TY - JOUR AU - Thun, M. J. AU - Carter, B. D. AU - Feskanich, D. AU - Freedman, N. D. AU - Prentice, R. AU - Lopez, A. D. PY - 2013 DA - 2013// TI - 50-year trends in smoking-related mortality in the United States JO - N Engl J Med VL - 368 UR - https://doi.org/10.1056/NEJMsa1211127 DO - 10.1056/NEJMsa1211127 ID - Thun2013 ER - TY - JOUR AU - Ferreira Antunes, J. L. AU - Toporcov, T. N. AU - Biazevic, M. G. AU - Boing, A. F. AU - Scully, C. AU - Petti, S. PY - 2013 DA - 2013// TI - Joint and independent effects of alcohol drinking and tobacco smoking on oral cancer: a large case-control study JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0068132 DO - 10.1371/journal.pone.0068132 ID - Ferreira Antunes2013 ER - TY - JOUR AU - Tonetti, M. S. AU - Claffey, N. PY - 2005 DA - 2005// TI - Advances in the progression of periodontitis and proposal of definitions of a periodontitis case and disease progression for use in risk factor research. Group C consensus report of the 5th European Workshop in Periodontology JO - J Clin Periodontol VL - 32 UR - https://doi.org/10.1111/j.1600-051X.2005.00822.x DO - 10.1111/j.1600-051X.2005.00822.x ID - Tonetti2005 ER - TY - JOUR AU - Portela, A. AU - Esteller, M. PY - 2010 DA - 2010// TI - Epigenetic modifications and human disease JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1685 DO - 10.1038/nbt.1685 ID - Portela2010 ER - TY - JOUR AU - Feinberg, A. P. PY - 2007 DA - 2007// TI - Phenotypic plasticity and the epigenetics of human disease JO - Nature. VL - 447 UR - https://doi.org/10.1038/nature05919 DO - 10.1038/nature05919 ID - Feinberg2007 ER - TY - JOUR AU - Fraga, M. F. AU - Ballestar, E. AU - Paz, M. F. AU - Ropero, S. AU - Setien, F. AU - Ballestar, M. L. PY - 2005 DA - 2005// TI - Epigenetic differences arise during the lifetime of monozygotic twins JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0500398102 DO - 10.1073/pnas.0500398102 ID - Fraga2005 ER - TY - JOUR AU - Flanagan, J. M. PY - 2015 DA - 2015// TI - Epigenome-wide association studies (EWAS): past, present, and future JO - Methods Mol Biol VL - 1238 UR - https://doi.org/10.1007/978-1-4939-1804-1_3 DO - 10.1007/978-1-4939-1804-1_3 ID - Flanagan2015 ER - TY - JOUR AU - Ambatipudi, S. AU - Cuenin, C. AU - Hernandez-Vargas, H. AU - Ghantous, A. AU - Calvez-Kelm, F. AU - Kaaks, R. PY - 2016 DA - 2016// TI - Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study JO - Epigenomics. VL - 8 UR - https://doi.org/10.2217/epi-2016-0001 DO - 10.2217/epi-2016-0001 ID - Ambatipudi2016 ER - TY - JOUR AU - Breitling, L. P. AU - Yang, R. AU - Korn, B. AU - Burwinkel, B. AU - Brenner, H. PY - 2011 DA - 2011// TI - Tobacco-smoking-related differential DNA methylation: 27K discovery and replication JO - Am J Hum Genet VL - 88 UR - https://doi.org/10.1016/j.ajhg.2011.03.003 DO - 10.1016/j.ajhg.2011.03.003 ID - Breitling2011 ER - TY - JOUR AU - Vries, M. AU - Plaat, D. A. AU - Nedeljkovic, I. AU - Verkaik-Schakel, R. N. AU - Kooistra, W. AU - Amin, N. PY - 2018 DA - 2018// TI - From blood to lung tissue: effect of cigarette smoke on DNA methylation and lung function JO - Respir Res VL - 