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Duncan Campbell Thomas, PhD

TitleProfessor of Preventive Medicine
InstitutionUniversity of Southern California
DepartmentPreventive Medicine
AddressSSB 202 2001 N. Soto Street
Health Sciences Campus
Los Angeles CA 90033
Phone+1 323 442 1218
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    Other Positions
    TitleVerna R. Richter Chair in Cancer Research


    Collapse Overview 
    Collapse Overview
    My primary research interest has been in the development of statistical methods for genetic and environmental epidemiology, with wide involvement in numerous studies in both areas. My statistical contributions include methods for analysis of nested case-control studies, approaches to modeling exposure-time-response relationships and interaction effects, exposure modeling and measurement error, and the use of Markov chain Monte Carlo (MCMC) methods and Generalized Estimating Equations (GEE) methods in genetics.On the environmental side, I have been particularly active in air pollution and radiation carcinogenesis. I was one of the founding investigators of the Southern California Children’s Health Study, a major cohort study of the health effects of air pollution on schoolchildren’s lung development. I have also collaborated on studies of cancer in residents downwind of the Nevada Test Site, uranium miners, medical irradiation, and the atomic bomb survivors. I was a member of President Clinton’s Advisory Committee on Human Radiation Experiments, as well as the National Academy of Sciences Committee on the Biological Effects of Ionizing Radiation (BEIR V), and radiation advisory committees for numerous other governmental agencies. Other environmental activities include studies of asbestos, malathion spraying in California, electromagnetic fields, and air pollution; I am a Co-Director of the Southern California Environmental Health Research Center.On the genetic side, I have numerous publications in the area of statistical genetics and am collaborating on family studies of breast and colon cancer, pathway based modeling, several genome-wide association studies, next generation sequencing, and epigenetics. I chaired organizing committees for the Genetic Analysis Workshop, and am a Past President of the International Genetic Epidemiology Society.I have authored two textbooks: Statistical Methods in Genetic Epidemiology (Oxford University Press, 2003) and Statistical Methods in Environmental Epidemiology (Oxford University Press, 2009).I feel that these three broad areas of interest make me uniquely qualified to address methodological challenges in studying gene-environment interactions.


    Collapse Research 
    Collapse Research Activities and Funding
    Statistical Methods for Integrative Genomics in Cancer
    NIH/NCI P01CA196569Jul 1, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Statistical Methods for Epigenetic Mediation of Exposure-response Relations
    NIH/NIEHS R21ES020794Jan 18, 2012 - Dec 31, 2014
    Role: Principal Investigator
    Methods for Pathway Modeling with Application to Folate
    NIH/NIEHS R01ES019876Aug 16, 2010 - Mar 31, 2015
    Role: Principal Investigator
    DESIGN AND ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES
    NIH/NIEHS U01ES015090Sep 1, 2006 - Jul 31, 2010
    Role: Principal Investigator
    Environmental Genomics
    NIH/NIEHS T32ES013678Apr 30, 2005 - Jun 30, 2018
    Role: Co-Principal Investigator
    COMPUTATIONAL METHODS IN GENETIC EPIDEMIOLOGY
    NIH/NIGMS R01GM058897Feb 1, 2000 - Aug 31, 2004
    Role: Principal Investigator
    CHILD WELL BEING AND PUBLIC POLICY
    NIH/NICHD R01HD031722Sep 1, 1995 - Aug 31, 2001
    Role: Principal Investigator
    PEDIGREE ANALYSIS USING GIBBS SAMPLING
    NIH/NIGMS R44GM048326Sep 1, 1992 - Sep 19, 1996
    Role: Principal Investigator
    INCOME, ECONOMIC SHOCKS, INFRASTRUCTURE AND CHILD GROWTH
    NIH/NICHD R01HD027560Aug 1, 1991 - Jul 31, 1996
    Role: Principal Investigator
    Survival Models for Genetic Epidemiology
    NIH/NCI R01CA052862Apr 1, 1991 - Mar 31, 2008
    Role: Principal Investigator
    Time Related Factors in Cancer Epidemiology
    NIH/NCI R01CA042949Jul 1, 1986 - Aug 31, 2008
    Role: Co-Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Thomas D. Re: Kheifets et al. (2017): Residential magnetic fields exposure and childhood leukemia: a population-based case-control study in California. Cancer Causes Control. 2018 May 07. PMID: 29736896.
      View in: PubMed
    2. Reiner AS, Sisti J, John EM, Lynch CF, Brooks JD, Mellemkjær L, Boice JD, Knight JA, Concannon P, Capanu M, Tischkowitz M, Robson M, Liang X, Woods M, Conti DV, Duggan D, Shore R, Stram DO, Thomas D, Malone KE, Bernstein L, Bernstein JL. Breast Cancer Family History and Contralateral Breast Cancer Risk in Young Women: An Update From the Women's Environmental Cancer and Radiation Epidemiology Study. J Clin Oncol. 2018 May 20; 36(15):1513-1520. PMID: 29620998.
      View in: PubMed
    3. Assi N, Thomas D, Leitzmann M, Stepien M, Chajès V, Philip T, Vineis P, Bamia C, Boutron-Ruault MC, Sandanger TM, Molinuevo A, Boshuizen HC, Sundkvist A, Kühn T, Travis RC, Overvad K, Riboli E, Gunter MJ, Scalbert A, Jenab M, Ferrari P, Viallon V. Are Metabolic Signatures Mediating the Relationship between Lifestyle Factors and Hepatocellular Carcinoma Risk? Results from a Nested Case-Control Study in EPIC. Cancer Epidemiol Biomarkers Prev. 2018 May; 27(5):531-540. PMID: 29563134.
