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Thomas Hoffmann, PhD

Title(s)Associate Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
Phone415-476-2475
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    Collapse Biography 
    Collapse Education and Training
    University of Wisconsin MadisonBS06/2004Computer Science, Mathematics, Statistics
    Harvard UniversityAM06/2006Biostatistics
    Harvard UniversityPhD06/2009Biostatistics
    University of California San FranciscoPost-doc08/2011Biostatistics and Genetic Epidemiology

    Collapse Overview 
    Collapse Overview
    I have a broad background in statistics, genetics, and computer science, have been involved in a wide variety of theoretical and applied projects. My my applied work encompasses a wide variety of genetic association studies related to human health, including work on age-related hearing impairment, cardiovascular disease, and cancer. Driven by my applied research, my methodological work includes imputation, array design, rare variants, gene-environment interaction, and study design, and I have produced software packages that implement the methodology in these works so other researchers can freely use them.

    Collapse Research 
    Collapse Research Activities and Funding
    Sequencing not required: Imputing rare variants into a cohort of 100,000 on aging
    NIH/NIA R21AG046616Sep 30, 2013 - Jun 30, 2015
    Role: Principal Investigator
    Genome-wide Study of Hearing Impairment
    NIH/NIDCD K01DC013300Jul 1, 2013 - Jun 30, 2018
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    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.
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    1. Ley B, Torgerson DG, Oldham JM, Adegunsoye A, Liu S, Li J, Elicker BM, Henry TS, Golden JA, Jones KD, Dressen A, Yaspan BL, Arron JR, Noth I, Hoffmann TJ, Wolters PJ. Rare Protein-altering Telomere-related Gene Variants in Patients with Chronic Hypersensitivity Pneumonitis. Am J Respir Crit Care Med. 2019 Jul 03. PMID: 31268371.
      View in: PubMed
    2. Du Z, Hopp H, Ingles SA, Huff C, Sheng X, Weaver B, Stern M, Hoffmann TJ, John EM, Van Den Eeden SK, Strom S, Leach RJ, Thompson IM, Witte JS, Conti DV, Haiman CA. A genome-wide association study of prostate cancer in Latinos. Int J Cancer. 2019 Jun 21. PMID: 31226226.
      View in: PubMed
    3. Jorgenson E, Matharu N, Palmer MR, Yin J, Shan J, Hoffmann TJ, Thai KK, Zhou X, Hotaling JM, Jarvik GP, Ahituv N, Wessells H, Van Den Eeden SK. Reply to Liu et al.: Tissue specificity of SIM1 gene expression and erectile dysfunction. Proc Natl Acad Sci U S A. 2019 02 26; 116(9):3349-3350. PMID: 30755537.
      View in: PubMed
    4. Jorgenson E, Matharu N, Palmer MR, Yin J, Shan J, Hoffmann TJ, Thai KK, Zhou X, Hotaling JM, Jarvik GP, Ahituv N, Wessells H, Van Den Eeden SK. Genetic variation in the SIM1 locus is associated with erectile dysfunction. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11018-11023. PMID: 30297428.
      View in: PubMed
    5. Oni-Orisan A, Hoffmann TJ, Ranatunga D, Medina MW, Jorgenson E, Schaefer C, Krauss RM, Iribarren C, Risch N. Characterization of Statin Low-Density Lipoprotein Cholesterol Dose-Response Using Electronic Health Records in a Large Population-Based Cohort. Circ Genom Precis Med. 2018 Sep; 11(9):e002043. PMID: 30354326.
      View in: PubMed
    6. Hoffmann TJ, Choquet H, Yin J, Banda Y, Kvale MN, Glymour M, Schaefer C, Risch N, Jorgenson E. A Large Multiethnic Genome-Wide Association Study of Adult Body Mass Index Identifies Novel Loci. Genetics. 2018 10; 210(2):499-515. PMID: 30108127.