19 UR - https://doi.org/10.1186/s12931-018-0904-y DO - 10.1186/s12931-018-0904-y ID - Vries2018 ER - TY - JOUR AU - Guida, F. AU - Sandanger, T. M. AU - Castagne, R. AU - Campanella, G. AU - Polidoro, S. AU - Palli, D. PY - 2015 DA - 2015// TI - Dynamics of smoking-induced genome-wide methylation changes with time since smoking cessation JO - Hum Mol Genet VL - 24 UR - https://doi.org/10.1093/hmg/ddu751 DO - 10.1093/hmg/ddu751 ID - Guida2015 ER - TY - JOUR AU - Jessen, W. J. AU - Borgerding, M. F. AU - Prasad, G. L. PY - 2018 DA - 2018// TI - Global methylation profiles in buccal cells of long-term smokers and moist snuff consumers JO - Biomarkers. VL - 23 UR - https://doi.org/10.1080/1354750X.2018.1466367 DO - 10.1080/1354750X.2018.1466367 ID - Jessen2018 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. 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 - 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 - Rzehak, P. AU - Saffery, R. AU - Reischl, E. AU - Covic, M. AU - Wahl, S. AU - Grote, V. PY - 2016 DA - 2016// TI - Maternal smoking during pregnancy and DNA-methylation in children at age 5.5 years: epigenome-wide-analysis in the European childhood obesity project (CHOP)-study JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0155554 DO - 10.1371/journal.pone.0155554 ID - Rzehak2016 ER - TY - JOUR AU - Sayols-Baixeras, S. AU - Lluis-Ganella, C. AU - Subirana, I. AU - Salas, L. A. AU - Vilahur, N. AU - Corella, D. PY - 2015 DA - 2015// TI - Identification of a new locus and validation of previously reported loci showing differential methylation associated with smoking. The REGICOR study JO - Epigenetics. VL - 10 UR - https://doi.org/10.1080/15592294.2015.1115175 DO - 10.1080/15592294.2015.1115175 ID - Sayols-Baixeras2015 ER - TY - JOUR AU - Shenker, N. S. AU - Polidoro, S. AU - Veldhoven, K. AU - Sacerdote, C. AU - Ricceri, F. AU - Birrell, M. A. PY - 2013 DA - 2013// TI - Epigenome-wide association study in the European Prospective Investigation into Cancer and Nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking JO - Hum Mol Genet VL - 22 UR - https://doi.org/10.1093/hmg/dds488 DO - 10.1093/hmg/dds488 ID - Shenker2013 ER - TY - JOUR AU - Sun, Y. V. AU - Smith, A. K. AU - Conneely, K. N. AU - Chang, Q. AU - Li, W. AU - Lazarus, A. PY - 2013 DA - 2013// TI - Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans JO - Hum Genet VL - 132 UR - https://doi.org/10.1007/s00439-013-1311-6 DO - 10.1007/s00439-013-1311-6 ID - Sun2013 ER - TY - JOUR AU - Tsai, P. C. AU - Glastonbury, C. A. AU - Eliot, M. N. AU - Bollepalli, S. AU - Yet, I. AU - Castillo-Fernandez, J. E. PY - 2018 DA - 2018// TI - Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health JO - Clin Epigenetics VL - 10 UR - https://doi.org/10.1186/s13148-018-0558-0 DO - 10.1186/s13148-018-0558-0 ID - Tsai2018 ER - TY - JOUR AU - Tsaprouni, L. G. AU - Yang, T. P. AU - Bell, J. AU - Dick, K. J. AU - Kanoni, S. AU - Nisbet, J. 