      View in: PubMed
    4. Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas D, Wei P, Montgomery SB. Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. Am J Epidemiol. 2017 Oct 01; 186(7):771-777. PMID: 28978191.
      View in: PubMed
    5. McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas D, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol. 2017 Oct 01; 186(7):753-761. PMID: 28978193.
      View in: PubMed
    6. Robson ME, Reiner AS, Brooks JD, Concannon PJ, John EM, Mellemkjaer L, Bernstein L, Malone KE, Knight JA, Lynch CF, Woods M, Liang X, Haile RW, Duggan DJ, Shore RE, Smith SA, Thomas D, Stram DO, Bernstein JL. Association of Common Genetic Variants With Contralateral Breast Cancer Risk in the WECARE Study. J Natl Cancer Inst. 2017 10 01; 109(10). PMID: 28521362.
      View in: PubMed
    7. Patel CJ, Kerr J, Thomas D, Mukherjee B, Ritz B, Chatterjee N, Jankowska M, Madan J, Karagas MR, McAllister KA, Mechanic LE, Fallin MD, Ladd-Acosta C, Blair IA, Teitelbaum SL, Amos CI. Opportunities and Challenges for Environmental Exposure Assessment in Population-Based Studies. Cancer Epidemiol Biomarkers Prev. 2017 Sep; 26(9):1370-1380. PMID: 28710076.
      View in: PubMed
    8. Thomas D. What Does "Precision Medicine" Have to Say About Prevention? Epidemiology. 2017 07; 28(4):479-483. PMID: 28368942.
      View in: PubMed
    9. Thomas D. Estimating the Effect of Targeted Screening Strategies: An Application to Colonoscopy and Colorectal Cancer. Epidemiology. 2017 07; 28(4):470-478. PMID: 28368944.
      View in: PubMed
    10. Pereira M, Thompson JR, Weichenberger CX, Thomas D, Minelli C. Inclusion of biological knowledge in a Bayesian shrinkage model for joint estimation of SNP effects. Genet Epidemiol. 2017 05; 41(4):320-331. PMID: 28393391.
      View in: PubMed
    11. Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas D, Wishart D, Balshaw DM, Patel CJ. Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. Annu Rev Public Health. 2017 Mar 20; 38:279-294. PMID: 28068484.
      View in: PubMed
    12. Salomon MP, Li WL, Edlund CK, Morrison J, Fortini BK, Win AK, Conti DV, Thomas D, Duggan D, Buchanan DD, Jenkins MA, Hopper JL, Gallinger S, Le Marchand L, Newcomb PA, Casey G, Marjoram P. GWASeq: targeted re-sequencing follow up to GWAS. BMC Genomics. 2016 Mar 03; 17:176. PMID: 26940994; PMCID: PMC4776370.
    13. Schumacher FR, Schmit SL, Jiao S, Edlund CK, Wang H, Zhang B, Hsu L, Huang SC, Fischer CP, Harju JF, Idos GE, Lejbkowicz F, Manion FJ, McDonnell K, McNeil CE, Melas M, Rennert HS, Shi W, Thomas D, Van Den Berg DJ, Hutter CM, Aragaki AK, Butterbach K, Caan BJ, Carlson CS, Chanock SJ, Curtis KR, Fuchs CS, Gala M, Giovannucci EL, Gogarten SM, Hayes RB, Henderson B, Hunter DJ, Jackson RD, Kolonel LN, Kooperberg C, Küry S, LaCroix A, Laurie CC, Laurie CA, Lemire M, Levine D, Ma J, Makar KW, Qu C, Taverna D, Ulrich CM, Wu K, Kono S, West DW, Berndt SI, Bezieau S, Brenner H, Campbell PT, Chan AT, Chang-Claude J, Coetzee GA, Conti DV, Duggan D, Figueiredo JC, Fortini BK, Gallinger SJ, Gauderman WJ, Giles G, Green R, Haile R, Harrison TA, Hoffmeister M, Hopper JL, Hudson TJ, Jacobs E, Iwasaki M, Jee SH, Jenkins M, Jia WH, Joshi A, Li L, Lindor NM, Matsuo K, Moreno V, Mukherjee B, Newcomb PA, Potter JD, Raskin L, Rennert G, Rosse S, Severi G, Schoen RE, Seminara D, Shu XO, Slattery ML, Tsugane S, White E, Xiang YB, Zanke BW, Zheng W, Le Marchand L, Casey G, Gruber SB, Peters U. Corrigendum: genome-wide association study of colorectal cancer identifies six new susceptibility loci. Nat Commun. 2015 Oct 26; 6:8739. PMID: 26498495.
      View in: PubMed
    14. Schmit SL, Figueiredo JC, Cortessis VK, Thomas D. The Influence of Screening for Precancerous Lesions on Family-Based Genetic Association Tests: An Example of Colorectal Polyps and Cancer. Am J Epidemiol. 2015 Oct 15; 182(8):714-22. PMID: 26306664; PMCID: PMC4597802 [Available on 10/15/16].
    15. Gribble MO, Voruganti VS, Cole SA, Haack K, Balakrishnan P, Laston SL, Tellez-Plaza M, Francesconi KA, Goessler W, Umans JG, Thomas D, Gilliland F, North KE, Franceschini N, Navas-Acien A. Linkage Analysis of Urine Arsenic Species Patterns in the Strong Heart Family Study. Toxicol Sci. 2015 Nov; 148(1):89-100. PMID: 26209557; PMCID: PMC4731407 [Available on 11/01/16].