      View in: PubMed
    7. Choquet H, Paylakhi S, Kneeland SC, Thai KK, Hoffmann TJ, Yin J, Kvale MN, Banda Y, Tolman NG, Williams PA, Schaefer C, Melles RB, Risch N, John SWM, Nair KS, Jorgenson E. A multiethnic genome-wide association study of primary open-angle glaucoma identifies novel risk loci. Nat Commun. 2018 06 11; 9(1):2278. PMID: 29891935.
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    8. Hoffmann TJ, Theusch E, Haldar T, Ranatunga DK, Jorgenson E, Medina MW, Kvale MN, Kwok PY, Schaefer C, Krauss RM, Iribarren C, Risch N. A large electronic-health-record-based genome-wide study of serum lipids. Nat Genet. 2018 Mar; 50(3):401-413. PMID: 29507422.
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    9. Choquet H, Thai KK, Yin J, Hoffmann TJ, Kvale MN, Banda Y, Schaefer C, Risch N, Nair KS, Melles R, Jorgenson E. A large multi-ethnic genome-wide association study identifies novel genetic loci for intraocular pressure. Nat Commun. 2017 12 13; 8(1):2108. PMID: 29235454.
      View in: PubMed
    10. Wu YH, Graff RE, Passarelli MN, Hoffman JD, Ziv E, Hoffmann TJ, Witte JS. Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics. Cancer Epidemiol Biomarkers Prev. 2018 01; 27(1):75-85. PMID: 29150481.
      View in: PubMed
    11. Conti DV, Wang K, Sheng X, Bensen JT, Hazelett DJ, Cook MB, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Stevens VL, Berndt SI, Huff CD, Wang Z, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas C, Stern MC, Jarai ZK, Govindasami K, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann T, Drake BF, Hu JJ, Clark PE, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJM, Han Y, Lubwama A, Thompson IM, Leach R, Easton DF, Schumacher F, Van den Berg DJ, Gundell SM, Stram A, Wan P, Xia L, Pooler LC, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten J, Kibel AS, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Klein EA, Brureau L, Stram DO, Watya S, Chanock SJ, Witte JS, Blot WJ, Henderson BE, Haiman CA. Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry. J Natl Cancer Inst. 2017 08 01; 109(8). PMID: 29117387.
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    12. Wade M, Prime H, Hoffmann TJ, Schmidt LA, O'Connor TG, Jenkins JM. Birth weight interacts with a functional variant of the oxytocin receptor gene (OXTR) to predict executive functioning in children. Dev Psychopathol. 2018 02; 30(1):203-211. PMID: 28511728.
      View in: PubMed
    13. Jorgenson E, Thai KK, Hoffmann TJ, Sakoda LC, Kvale MN, Banda Y, Schaefer C, Risch N, Mertens J, Weisner C, Choquet H. Genetic contributors to variation in alcohol consumption vary by race/ethnicity in a large multi-ethnic genome-wide association study. Mol Psychiatry. 2017 09; 22(9):1359-1367. PMID: 28485404.
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    14. Hoffmann TJ, Passarelli MN, Graff RE, Emami NC, Sakoda LC, Jorgenson E, Habel LA, Shan J, Ranatunga DK, Quesenberry CP, Chao CR, Ghai NR, Aaronson D, Presti J, Nordström T, Wang Z, Berndt SI, Chanock SJ, Mosley JD, Klein RJ, Middha M, Lilja H, Melander O, Kvale MN, Kwok PY, Schaefer C, Risch N, Van Den Eeden SK, Witte JS. Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer. Nat Commun. 2017 01 31; 8:14248. PMID: 28139693.
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    15. Hoffmann TJ, Ehret GB, Nandakumar P, Ranatunga D, Schaefer C, Kwok PY, Iribarren C, Chakravarti A, Risch N. Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. Nat Genet. 2017 01; 49(1):54-64. PMID: 27841878.
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    16. Hoffmann TJ, Keats BJ, Yoshikawa N, Schaefer C, Risch N, Lustig LR. A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records. PLoS Genet. 2016 Oct; 12(10):e1006371. PMID: 27764096.
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    17. Wade M, Hoffmann TJ, Knafo-Noam A, O'Connor TG, Jenkins JM. Oxytocin and vasopressin hormone genes in children's externalizing problems: A cognitive endophenotype approach. Horm Behav. 2016 06; 82:78-86. PMID: 27155104.