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 - Wan, E. S. AU - Qiu, W. AU - Carey, V. J. AU - Morrow, J. AU - Bacherman, H. AU - Foreman, M. G. PY - 2015 DA - 2015// TI - Smoking-associated site-specific differential methylation in buccal mucosa in the COPDGene study JO - Am J Respir Cell Mol Biol VL - 53 UR - https://doi.org/10.1165/rcmb.2014-0103OC DO - 10.1165/rcmb.2014-0103OC ID - Wan2015 ER - TY - JOUR AU - Teschendorff, A. E. AU - Yang, Z. AU - Wong, A. AU - Pipinikas, C. P. AU - Jiao, Y. AU - Jones, A. PY - 2015 DA - 2015// TI - Correlation of smoking-associated DNA methylation changes in buccal cells with DNA methylation changes in epithelial cancer JO - JAMA Oncol VL - 1 UR - https://doi.org/10.1001/jamaoncol.2015.1053 DO - 10.1001/jamaoncol.2015.1053 ID - Teschendorff2015 ER - TY - JOUR AU - Stueve, T. R. AU - Li, W. Q. AU - Shi, J. AU - Marconett, C. N. AU - Zhang, T. AU - Yang, C. PY - 2017 DA - 2017// TI - Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers JO - Hum Mol Genet VL - 26 UR - https://doi.org/10.1093/hmg/ddx188 DO - 10.1093/hmg/ddx188 ID - Stueve2017 ER - TY - JOUR AU - Monick, M. M. AU - Beach, S. R. AU - Plume, J. AU - Sears, R. AU - Gerrard, M. AU - Brody, G. H. PY - 2012 DA - 2012// TI - Coordinated changes in AHRR methylation in lymphoblasts and pulmonary macrophages from smokers JO - Am J Med Genet B Neuropsychiatr Genet VL - 159B UR - https://doi.org/10.1002/ajmg.b.32021 DO - 10.1002/ajmg.b.32021 ID - Monick2012 ER - TY - JOUR AU - Zeilinger, S. AU - Kuhnel, B. AU - Klopp, N. AU - Baurecht, H. AU - Kleinschmidt, A. AU - Gieger, C. PY - 2013 DA - 2013// TI - Tobacco smoking leads to extensive genome-wide changes in DNA methylation JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0063812 DO - 10.1371/journal.pone.0063812 ID - Zeilinger2013 ER - TY - JOUR AU - Vogel, C. F. A. AU - Haarmann-Stemmann, T. PY - 2017 DA - 2017// TI - The aryl hydrocarbon receptor repressor—more than a simple feedback inhibitor of AhR signaling: clues for its role in inflammation and cancer JO - Curr Opin Toxicol VL - 2 UR - https://doi.org/10.1016/j.cotox.2017.02.004 DO - 10.1016/j.cotox.2017.02.004 ID - Vogel2017 ER - TY - JOUR AU - Buro-Auriemma, L. J. AU - Salit, J. AU - Hackett, N. R. AU - Walters, M. S. AU - Strulovici-Barel, Y. AU - Staudt, M. R. PY - 2013 DA - 2013// TI - Cigarette smoking induces small airway epithelial epigenetic changes with corresponding modulation of gene expression JO - Hum Mol Genet VL - 22 UR - https://doi.org/10.1093/hmg/ddt326 DO - 10.1093/hmg/ddt326 ID - Buro-Auriemma2013 ER - TY - JOUR AU - Squier, C. A. AU - Kremer, M. J. PY - 2001 DA - 2001// TI - Biology of Oral Mucosa and Esophagus JO - JNCI Monographs VL - 2001 UR - https://doi.org/10.1093/oxfordjournals.jncimonographs.a003443 DO - 10.1093/oxfordjournals.jncimonographs.a003443 ID - Squier2001 ER - TY - CHAP AU - Bergmeier, L. e. s. l. e. y. A. n. n. PY - 2018 DA - 2018// TI - Immunology of the Oral Mucosa BT - Oral Mucosa in Health and Disease PB - Springer International Publishing CY - Cham UR - https://doi.org/10.1007/978-3-319-56065-6_4 DO - 10.1007/978-3-319-56065-6_4 ID - Bergmeier2018 ER - TY - JOUR AU - Lesch, C. A. AU - Squier, C. A. AU - Cruchley, A. AU - Williams, D. M. AU - Speight, P. PY - 1989 DA - 1989// TI - The permeability of human oral