    16. Schumacher FR, Schmit SL, Jiao S, Edlund CK, Wang H, Zhang B, Hsu L, Huang SC, Fischer CP, Harju JF, Idos GE, Lejbkowicz F, Manion FJ, McDonnell K, McNeil CE, Melas M, Rennert HS, Shi W, Thomas D, Van Den Berg DJ, Hutter CM, Aragaki AK, Butterbach K, Caan BJ, Carlson CS, Chanock SJ, Curtis KR, Fuchs CS, Gala M, Giovannucc EL, Giocannucci EL, Gogarten SM, Hayes RB, Henderson B, Hunter DJ, Jackson RD, Kolonel LN, Kooperberg C, Küry S, Kury S, LaCroix A, Laurie CC, Laurie CA, Lemire M, Lemire M, Levine D, Ma J, Makar KW, Qu C, Taverna D, Ulrich CM, Wu K, Kono S, West DW, Berndt SI, Bezieau S, Brenner H, Campbell PT, Chan AT, Chang-Claude J, Coetzee GA, Conti DV, Duggan D, Figueiredo JC, Fortini BK, Gallinger SJ, Gauderman WJ, Giles G, Green R, Haile R, Harrison TA, Hoffmeister M, Hopper JL, Hudson TJ, Jacobs E, Iwasaki M, Jee SH, Jenkins M, Jia WH, Joshi A, Li L, Lindor NM, Matsuo K, Moreno V, Mukherjee B, Newcomb PA, Potter JD, Raskin L, Rennert G, Rosse S, Severi G, Schoen RE, Seminara D, Shu XO, Slattery ML, Tsugane S, White E, Xiang YB, Zanke BW, Zheng W, Le Marchand L, Casey G, Gruber SB, Peters U. Genome-wide association study of colorectal cancer identifies six new susceptibility loci. Nat Commun. 2015 Jul 07; 6:7138. PMID: 26151821; PMCID: PMC4967357.
    17. Hsu L, Jeon J, Brenner H, Gruber SB, Schoen RE, Berndt SI, Chan AT, Chang-Claude J, Du M, Gong J, Harrison TA, Hayes RB, Hoffmeister M, Hutter CM, Lin Y, Nishihara R, Ogino S, Prentice RL, Schumacher FR, Seminara D, Slattery ML, Thomas D, Thornquist M, Newcomb PA, Potter JD, Zheng Y, White E, Peters U. A model to determine colorectal cancer risk using common genetic susceptibility loci. Gastroenterology. 2015 Jun; 148(7):1330-9.e14. PMID: 25683114.
      View in: PubMed
    18. Roy A, Gong J, Thomas D, Zhang J, Kipen HM, Rich DQ, Zhu T, Huang W, Hu M, Wang G, Wang Y, Zhu P, Lu SE, Ohman-Strickland P, Diehl SR, Eckel SP. The cardiopulmonary effects of ambient air pollution and mechanistic pathways: a comparative hierarchical pathway analysis. PLoS One. 2014; 9(12):e114913. PMID: 25502951; PMCID: PMC4264846.
    19. Li D, Zhou J, Thomas D, Fardo DW. Complex pedigrees in the sequencing era: to track transmissions or decorrelate? Genet Epidemiol. 2014 Sep; 38 Suppl 1:S29-36. PMID: 25112185; PMCID: PMC4272198.
    20. Yang Z, Thomas D. Two-stage family-based designs for sequencing studies. BMC Proc. 2014; 8(Suppl 1):S32. PMID: 25519319; PMCID: PMC4143728.
    21. Cortessis VK, Phay Johnson Thomas J, Thomas D. Three authors reply. Am J Epidemiol. 2014 Apr 15; 179(8):1037. PMID: 24647848.
      View in: PubMed
    22. Ahsan H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, Andrulis I, Hopper JL, John EM, Malone K, Ursin G, Gammon MD, Thomas D, Seminara D, Casey G, Knight JA, Southey MC, Giles GG, Santella RM, Lee E, Conti D, Duggan D, Gallinger S, Haile R, Jenkins M, Lindor NM, Newcomb P, Michailidou K, Apicella C, Park DJ, Peto J, Fletcher O, dos Santos Silva I, Lathrop M, Hunter DJ, Chanock SJ, Meindl A, Schmutzler RK, Müller-Myhsok B, Lochmann M, Beckmann L, Hein R, Makalic E, Schmidt DF, Bui QM, Stone J, Flesch-Janys D, Dahmen N, Nevanlinna H, Aittomäki K, Blomqvist C, Hall P, Czene K, Irwanto A, Liu J, Rahman N, Turnbull C. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Cancer Epidemiol Biomarkers Prev. 2014 Apr; 23(4):658-69. PMID: 24493630; PMCID: PMC3990360.
    23. Corral R, Lewinger JP, Van Den Berg D, Joshi AD, Yuan JM, Gago-Dominguez M, Cortessis VK, Pike MC, Conti DV, Thomas D, Edlund CK, Gao YT, Xiang YB, Zhang W, Su YC, Stern MC. Comprehensive analyses of DNA repair pathways, smoking and bladder cancer risk in Los Angeles and Shanghai. Int J Cancer. 2014 Jul 15; 135(2):335-47. PMID: 24382701; PMCID: PMC4016180.
    24. Duan L, Thomas D. A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk. Int J Genomics. 2013; 2013:406217. PMID: 24490143; PMCID: PMC3892936.
    25. Thomas D. Invited commentary: is it time to retire the "pack-years" variable? Maybe not! Am J Epidemiol. 2014 Feb 01; 179(3):299-302. PMID: 24355333; PMCID: PMC3895098.