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    18. Lindquist KJ, Paris PL, Hoffmann TJ, Cardin NJ, Kazma R, Mefford JA, Simko JP, Ngo V, Chen Y, Levin AM, Chitale D, Helfand BT, Catalona WJ, Rybicki BA, Witte JS. Mutational Landscape of Aggressive Prostate Tumors in African American Men. Cancer Res. 2016 04 01; 76(7):1860-8. PMID: 26921337; PMCID: PMC4772140 [Available on 04/01/17].
    19. Roberts JD, Dewland TA, Glidden DV, Hoffmann TJ, Arking DE, Chen LY, Psaty BM, Olgin JE, Alonso A, Heckbert SR, Marcus GM. Impact of genetic variants on the upstream efficacy of renin-angiotensin system inhibitors for the prevention of atrial fibrillation. Am Heart J. 2016 05; 175:9-17. PMID: 27179719.
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    20. Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol. 2016 05; 136(5):930-937. PMID: 26829030.
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    21. Jorgenson E, Melles RB, Hoffmann TJ, Jia X, Sakoda LC, Kvale MN, Banda Y, Schaefer C, Risch N, Shen L. Common coding variants in the HLA-DQB1 region confer susceptibility to age-related macular degeneration. Eur J Hum Genet. 2016 07; 24(7):1049-55. PMID: 26733291.
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    22. Domingue BW, Wedow R, Conley D, McQueen M, Hoffmann TJ, Boardman JD. Genome-Wide Estimates of Heritability for Social Demographic Outcomes. Biodemography Soc Biol. 2016; 62(1):1-18. PMID: 27050030.
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    23. Hoffmann TJ, Witte JS. Strategies for Imputing and Analyzing Rare Variants in Association Studies. Trends Genet. 2015 Oct; 31(10):556-563. PMID: 26450338.
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    24. Shen L, Hoffmann TJ, Melles RB, Sakoda LC, Kvale MN, Banda Y, Schaefer C, Risch N, Jorgenson E. Differences in the Genetic Susceptibility to Age-Related Macular Degeneration Clinical Subtypes. Invest Ophthalmol Vis Sci. 2015 Jul; 56(8):4290-9. PMID: 26176866; PMCID: PMC4509058.
    25. Lapham K, Kvale MN, Lin J, Connell S, Croen LA, Dispensa BP, Fang L, Hesselson S, Hoffmann TJ, Iribarren C, Jorgenson E, Kushi LH, Ludwig D, Matsuguchi T, McGuire WB, Miles S, Quesenberry CP, Rowell S, Sadler M, Sakoda LC, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Whitmer RA, Kwok PY, Risch N, Schaefer C, Blackburn EH. Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1061-72. PMID: 26092717.
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    26. Banda Y, Kvale MN, Hoffmann TJ, Hesselson SE, Ranatunga D, Tang H, Sabatti C, Croen LA, Dispensa BP, Henderson M, Iribarren C, Jorgenson E, Kushi LH, Ludwig D, Olberg D, Quesenberry CP, Rowell S, Sadler M, Sakoda LC, Sciortino S, Shen L, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Whitmer RA, Kwok PY, Schaefer C, Risch N. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1285-95. PMID: 26092716; PMCID: PMC4574246.
    27. Kvale MN, Hesselson S, Hoffmann TJ, Cao Y, Chan D, Connell S, Croen LA, Dispensa BP, Eshragh J, Finn A, Gollub J, Iribarren C, Jorgenson E, Kushi LH, Lao R, Lu Y, Ludwig D, Mathauda GK, McGuire WB, Mei G, Miles S, Mittman M, Patil M, Quesenberry CP, Ranatunga D, Rowell S, Sadler M, Sakoda LC, Shapero M, Shen L, Shenoy T, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Wan E, Webster T, Whitmer RA, Wong S, Zau C, Zhan Y, Schaefer C, Kwok PY, Risch N. Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1051-60. PMID: 26092718; PMCID: PMC4574249.
