McCartney DL, Hillary RF, Stevenson AJ, Ritchie SJ, Walker RM, Zhang Q, Morris SW, Bermingham ML, Campbell A, Murray AD, et al. Epigenetic prediction of complex traits and death. Genome Biol. 2018;19:136.
Article
Google Scholar
Justice AC, Gordon K, Skanderson M, Edelman EJ, Akgun KM, Gibert CL, Lo Re V 3rd, Rimland D, Womack JA, Wyatt CM, Tate JP. Non antiretroviral polypharmacy and adverse health outcomes among HIV-infected and uninfected individuals. AIDS. 2018:32(6):739–49.
Justice AC, McGinnis KA, Tate JP, Braithwaite RS, Bryant KJ, Cook RL, Edelman EJ, Fiellin LE, Freiberg MS, Gordon AJ, et al. Risk of mortality and physiologic injury evident with lower alcohol exposure among HIV infected compared with uninfected men. Drug Alcohol Depend. 2016;161:95–103.
Article
Google Scholar
Lehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan ST, Afzal U, Scott J, Jarvelin MR, Elliott P, et al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol. 2015;16:37.
Article
Google Scholar
Houseman EA, Kelsey KT, Wiencke JK, Marsit CJ. Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective. BMC Bioinformatics. 2015;16:95.
Article
Google Scholar
Gao X, Zhang Y, Breitling LP, Brenner H. Relationship of tobacco smoking and smoking-related DNA methylation with epigenetic age acceleration. Oncotarget. 2016;7:46878–89.
PubMed
PubMed Central
Google Scholar