    26. Thomas D, Yang Z, Yang F. Two-phase and family-based designs for next-generation sequencing studies. Front Genet. 2013 Dec 13; 4:276. PMID: 24379824; PMCID: PMC3861783.
    27. Thomas D. Measurement Error in Spatial Exposure Models: Study Design Implications. Environmetrics. 2013 Dec 01; 24(8):518-520. PMID: 24729740.
      View in: PubMed
    28. Thomas JP, Davis-Dao C, Lewinger JP, Siegmund KD, Hamilton AS, Daneshmand S, Skinner EC, Thomas D, Cortessis VK. Null association between histology of first and second primary malignancies in men with bilateral testicular germ cell tumors. Am J Epidemiol. 2013 Oct 15; 178(8):1240-5. PMID: 23928263; PMCID: PMC3792726.
    29. Bernstein JL, Thomas D, Shore RE, Robson M, Boice JD, Stovall M, Andersson M, Bernstein L, Malone KE, Reiner AS, Lynch CF, Capanu M, Smith SA, Tellhed L, Teraoka SN, Begg CB, Olsen JH, Mellemkjaer L, Liang X, Diep AT, Borg A, Concannon P, Haile RW. Contralateral breast cancer after radiotherapy among BRCA1 and BRCA2 mutation carriers: a WECARE study report. Eur J Cancer. 2013 Sep; 49(14):2979-85. PMID: 23706288; PMCID: PMC3755053.
    30. Chung CC, Kanetsky PA, Wang Z, Hildebrandt MA, Koster R, Skotheim RI, Kratz CP, Turnbull C, Cortessis VK, Bakken AC, Bishop DT, Cook MB, Erickson RL, Fosså SD, Jacobs KB, Korde LA, Kraggerud SM, Lothe RA, Loud JT, Rahman N, Skinner EC, Thomas D, Wu X, Yeager M, Schumacher FR, Greene MH, Schwartz SM, McGlynn KA, Chanock SJ, Nathanson KL. Meta-analysis identifies four new loci associated with testicular germ cell tumor. Nat Genet. 2013 Jun; 45(6):680-5. PMID: 23666239; PMCID: PMC3723930.
    31. Lewinger JP, Morrison JL, Thomas D, Murcray CE, Conti DV, Li D, Gauderman WJ. Efficient two-step testing of gene-gene interactions in genome-wide association studies. Genet Epidemiol. 2013 Jul; 37(5):440-51. PMID: 23633124.
      View in: PubMed
    32. Thomas D. Some surprising twists on the road to discovering the contribution of rare variants to complex diseases. Hum Hered. 2012; 74(3-4):113-7. PMID: 23594489; PMCID: PMC3704173.
    33. Li R, Conti DV, Diaz-Sanchez D, Gilliland F, Thomas D. Joint analysis for integrating two related studies of different data types and different study designs using hierarchical modeling approaches. Hum Hered. 2012; 74(2):83-96. PMID: 23343600; PMCID: PMC4106669.
    34. Reiner AS, John EM, Brooks JD, Lynch CF, Bernstein L, Mellemkjær L, Malone KE, Knight JA, Capanu M, Teraoka SN, Concannon P, Liang X, Figueiredo JC, Smith SA, Stovall M, Pike MC, Haile RW, Thomas D, Begg CB, Bernstein JL. Risk of asynchronous contralateral breast cancer in noncarriers of BRCA1 and BRCA2 mutations with a family history of breast cancer: a report from the Women's Environmental Cancer and Radiation Epidemiology Study. J Clin Oncol. 2013 Feb 01; 31(4):433-9. PMID: 23269995; PMCID: PMC3731919.
    35. Liang WE, Thomas D, Conti DV. Analysis and optimal design for association studies using next-generation sequencing with case-control pools. Genet Epidemiol. 2012 Dec; 36(8):870-81. PMID: 22972696; PMCID: PMC4139478.
    36. Cortessis VK, Thomas D, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, Laird PW. Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet. 2012 Oct; 131(10):1565-89. PMID: 22740325; PMCID: PMC3432200.
    37. Cicek MS, Cunningham JM, Fridley BL, Serie DJ, Bamlet WR, Diergaarde B, Haile RW, Le Marchand L, Krontiris TG, Younghusband HB, Gallinger S, Newcomb PA, Hopper JL, Jenkins MA, Casey G, Schumacher F, Chen Z, DeRycke MS, Templeton AS, Winship I, Green RC, Green JS, Macrae FA, Parry S, Young GP, Young JP, Buchanan D, Thomas D, Bishop DT, Lindor NM, Thibodeau SN, Potter JD, Goode EL. Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22. PLoS One. 2012; 7(5):e38175. PMID: 22675446; PMCID: PMC3364975.
    38. Boffetta P, Winn DM, Ioannidis JP, Thomas D, Little J, Smith GD, Cogliano VJ, Hecht SS, Seminara D, Vineis P, Khoury MJ. Recommendations and proposed guidelines for assessing the cumulative evidence on joint effects of genes and environments on cancer occurrence in humans. Int J Epidemiol. 2012 Jun; 41(3):686-704. PMID: 22596931; PMCID: PMC3481885.
    39. Brooks JD, Boice JD, Stovall M, Reiner AS, Bernstein L, John EM, Lynch CF, Mellemkjær L, Knight JA, Thomas D, Haile RW, Smith SA, Capanu M, Bernstein JL, Shore RE. Reproductive status at first diagnosis influences risk of radiation-induced second primary contralateral breast cancer in the WECARE study. Int J Radiat Oncol Biol Phys. 2012 Nov 15; 84(4):917-24. PMID: 22483700; PMCID: PMC3394928.