    28. Hoffmann TJ, Van Den Eeden SK, Sakoda LC, Jorgenson E, Habel LA, Graff RE, Passarelli MN, Cario CL, Emami NC, Chao CR, Ghai NR, Shan J, Ranatunga DK, Quesenberry CP, Aaronson D, Presti J, Wang Z, Berndt SI, Chanock SJ, McDonnell SK, French AJ, Schaid DJ, Thibodeau SN, Li Q, Freedman ML, Penney KL, Mucci LA, Haiman CA, Henderson BE, Seminara D, Kvale MN, Kwok PY, Schaefer C, Risch N, Witte JS. A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences. Cancer Discov. 2015 Aug; 5(8):878-91. PMID: 26034056; PMCID: PMC4527942.
    29. Tai CG, Graff RE, Liu J, Passarelli MN, Mefford JA, Shaw GM, Hoffmann TJ, Witte JS. Detecting gene-environment interactions in human birth defects: Study designs and statistical methods. Birth Defects Res A Clin Mol Teratol. 2015 Aug; 103(8):692-702. PMID: 26010994; PMCID: PMC4537677.
    30. Wade M, Hoffmann TJ, Jenkins JM. Gene-environment interaction between the oxytocin receptor (OXTR) gene and parenting behaviour on children's theory of mind. Soc Cogn Affect Neurosci. 2015 Dec; 10(12):1749-57. PMID: 25977357.
      View in: PubMed
    31. Wen CC, Yee SW, Liang X, Hoffmann TJ, Kvale MN, Banda Y, Jorgenson E, Schaefer C, Risch N, Giacomini KM. Genome-wide association study identifies ABCG2 (BCRP) as an allopurinol transporter and a determinant of drug response. Clin Pharmacol Ther. 2015 May; 97(5):518-25. PMID: 25676789; PMCID: PMC4479153.
    32. Virlogeux V, Graff RE, Hoffmann TJ, Witte JS. Replication and heritability of prostate cancer risk variants: impact of population-specific factors. Cancer Epidemiol Biomarkers Prev. 2015 Jun; 24(6):938-43. PMID: 25809866.
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    33. Hoffmann TJ, Sakoda LC, Shen L, Jorgenson E, Habel LA, Liu J, Kvale MN, Asgari MM, Banda Y, Corley D, Kushi LH, Quesenberry CP, Schaefer C, Van Den Eeden SK, Risch N, Witte JS. Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort. PLoS Genet. 2015 Jan; 11(1):e1004930. PMID: 25629170.
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    34. Risch N, Hoffmann TJ, Anderson M, Croen LA, Grether JK, Windham GC. Familial recurrence of autism spectrum disorder: evaluating genetic and environmental contributions. Am J Psychiatry. 2014 Nov 01; 171(11):1206-13. PMID: 24969362.
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    35. Smith RP, Eckalbar WL, Morrissey KM, Luizon MR, Hoffmann TJ, Sun X, Jones SL, Force Aldred S, Ramamoorthy A, Desta Z, Liu Y, Skaar TC, Trinklein ND, Giacomini KM, Ahituv N. Genome-wide discovery of drug-dependent human liver regulatory elements. PLoS Genet. 2014 Oct; 10(10):e1004648. PMID: 25275310.
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    36. Hoffmann TJ, Windham GC, Anderson M, Croen LA, Grether JK, Risch N. Evidence of reproductive stoppage in families with autism spectrum disorder: a large, population-based cohort study. JAMA Psychiatry. 2014 Aug; 71(8):943-51. PMID: 24942798.
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    37. Wade M, Hoffmann TJ, Wigg K, Jenkins JM. Association between the oxytocin receptor (OXTR) gene and children's social cognition at 18 months. Genes Brain Behav. 2014 Sep; 13(7):603-10. PMID: 24916666.
      View in: PubMed
    38. Hoffmann TJ, Tang H, Thornton TA, Caan B, Haan M, Millen AE, Thomas F, Risch N. Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative. Hum Mol Genet. 2014 Dec 15; 23(24):6634-43. PMID: 25027321; PMCID: PMC4240199.