mucosa and skin to water JO - J Dent Res VL - 68 UR - https://doi.org/10.1177/00220345890680091101 DO - 10.1177/00220345890680091101 ID - Lesch1989 ER - TY - JOUR AU - Winning, T. A. AU - Townsend, G. C. PY - 2000 DA - 2000// TI - Oral mucosal embryology and histology JO - Clin Dermatol VL - 18 UR - https://doi.org/10.1016/S0738-081X(00)00140-1 DO - 10.1016/S0738-081X(00)00140-1 ID - Winning2000 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 - Sutter, T. R. AU - Tang, Y. M. AU - Hayes, C. L. AU - Wo, Y. Y. AU - Jabs, E. W. AU - Li, X. PY - 1994 DA - 1994// TI - Complete cDNA sequence of a human dioxin-inducible mRNA identifies a new gene subfamily of cytochrome P450 that maps to chromosome 2 JO - J Biol Chem VL - 269 ID - Sutter1994 ER - TY - JOUR AU - Hopper, J. L. AU - Seeman, E. PY - 1994 DA - 1994// TI - The bone density of female twins discordant for tobacco use JO - N Engl J Med VL - 330 UR - https://doi.org/10.1056/NEJM199402103300603 DO - 10.1056/NEJM199402103300603 ID - Hopper1994 ER - TY - JOUR AU - Law, M. R. AU - Hackshaw, A. K. PY - 1997 DA - 1997// TI - A meta-analysis of cigarette smoking, bone mineral density and risk of hip fracture: recognition of a major effect JO - BMJ. VL - 315 UR - https://doi.org/10.1136/bmj.315.7112.841 DO - 10.1136/bmj.315.7112.841 ID - Law1997 ER - TY - JOUR AU - Szulc, P. AU - Garnero, P. AU - Claustrat, B. AU - Marchand, F. AU - Duboeuf, F. AU - Delmas, P. D. PY - 2002 DA - 2002// TI - Increased bone resorption in moderate smokers with low body weight: the Minos study JO - J Clin Endocrinol Metab VL - 87 UR - https://doi.org/10.1210/jcem.87.2.8232 DO - 10.1210/jcem.87.2.8232 ID - Szulc2002 ER - TY - JOUR AU - Iqbal, J. AU - Sun, L. AU - Cao, J. AU - Yuen, T. AU - Lu, P. AU - Bab, I. PY - 2013 DA - 2013// TI - Smoke carcinogens cause bone loss through the aryl hydrocarbon receptor and induction of Cyp1 enzymes JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1220919110 DO - 10.1073/pnas.1220919110 ID - Iqbal2013 ER - TY - JOUR AU - Yu, J. AU - Liu, Y. AU - Gong, Z. AU - Zhang, S. AU - Guo, C. AU - Li, X. PY - 2017 DA - 2017// TI - Overexpression long non-coding RNA LINC00673 is associated with poor prognosis and promotes invasion and metastasis in tongue squamous cell carcinoma JO - Oncotarget. VL - 8 UR - https://doi.org/10.18632/oncotarget.14200 DO - 10.18632/oncotarget.14200 ID - Yu2017 ER - TY - JOUR AU - Spivack, S. D. AU - Hurteau, G. J. AU - Jain, R. AU - Kumar, S. V. AU - Aldous, K. M. AU - Gierthy, J. F. PY - 2004 DA - 2004// TI - Gene-environment interaction signatures by quantitative mRNA profiling in exfoliated buccal mucosal cells JO - Cancer Res VL - 64 UR - https://doi.org/10.1158/0008-5472.CAN-04-1771 DO - 10.1158/0008-5472.CAN-04-1771 ID - Spivack2004 ER - TY - JOUR AU - Spira, A. AU - Beane, J. AU - Shah, V. AU - Liu, G. AU - Schembri, F. AU - Yang, X. PY - 2004 DA - 2004// TI - Effects of cigarette smoke on the human airway epithelial cell transcriptome JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0401422101 DO - 10.1073/pnas.0401422101 ID - Spira2004 ER - TY - JOUR AU - Cornelis, M. C. AU - Monda, K. L. AU - Yu, K. AU - Paynter, N. AU - Azzato, E. M. AU - Bennett, S. N. PY - 2011 DA - 2011// TI - Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption JO - PLoS Genet VL - 7 UR - https://doi.org/10.1371/journal.pgen.1002033 DO - 10.1371/journal.pgen.1002033 ID - Cornelis2011 ER - TY - JOUR AU - Pradhan, S. AU - Nagashri, M. N. AU - Gopinath, K. S. AU - Kumar, A. PY - 2011 DA - 2011// TI - Expression profiling of CYP1B1 in oral squamous cell carcinoma: counterintuitive downregulation in tumors JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0027914 DO - 10.1371/journal.pone.0027914 ID - Pradhan2011 ER - TY - JOUR AU - Murray, G. I. AU - Taylor, M. C. AU - McFadyen, M. C. AU - McKay, J. A. AU - Greenlee, W. F. AU - Burke, M. D. PY - 1997 DA - 1997// TI - Tumor-specific expression of cytochrome P450 CYP1B1 JO - Cancer Res VL - 57 ID - Murray1997 ER - TY - JOUR AU - Chang, I. AU - Mitsui, Y. AU - Kim, S. K. AU - Sun, J. S. AU - Jeon, H. S. AU - Kang, J. Y. PY - 2017 DA - 2017// TI - Cytochrome P450 1B1 inhibition suppresses tumorigenicity of prostate cancer via caspase-1 activation JO - Oncotarget. VL - 8 UR - https://doi.org/10.18632/oncotarget.16598 DO - 10.18632/oncotarget.16598 ID - Chang2017 ER - TY - BOOK AU - Brand, R. W. AU - Isselhard, D. E. PY - 2019 DA - 2019// TI - Anatomy of orofacial structures : a comprehensive approach PB - Elsevier CY - St. Louis ID - Brand2019 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. PY - 2014 DA - 2014// TI - Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu049 DO - 10.1093/bioinformatics/btu049 ID - Aryee2014 ER - TY - JOUR AU - Smyth, G. K. AU - Michaud, J. AU - Scott, H. S. PY - 2005 DA - 2005// TI - Use of within-array replicate spots for assessing differential expression in microarray experiments JO - Bioinformatics. VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti270 DO - 10.1093/bioinformatics/bti270 ID - Smyth2005 ER - TY - JOUR AU - Pidsley, R. AU - Zotenko, E. AU - Peters, T. J. AU - Lawrence, M. G. AU - Risbridger, G. P. AU - Molloy, P. PY - 2016 DA - 2016// TI - Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1066-1 DO - 10.1186/s13059-016-1066-1 ID - Pidsley2016 ER - TY - JOUR AU - McCartney, D. L. AU - Walker, R. M. AU - Morris, S. W. AU - McIntosh, A. M. AU - Porteous, D. J. AU - Evans, K. L. PY - 2016 DA - 2016// TI - Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip JO - Genom Data VL - 9 UR - https://doi.org/10.1016/j.gdata.2016.05.012 DO - 10.1016/j.gdata.2016.05.012 ID - McCartney2016 ER - TY - JOUR AU - Du, P. AU - Zhang, X. AU - Huang, C. C. AU - Jafari, N. AU - Kibbe, W. A. AU - Hou, L. 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 - JOUR AU - Fortin, J. P. AU - Labbe, A. AU - Lemire, M. AU - Zanke, B. W. AU - Hudson, T. J. AU - Fertig, E. J. PY - 2014 DA - 2014// TI - Functional normalization of 450k methylation array data improves replication in large cancer studies JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0503-2 DO - 10.1186/s13059-014-0503-2 ID - Fortin2014 ER - TY - JOUR AU - Manimaran, S. AU - Selby, H. M. AU - Okrah, K. AU - Ruberman, C. AU - Leek, J. T. AU - Quackenbush, J. PY - 2016 DA - 2016// TI - BatchQC: interactive software for evaluating sample and batch effects in genomic data JO - Bioinformatics. VL - 32 UR - https://doi.org/10.1093/bioinformatics/btw538 DO - 10.1093/bioinformatics/btw538 ID - Manimaran2016 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 Methodol VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Zheng, S. C. AU - Webster, A. P. AU - Dong, D. AU - Feber, A. AU - Graham, D. G. AU - Sullivan, R. PY - 2018 DA - 2018// TI - A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix JO - Epigenomics. VL - 10 UR - https://doi.org/10.2217/epi-2018-0037 DO - 10.2217/epi-2018-0037 ID - Zheng2018 ER - TY - JOUR AU - Patro, R. AU - Duggal, G. AU - Love, M. I. AU - Irizarry, R. A. AU - Kingsford, C. PY - 2017 DA - 2017// TI - Salmon provides fast and bias-aware quantification of transcript expression JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4197 DO - 10.1038/nmeth.4197 ID - Patro2017 ER - TY - JOUR AU - Soneson, C. AU - Love, M. I. AU - Robinson, M. D. PY - 2015 DA - 2015// TI - Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences JO - F1000Res. VL - 4 UR - https://doi.org/10.12688/f1000research.7563.1 DO - 10.12688/f1000research.7563.1 ID - Soneson2015 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Liberzon, A. AU - Birger, C. AU - Thorvaldsdottir, H. AU - Ghandi, M. AU - Mesirov, J. P. AU - Tamayo, P. PY - 2015 DA - 2015// TI - The molecular signatures database (MSigDB) hallmark gene set collection JO - Cell Syst VL - 1 UR - https://doi.org/10.1016/j.cels.2015.12.004 DO - 10.1016/j.cels.2015.12.004 ID - Liberzon2015 ER - TY - JOUR AU - Subramanian, A. AU - Tamayo, P. AU - Mootha, V. K. AU - Mukherjee, S. AU - Ebert, B. L. AU - Gillette, M. A. PY - 2005 DA - 2005// TI - Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0506580102 DO - 10.1073/pnas.0506580102 ID - Subramanian2005 ER - TY - JOUR AU - Luo, W. AU - Friedman, M. S. AU - Shedden, K. AU - Hankenson, K. D. AU - Woolf, P. J. PY - 2009 DA - 2009// TI - GAGE: generally applicable gene set enrichment for pathway analysis JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-161 DO - 10.1186/1471-2105-10-161 ID - Luo2009 ER - TY - JOUR AU - Gellner, C. A. AU - Reynaga, D. D. AU - Leslie, F. M. PY - 2016 DA - 2016// TI - Cigarette smoke extract: a preclinical model of tobacco dependence JO - Curr Protoc Neurosci VL - 77 UR - https://doi.org/10.1002/cpns.14 DO - 10.1002/cpns.14 ID - Gellner2016 ER - TY - JOUR AU - Weinstein, J. N. AU - Collisson, E. A. AU - Mills, G. B. AU - Shaw, K. R. AU - Ozenberger, B. A. PY - 2013 DA - 2013// TI - The cancer genome Atlas pan-cancer analysis project JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2764 DO - 10.1038/ng.2764 ID - Weinstein2013 ER - TY - JOUR AU - Leek, J. T. AU - Johnson, W. E. AU - Parker, H. S. AU - Jaffe, A. E. AU - Storey, J. D. PY - 2012 DA - 2012// TI - The sva package for removing batch effects and other unwanted variation in high-throughput experiments JO - Bioinformatics. VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts034 DO - 10.1093/bioinformatics/bts034 ID - Leek2012 ER -