    40. Thomas D. Genetic epidemiology with a capital E: where will we be in another 10 years? Genet Epidemiol. 2012 Apr; 36(3):179-82. PMID: 22311722; PMCID: PMC3781009.
    41. Haile RW, John EM, Levine AJ, Cortessis VK, Unger JB, Gonzales M, Ziv E, Thompson P, Spruijt-Metz D, Tucker KL, Bernstein JL, Rohan TE, Ho GY, Bondy ML, Martinez ME, Cook L, Stern MC, Correa MC, Wright J, Schwartz SJ, Baezconde-Garbanati L, Blinder V, Miranda P, Hayes R, Friedman-Jiménez G, Monroe KR, Haiman CA, Henderson BE, Thomas D, Boffetta P. A review of cancer in U.S. Hispanic populations. Cancer Prev Res (Phila). 2012 Feb; 5(2):150-63. PMID: 22307564.
      View in: PubMed
    42. Thomas D, Lewinger JP, Murcray CE, Gauderman WJ. Invited commentary: GE-Whiz! Ratcheting gene-environment studies up to the whole genome and the whole exposome. Am J Epidemiol. 2012 Feb 01; 175(3):203-7; discussion 208-9. PMID: 22199029; PMCID: PMC3261438.
    43. Mechanic LE, Chen HS, Amos CI, Chatterjee N, Cox NJ, Divi RL, Fan R, Harris EL, Jacobs K, Kraft P, Leal SM, McAllister K, Moore JH, Paltoo DN, Province MA, Ramos EM, Ritchie MD, Roeder K, Schaid DJ, Stephens M, Thomas D, Weinberg CR, Witte JS, Zhang S, Zöllner S, Feuer EJ, Gillanders EM. Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol. 2012 Jan; 36(1):22-35. PMID: 22147673; PMCID: PMC3368075.
    44. Teraoka SN, Bernstein JL, Reiner AS, Haile RW, Bernstein L, Lynch CF, Malone KE, Stovall M, Capanu M, Liang X, Smith SA, Mychaleckyj J, Hou X, Mellemkjaer L, Boice JD, Siniard A, Duggan D, Thomas D. Single nucleotide polymorphisms associated with risk for contralateral breast cancer in the Women's Environment, Cancer, and Radiation Epidemiology (WECARE) Study. Breast Cancer Res. 2011; 13(6):R114. PMID: 22087758; PMCID: PMC3326556.
    45. Brooks JD, Teraoka SN, Reiner AS, Satagopan JM, Bernstein L, Thomas D, Capanu M, Stovall M, Smith SA, Wei S, Shore RE, Boice JD, Lynch CF, Mellemkjaer L, Malone KE, Liang X. Variants in activators and downstream targets of ATM, radiation exposure, and contralateral breast cancer risk in the WECARE study. Hum Mutat. 2012 Jan; 33(1):158-64. PMID: 21898661; PMCID: PMC3240722.
    46. Quintana MA, Berstein JL, Thomas D, Conti DV. Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol. 2011 Nov; 35(7):638-49. PMID: 22009789; PMCID: PMC3936341.
    47. Tzeng JY, Zhang D, Pongpanich M, Smith C, McCarthy MI, Sale MM, Worrall BB, Hsu FC, Thomas D, Sullivan PF. Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression. Am J Hum Genet. 2011 Aug 12; 89(2):277-88. PMID: 21835306.
      View in: PubMed
    48. Yang F, Thomas D. Two-stage design of sequencing studies for testing association with rare variants. Hum Hered. 2011; 71(4):209-20. PMID: 21734405; PMCID: PMC3136374.
    49. Davis-Dao CA, Siegmund KD, Vandenberg DJ, Skinner EC, Coetzee GA, Thomas D, Pike MC, Cortessis VK. Heterogenous effect of androgen receptor CAG tract length on testicular germ cell tumor risk: shorter repeats associated with seminoma but not other histologic types. Carcinogenesis. 2011 Aug; 32(8):1238-43. PMID: 21642359; PMCID: PMC3202310.
    50. Capanu M, Concannon P, Haile RW, Bernstein L, Malone KE, Lynch CF, Liang X, Teraoka SN, Diep AT, Thomas D, Bernstein JL. Assessment of rare BRCA1 and BRCA2 variants of unknown significance using hierarchical modeling. Genet Epidemiol. 2011 Jul; 35(5):389-97. PMID: 21520273; PMCID: PMC3111904.
    51. Murcray CE, Lewinger JP, Conti DV, Thomas D, Gauderman WJ. Sample size requirements to detect gene-environment interactions in genome-wide association studies. Genet Epidemiol. 2011 Apr; 35(3):201-10. PMID: 21308767.
      View in: PubMed
    52. Chen GK, Thomas D. Using biological knowledge to discover higher order interactions in genetic association studies. Genet Epidemiol. 2010 Dec; 34(8):863-78. PMID: 21104889.
      View in: PubMed
    53. Baurley JW, Conti DV, Gauderman WJ, Thomas D. Discovery of complex pathways from observational data. Stat Med. 2010 Aug 30; 29(19):1998-2011. PMID: 20683892; PMCID: PMC2922970.
    54. Gauderman WJ, Thomas D, Murcray CE, Conti D, Li D, Lewinger JP. Efficient genome-wide association testing of gene-environment interaction in case-parent trios. Am J Epidemiol. 2010 Jul 01; 172(1):116-22. PMID: 20543031; PMCID: PMC2915477.