    39. Wade M, Hoffmann TJ, Jenkins JM. Association between the arginine vasopressin receptor 1A (AVPR1A) gene and preschoolers' executive functioning. Brain Cogn. 2014 Oct; 90:116-23. PMID: 25016245.
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    40. Hoffmann TJ, Shaw GM, Stevenson DK, Wang H, Quaintance CC, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Witte JS, O'Brodovich HM. Copy number variation in bronchopulmonary dysplasia. Am J Med Genet A. 2014 Oct; 164A(10):2672-5. PMID: 24975634; PMCID: PMC4167221.
    41. Jenkins MM, Reefhuis J, Gallagher ML, Mulle JG, Hoffmann TJ, Koontz DA, Sturchio C, Rasmussen SA, Witte JS, Richter P, Honein MA. Maternal smoking, xenobiotic metabolizing enzyme gene variants, and gastroschisis risk. Am J Med Genet A. 2014 Jun; 164A(6):1454-63. PMID: 24668907; PMCID: PMC4382863.
    42. Kim MJ, Oksenberg N, Hoffmann TJ, Vaisse C, Ahituv N. Functional characterization of SIM1-associated enhancers. Hum Mol Genet. 2014 Apr 01; 23(7):1700-8. PMID: 24203700.
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    43. Perez MV, Hoffmann TJ, Tang H, Thornton T, Stefanick ML, Larson JC, Kooperberg C, Reiner AP, Caan B, Iribarren C, Risch N. African American race but not genome-wide ancestry is negatively associated with atrial fibrillation among postmenopausal women in the Women's Health Initiative. Am Heart J. 2013 Sep; 166(3):566-72. PMID: 24016508.
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    44. Wang H, St Julien KR, Stevenson DK, Hoffmann TJ, Witte JS, Lazzeroni LC, Krasnow MA, Quaintance CC, Oehlert JW, Jelliffe-Pawlowski LL, Gould JB, Shaw GM, O'Brodovich HM. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. Pediatrics. 2013 Aug; 132(2):290-7. PMID: 23897914; PMCID: PMC3727675.
    45. Coram MA, Duan Q, Hoffmann TJ, Thornton T, Knowles JW, Johnson NA, Ochs-Balcom HM, Donlon TA, Martin LW, Eaton CB, Robinson JG, Risch NJ, Zhu X, Kooperberg C, Li Y, Reiner AP, Tang H. Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. Am J Hum Genet. 2013 Jun 06; 92(6):904-16. PMID: 23726366; PMCID: PMC3675231.
    46. Kaklamani VG, Hoffmann TJ, Thornton TA, Hayes G, Chlebowski R, Van Horn L, Mantzoros C. Adiponectin pathway polymorphisms and risk of breast cancer in African Americans and Hispanics in the Women's Health Initiative. Breast Cancer Res Treat. 2013 Jun; 139(2):461-8. PMID: 23624817.
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    47. Lindquist KJ, Jorgenson E, Hoffmann TJ, Witte JS. The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies. Genet Epidemiol. 2013 May; 37(4):383-92. PMID: 23529720; PMCID: PMC4291231.
    48. Ochs-Balcom HM, Preus L, Wactawski-Wende J, Nie J, Johnson NA, Zakharia F, Tang H, Carlson C, Carty C, Chen Z, Hoffman T, Hutter CM, Jackson RD, Kaplan RC, Li L, Liu S, Neuhouser ML, Peters U, Robbins J, Seldin MF, Thornton TA, Thompson CL, Kooperberg C, Sucheston LE. Association of DXA-derived bone mineral density and fat mass with African ancestry. J Clin Endocrinol Metab. 2013 Apr; 98(4):E713-7. PMID: 23436924; PMCID: PMC3615193.
    49. Thornton T, Tang H, Hoffmann TJ, Ochs-Balcom HM, Caan BJ, Risch N. Estimating kinship in admixed populations. Am J Hum Genet. 2012 Jul 13; 91(1):122-38. PMID: 22748210.
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    50. Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, Lazaruk K, Stein JB, Gilbert DA, Wright C, Lipzen A, Pennacchio LA, Carmichael SL, Witte JS, Shaw GM, Rine J. A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One. 2011; 6(11):e28408. PMID: 22140583; PMCID: PMC3227667.