    55. Malone KE, Begg CB, Haile RW, Borg A, Concannon P, Tellhed L, Xue S, Teraoka S, Bernstein L, Capanu M, Reiner AS, Riedel ER, Thomas D, Mellemkjaer L, Lynch CF, Boice JD, Anton-Culver H, Bernstein JL. Population-based study of the risk of second primary contralateral breast cancer associated with carrying a mutation in BRCA1 or BRCA2. J Clin Oncol. 2010 May 10; 28(14):2404-10. PMID: 20368571; PMCID: PMC2881721.
    56. Thomas D. Gene--environment-wide association studies: emerging approaches. Nat Rev Genet. 2010 Apr; 11(4):259-72. PMID: 20212493; PMCID: PMC2891422.
    57. Bernstein JL, Haile RW, Stovall M, Boice JD, Shore RE, Langholz B, Thomas D, Bernstein L, Lynch CF, Olsen JH, Malone KE, Mellemkjaer L, Borresen-Dale AL, Rosenstein BS, Teraoka SN, Diep AT, Smith SA, Capanu M, Reiner AS, Liang X, Gatti RA, Concannon P. Radiation exposure, the ATM Gene, and contralateral breast cancer in the women's environmental cancer and radiation epidemiology study. J Natl Cancer Inst. 2010 Apr 07; 102(7):475-83. PMID: 20305132; PMCID: PMC2902825.
    58. Borg A, Haile RW, Malone KE, Capanu M, Diep A, Törngren T, Teraoka S, Begg CB, Thomas D, Concannon P, Mellemkjaer L, Bernstein L, Tellhed L, Xue S, Olson ER, Liang X, Dolle J, Børresen-Dale AL, Bernstein JL. Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. Hum Mutat. 2010 Mar; 31(3):E1200-40. PMID: 20104584; PMCID: PMC2928257.
    59. Wilson MA, Baurley JW, Thomas D, Conti DV. Complex system approaches to genetic analysis Bayesian approaches. Adv Genet. 2010; 72:47-71. PMID: 21029848; PMCID: PMC4190044.
    60. Thomas D. Methods for investigating gene-environment interactions in candidate pathway and genome-wide association studies. Annu Rev Public Health. 2010; 31:21-36. PMID: 20070199; PMCID: PMC2847610.
    61. Thomas D, Casey G, Conti DV, Haile RW, Lewinger JP, Stram DO. Methodological Issues in Multistage Genome-wide Association Studies. Stat Sci. 2009 Nov 01; 24(4):414-429. PMID: 20607129.
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    62. Thomas D, Conti DV, Baurley J, Nijhout F, Reed M, Ulrich CM. Use of pathway information in molecular epidemiology. Hum Genomics. 2009 Oct; 4(1):21-42. PMID: 21072972; PMCID: PMC2999471.
    63. Tzeng JY, Zhang D, Chang SM, Thomas D, Davidian M. Gene-trait similarity regression for multimarker-based association analysis. Biometrics. 2009 Sep; 65(3):822-32. PMID: 19210740; PMCID: PMC2748404.
    64. Thomas D. Genome-wide association studies for discrete traits. Genet Epidemiol. 2009; 33 Suppl 1:S8-12. PMID: 19924710; PMCID: PMC2920891.
    65. Thomas D, Baurley JW, Brown EE, Figueiredo JC, Goldstein A, Hazra A, Wilson RT, Rothman N. Approaches to complex pathways in molecular epidemiology: summary of a special conference of the American Association for Cancer Research. Cancer Res. 2008 Dec 15; 68(24):10028-30. PMID: 19074865.
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    66. Concannon P, Haile RW, Børresen-Dale AL, Rosenstein BS, Gatti RA, Teraoka SN, Diep TA, Jansen L, Atencio DP, Langholz B, Capanu M, Liang X, Begg CB, Thomas D, Bernstein L, Olsen JH, Malone KE, Lynch CF, Anton-Culver H, Bernstein JL. Variants in the ATM gene associated with a reduced risk of contralateral breast cancer. Cancer Res. 2008 Aug 15; 68(16):6486-91. PMID: 18701470; PMCID: PMC2562548.
    67. Langholz B, Thomas D, Stovall M, Smith SA, Boice JD, Shore RE, Bernstein L, Lynch CF, Zhang X, Bernstein JL. Statistical methods for analysis of radiation effects with tumor and dose location-specific information with application to the WECARE study of asynchronous contralateral breast cancer. Biometrics. 2009 Jun; 65(2):599-608. PMID: 18647297; PMCID: PMC2728135.
    68. Kerber RA, Amos CI, Yeap BY, Finkelstein DM, Thomas D. Design considerations in a sib-pair study of linkage for susceptibility loci in cancer. BMC Med Genet. 2008 Jul 10; 9:64. PMID: 18616822; PMCID: PMC2488325.
    69. Jerrett M, Shankardass K, Berhane K, Gauderman WJ, Künzli N, Avol E, Gilliland F, Lurmann F, Molitor JN, Molitor JT, Thomas D, Peters J, McConnell R. Traffic-related air pollution and asthma onset in children: a prospective cohort study with individual exposure measurement. Environ Health Perspect. 2008 Oct; 116(10):1433-8. PMID: 18941591; PMCID: PMC2569108.
    70. Stovall M, Smith SA, Langholz BM, Boice JD, Shore RE, Andersson M, Buchholz TA, Capanu M, Bernstein L, Lynch CF, Malone KE, Anton-Culver H, Haile RW, Rosenstein BS, Reiner AS, Thomas D, Bernstein JL. Dose to the contralateral breast from radiotherapy and risk of second primary breast cancer in the WECARE study. Int J Radiat Oncol Biol Phys. 2008 Nov 15; 72(4):1021-30. PMID: 18556141; PMCID: PMC3782859.
    71. Capanu M, Orlow I, Berwick M, Hummer AJ, Thomas D, Begg CB. The use of hierarchical models for estimating relative risks of individual genetic variants: an application to a study of melanoma. Stat Med. 2008 May 20; 27(11):1973-92. PMID: 18335566; PMCID: PMC2722963.
    72. Begg CB, Haile RW, Borg A, Malone KE, Concannon P, Thomas D, Langholz B, Bernstein L, Olsen JH, Lynch CF, Anton-Culver H, Capanu M, Liang X, Hummer AJ, Sima C, Bernstein JL. Variation of breast cancer risk among BRCA1/2 carriers. JAMA. 2008 Jan 09; 299(2):194-201. PMID: 18182601; PMCID: PMC2714486.
    73. Bertelsen L, Bernstein L, Olsen JH, Mellemkjaer L, Haile RW, Lynch CF, Malone KE, Anton-Culver H, Christensen J, Langholz B, Thomas D, Begg CB, Capanu M, Ejlertsen B, Stovall M, Boice JD, Shore RE. Effect of systemic adjuvant treatment on risk for contralateral breast cancer in the Women's Environment, Cancer and Radiation Epidemiology Study. J Natl Cancer Inst. 2008 Jan 02; 100(1):32-40. PMID: 18159070.
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    74. Pique-Regi R, Morrison J, Thomas D. Bayesian hierarchical modeling of means and covariances of gene expression data within families. BMC Proc. 2007; 1 Suppl 1:S111. PMID: 18466452; PMCID: PMC2367475.
    75. Lewinger JP, Conti DV, Baurley JW, Triche TJ, Thomas D. Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation. Genet Epidemiol. 2007 Dec; 31(8):871-82. PMID: 17654612.
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    76. Thomas D. Viewpoint: using gene-environment interactions to dissect the effects of complex mixtures. J Expo Sci Environ Epidemiol. 2007 Dec; 17 Suppl 2:S71-4. PMID: 18079767.
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    77. Thomas D. Multistage sampling for latent variable models. Lifetime Data Anal. 2007 Dec; 13(4):565-81. PMID: 17943440.
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    78. Stram DO, Thomas D, Kopecky KJ. Hypothesis testing, statistical power, and confidence limits in the presence of epistemic uncertainty. Health Phys. 2007 Oct; 93(4):326-7; author reply 327-8. PMID: 17846531.
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    79. Thomas D, Lawlor DA, Thompson JR. Re: Estimation of bias in nongenetic observational studies using "Mendelian triangulation" by Bautista et al. Ann Epidemiol. 2007 Jul; 17(7):511-3. PMID: 17466535.
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    80. Thomas D, Witte JS, Greenland S. Dissecting effects of complex mixtures: who's afraid of informative priors? Epidemiology. 2007 Mar; 18(2):186-90. PMID: 17301703.
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    81. Thomas D, Jerrett M, Kuenzli N, Louis TA, Dominici F, Zeger S, Schwarz J, Burnett RT, Krewski D, Bates D. Bayesian model averaging in time-series studies of air pollution and mortality. J Toxicol Environ Health A. 2007 Feb 01; 70(3-4):311-5. PMID: 17365593.
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    82. Swartz MD, Thomas D, Daw EW, Albers K, Charlesworth JC, Dyer TC, Fridley BL, Govil M, Kraft P, Kwon S, Logue MW, Oh C, Pique-Regi R, Saba L, Schumacher FR, Uh HW. Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15. Genet Epidemiol. 2007; 31 Suppl 1:S96-102. PMID: 18046760.
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    83. Haile RW, Thomas D, McGuire V, Felberg A, John EM, Milne RL, Hopper JL, Jenkins MA, Levine AJ, Daly MM, Buys SS, Senie RT, Andrulis IL, Knight JA, Godwin AK, Southey M, McCredie MR, Giles GG, Andrews L, Tucker K, Miron A, Apicella C, Tesoriero A, Bane A, Pike MC. BRCA1 and BRCA2 mutation carriers, oral contraceptive use, and breast cancer before age 50. Cancer Epidemiol Biomarkers Prev. 2006 Oct; 15(10):1863-70. PMID: 17021353.
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    84. Thomas D. High-volume "-omics" technologies and the future of molecular epidemiology. Epidemiology. 2006 Sep; 17(5):490-1. PMID: 16906051.
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    85. Thomas D, Stram DO. An utter refutation of the "Fundamental Theorem of the HapMap" by Terwilliger and Hiekkalinna. Eur J Hum Genet. 2006 Dec; 14(12):1238-9. PMID: 16883307.
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    86. McGuire V, John EM, Felberg A, Haile RW, Boyd NF, Thomas D, Jenkins MA, Milne RL, Daly MB, Ward J, Terry MB, Andrulis IL, Knight JA, Godwin AK, Giles GG, Southey M, West DW, Hopper JL, Whittemore AS. No increased risk of breast cancer associated with alcohol consumption among carriers of BRCA1 and BRCA2 mutations ages <50 years. Cancer Epidemiol Biomarkers Prev. 2006 Aug; 15(8):1565-7. PMID: 16896052.
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    87. Wang H, Thomas D, Pe'er I, Stram DO. Optimal two-stage genotyping designs for genome-wide association scans. Genet Epidemiol. 2006 May; 30(4):356-68. PMID: 16607626.
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    88. Thomas D. Are we ready for genome-wide association studies? Cancer Epidemiol Biomarkers Prev. 2006 Apr; 15(4):595-8. PMID: 16614096.
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    89. Thomas D, Haile RW, Duggan D. Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet. 2005 Sep; 77(3):337-45. PMID: 16080110; PMCID: PMC1226200.