    51. Kazma R, Hoffmann TJ, Witte JS. Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates. BMC Proc. 2011 Nov 29; 5 Suppl 9:S29. PMID: 22373382.
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    52. Hoffmann TJ, Zhan Y, Kvale MN, Hesselson SE, Gollub J, Iribarren C, Lu Y, Mei G, Purdy MM, Quesenberry C, Rowell S, Shapero MH, Smethurst D, Somkin CP, Van den Eeden SK, Walter L, Webster T, Whitmer RA, Finn A, Schaefer C, Kwok PY, Risch N. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics. 2011 Dec; 98(6):422-30. PMID: 21903159; PMCID: PMC3502750.
    53. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, Cawley S, Chung E, Connell S, Eshragh J, Ewing M, Gollub J, Henderson M, Hubbell E, Iribarren C, Kaufman J, Lao RZ, Lu Y, Ludwig D, Mathauda GK, McGuire W, Mei G, Miles S, Purdy MM, Quesenberry C, Ranatunga D, Rowell S, Sadler M, Shapero MH, Shen L, Shenoy TR, Smethurst D, Van den Eeden SK, Walter L, Wan E, Wearley R, Webster T, Wen CC, Weng L, Whitmer RA, Williams A, Wong SC, Zau C, Finn A, Schaefer C, Kwok PY, Risch N. Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics. 2011 Aug; 98(2):79-89. PMID: 21565264.
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    54. Kompass KS, Hoffmann TJ, Witte JS. Parallel biocomputing. Source Code Biol Med. 2011 Mar 18; 6:4. PMID: 21418580; PMCID: PMC3068083.
    55. Hoffmann TJ, Vansteelandt S, Lange C, Silverman EK, DeMeo DL, Laird NM. Combining disease models to test for gene-environment interaction in nuclear families. Biometrics. 2011 Dec; 67(4):1260-70. PMID: 21401569.
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    56. Hoffmann TJ.J Stat Softw. Parsing in command line arguments and parallel cluster/multicore batching in R with batch. 2011; 39.
    57. Hoffmann TJ. Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch. J Stat Softw. 2011 Mar; 39. PMID: 25431538.
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    58. Witte JS, Hoffmann TJ. Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer. OMICS. 2011 Jun; 15(6):393-8. PMID: 21348634; PMCID: PMC3125548.
    59. Hoffmann TJ, Marini NJ, Witte JS. Comprehensive approach to analyzing rare genetic variants. PLoS One. 2010 Nov 03; 5(11):e13584. PMID: 21072163; PMCID: PMC2972202.
    60. Sebro R, Hoffman TJ, Lange C, Rogus JJ, Risch NJ. Testing for non-random mating: evidence for ancestry-related assortative mating in the Framingham heart study. Genet Epidemiol. 2010 Nov; 34(7):674-9. PMID: 20842694; PMCID: PMC3775670.
    61. Cho MH, Washko GR, Hoffmann TJ, Criner GJ, Hoffman EA, Martinez FJ, Laird N, Reilly JJ, Silverman EK. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation. Respir Res. 2010 Mar 16; 11:30. PMID: 20233420.
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    62. Hoffmann TJ, Lange C, Vansteelandt S, Raby BA, DeMeo DL, Silverman EK, Weiss ST, Laird NM. Parsing the effects of individual SNPs in candidate genes with family data. Hum Hered. 2010; 69(2):91-103. PMID: 19996607.
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    63. Hoffmann TJ, Lange C, Vansteelandt S, Laird NM. Gene-environment interaction tests for dichotomous traits in trios and sibships. Genet Epidemiol. 2009 Dec; 33(8):691-9. PMID: 19365860.
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    64. Hoffmann TJ, Laird NM. fgui: A Method for Automatically Creating Graphical User Interfaces for Command-Line R Packages. J Stat Softw. 2009 Apr 01; 30(2). PMID: 21625291.
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    65. Hoffmann T, Lange C. P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R. Bioinformatics. 2006 Dec 15; 22(24):3103-5. PMID: 17021156.
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