    90. Thomas D. Why do estimates of the acute and chronic effects of air pollution on mortality differ? J Toxicol Environ Health A. 2005 Jul 9-23; 68(13-14):1167-74. PMID: 16024495.
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    91. Berstein JL, Concannon P, Langholz B, Thompson WD, Bernstein L, Stovall M, Thomas D. Multi-center screening of mutations in the ATM gene among women with breast cancer - the WECARE Study. Radiat Res. 2005 Jun; 163(6):698-9. PMID: 16044499.
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    92. Rondeau V, Berhane K, Thomas D. A three-level model for binary time-series data: the effects of air pollution on school absences in the Southern California Children's Health Study. Stat Med. 2005 Apr 15; 24(7):1103-15. PMID: 15558697.
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    93. Thomas D. The need for a systematic approach to complex pathways in molecular epidemiology. Cancer Epidemiol Biomarkers Prev. 2005 Mar; 14(3):557-9. PMID: 15767327.
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    94. McKean-Cowdin R, Spencer Feigelson H, Xia LY, Pearce CL, Thomas D, Stram DO, Henderson BE. BRCA1 variants in a family study of African-American and Latina women. Hum Genet. 2005 May; 116(6):497-506. PMID: 15726418.
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    95. Easton DF, Hopper JL, Thomas D, Antoniou A, Pharoah PD, Whittemore AS, Haile RW. Breast cancer risks for BRCA1/2 carriers. Science. 2004 Dec 24; 306(5705):2187-91; author reply 2187-91. PMID: 15622557.
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    96. Ahsan H, Thomas D. Lung cancer etiology: independent and joint effects of genetics, tobacco, and arsenic. JAMA. 2004 Dec 22; 292(24):3026-9. PMID: 15613673.
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    97. Kraft P, Thomas D. Case-sibling gene-association studies for diseases with variable age at onset. Stat Med. 2004 Dec 15; 23(23):3697-712. PMID: 15534888.
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    98. Thomas D, Xie R, Gebregziabher M. Two-Stage sampling designs for gene association studies. Genet Epidemiol. 2004 Dec; 27(4):401-14. PMID: 15543639.
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    99. Rebbeck TR, Ambrosone CB, Bell DA, Chanock SJ, Hayes RB, Kadlubar FF, Thomas D. SNPs, haplotypes, and cancer: applications in molecular epidemiology. Cancer Epidemiol Biomarkers Prev. 2004 May; 13(5):681-7. PMID: 15159297.
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    100. Thomas D, Clayton DG. Betting odds and genetic associations. J Natl Cancer Inst. 2004 Mar 17; 96(6):421-3. PMID: 15026459.
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    101. Bernstein JL, Langholz B, Haile RW, Bernstein L, Thomas D, Stovall M, Malone KE, Lynch CF, Olsen JH, Anton-Culver H, Shore RE, Boice JD, Berkowitz GS, Gatti RA, Teitelbaum SL, Smith SA, Rosenstein BS, Børresen-Dale AL, Concannon P, Thompson WD. Study design: evaluating gene-environment interactions in the etiology of breast cancer - the WECARE study. Breast Cancer Res. 2004; 6(3):R199-214. PMID: 15084244; PMCID: PMC400669.
    102. Thomas D, Conti DV. Commentary: the concept of 'Mendelian Randomization'. Int J Epidemiol. 2004 Feb; 33(1):21-5. PMID: 15075141.
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    103. Cortessis V, Thomas D. Toxicokinetic genetics: an approach to gene-environment and gene-gene interactions in complex metabolic pathways. IARC Sci Publ. 2004; (157):127-50. PMID: 15055294.
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    104. Gee C, Morrison JL, Thomas D, Gauderman WJ. Segregation and linkage analysis for longitudinal measurements of a quantitative trait. BMC Genet. 2003 Dec 31; 4 Suppl 1:S21. PMID: 14975089; PMCID: PMC1866456.
    105. Daw EW, Morrison J, Zhou X, Thomas D. Genetic Analysis Workshop 13: simulated longitudinal data on families for a system of oligogenic traits. BMC Genet. 2003 Dec 31; 4 Suppl 1:S3. PMID: 14975071; PMCID: PMC1866465.
    106. Conti DV, Cortessis V, Molitor J, Thomas D. Bayesian modeling of complex metabolic pathways. Hum Hered. 2003; 56(1-3):83-93. PMID: 14614242.
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    107. Stram DO, Leigh Pearce C, Bretsky P, Freedman M, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Thomas D. Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered. 2003; 55(4):179-90. PMID: 14566096.
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    108. Badzioch MD, Thomas D, Jarvik GP. Summary report: Missing data and pedigree and genotyping errors. Genet Epidemiol. 2003; 25 Suppl 1:S36-42. PMID: 14635167.
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    109. Thomas D, Stram DO, Conti D, Molitor J, Marjoram P. Bayesian spatial modeling of haplotype associations. Hum Hered. 2003; 56(1-3):32-40. PMID: 14614236.
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    110. Langholz B, Ebi KL, Thomas D, Peters JM, London SJ. Traffic density and the risk of childhood leukemia in a Los Angeles case-control study. Ann Epidemiol. 2002 Oct; 12(7):482-7. PMID: 12377426.
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    111. Thomas D, Witte JS. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 2002 Jun; 11(6):505-12. PMID: 12050090.
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    112. Berhane K, Thomas D. A two-stage model for multiple time series data of counts. Biostatistics. 2002 Mar; 3(1):21-32. PMID: 12933621.
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    113. Thomas D. Genetic epidemiology with a capital "E". Genet Epidemiol. 2000 Dec; 19(4):289-300. PMID: 11108640.
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