Highlighted Publications [first or senior or correspondence author]
- The full list of >80 publications can be downloaded here: James Dai’s Bibliography
Cancer genomics and genetic epidemiology
Wang X, Gharahkhani P, Levin DM, Fitzgerald RC, …, Whiteman DC, MacGregor S, Schumacher J, Vaughan TL, Buas MF, Dai JY. eQTL set-based association analysis identifies novel susceptibility loci for Barrett’s esophagus and esophageal adenocarcinoma. Cancer Epidemiology, Biomarker and Prevention 2022;31(9):1735-1745. PubMed Link
Wang X, Jordahl KM, Zhu C, Livingstone J, Rhie SK, Wright JL, Grady WM, Boutros PC, Stanford JL, Dai JY. Methylation subtypes of primary prostate cancer predict poor prognosis. Cancer Epidemiology, Biomarker and Prevention 2022;31(7):1473-1482. PubMed Link
Dai JY, Wang X, Wang B, Sun W, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Feng Z, Stanford JL. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. PLoS Genetics 2020;16(3):e1008667. PubMed Link
Wang X, Crasso CS, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Troyer DA, Lance R, Feng Z, Dai JY, Stanford JL. Copy number alterations are associated with metastatic lethal progression in prostate cancer. Prostate Cancer and Prostatic Diseases 2020;23:494-506.PubMed Link
Dai JY, Wang B, Wang X, Cheng A, Kolb S, Wright JL, Stanford JL. Physical activity is associated with lower risk of metastatic-lethal prostate cancer outcomes and hypomethylation in the CRACR2A gene. Cancer Epidemiology, Biomarker and Prevention 2019;28(2):258-264.PubMed Link
Vaughan TL, Onstad L, Dai JY. Interactive Decision Support for Esophageal Adenocarcinoma Screening and Surveillance. BMC Gastroenterology 2019;19(1):109. PubMed Link
Cheng A, Zhao S, Wright JL, Kolb S, Karnes RJ, Jenkins RB, Davicioni E, Feng Z, Fan J-B, Dai JY, Stanford JL. A four-gene transcript score to predict metastatic progression in men treated for localized prostate cancer: development and validation studies. Prostate 2019;79(14):1589-1596. PubMed Link
Dai JY, LeBlanc M, Goodman PJ, Lucia MS, Thompson IM, Tangen CM. Case-only methods identified genetic loci predicting a subgroup of men with reduced risk of high-grade prostate cancer by finasteride. Cancer Prevention Research 2019;12(2):113-120. PubMed Link
Dai JY, Wang X, Ma J, Wei B, Zhang C, Sun X, Self S, Yao L, Odze RD, Vaughan T, Guo Y. Whole-genome sequencing of esophageal adenocarcinoma in China reveals distinct mutation signatures and genomic alterations. Communication Biology 2018;1:174. PubMed Link
Dai JY, Tapsoba JDT, Buas MF, the BEACON Consortium, Risch H, Vaughan TL. Constrained score statistics identify genetic loci interacting with multiple risk factors in Barrett’s esophagus. American Journal of Human Genetics 2016;99(2):352-365. PubMed Link
Wang X, Li X, Paulson TG, Reid BJ, Kooperberg C, Dai JY. Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma. Human Genomics 2015; 9:22. PubMed Link
Dai JY, Tapsoba JDT, Buas MF, Onstad L, Levine DM, Risch HA, Chow WH, Bernstein L, Ye W, Lagergren J, Bird NC, Corley DA, Shaheen NJ, Wu AH, Hardie LJ, Reid BJ, Whiteman DC, Vaughan TL. A newly identified susceptibility locus near FOXP1 modifies the association of gastroesophageal reflux with Barrett’s esophagus. Cancer Epidemiology, Biomarker & Prevention 2015; 24(11):1739-47. 2015; 9:22. PubMed Link
Methodologies in causal inference, clinical trials, and precision medicine
Dai JY, Stanford JL. LeBlanc M. A multiple-testing procedure for high-dimensional mediation analyses. Journal of American Statistical Association: Theory and Methods 2022;117(537):198-213. PubMed Link
Dai JY, LeBlanc M. Case-only trees and random forests for exploring gene-treatment interactions in randomized clinical trials. Journal of Royal Statistical Society, Series C 2019;68(5):1371-1391. PubMed Link
Wang CY, Dai JY. Best linear inverse probability weighted estimation for two-phase designs and missing covariate regression. Statistics in Medicine 2019;38(15):2783-96. PubMed Link
Dai JY, Peters U, Wang X, Kocarnik J, Chang-Claude J, Slattery ML, Chan A, Lemire M, Berndt SI, Casey G, Song M, Jenkins MA, Brenner H, Thrift AP, White E, Hsu L. Diagnostics of pleiotropy in Mendelian randomization studies: global and individual tests for direct effects. American Journal of Epidemiology 2018;187(12):2672-2680. PubMed Link
Dai JY, Liang J, LeBlanc M, Prentice RL, Janes H. Case-only approach to identifying markers predicting treatment effects on the relative risk scale. Biometrics 2017;74(2):753-763. PubMed Link
Wang X, Dai JY. TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials. Bioinformatics 2016;32(21):3348-3350. PubMed Link
Dai JY, Zhang X, Wang CY, Kooperberg C. Augmented case-only design for randomized clinical trials with failure time endpoints. Biometrics 2016; 72(1):30-8. PubMed Link
Dai JY, Zhang X. Mendelian randomization studies for a continuous exposure under case-control sampling. American Journal of Epidemiology 2015;181(6):440-449. PubMed Link
Dai JY, Chan KC, Hsu L. Testing concordance of instrumental variable effects in generalized linear models with application to Mendelian randomization. Statistics in Medicine 2014; 33(23):3986-4007. PubMed Link
Tapsoba JD, Kooperberg C, Reiner AP, Wang CY, Dai JY. Robust estimation for secondary trait association in case-control genetic studies. American Journal of Epidemiology 2014;179(10):1264-72. PubMed Link
Dai JY, Li SS, Gilbert PB. Case-only methods for competing risks models with application to assessing differential vaccine efficacy by viral and host genetics. Biostatistics 2014; 15(1):196-203. PubMed Link
Dai JY, Gilbert PB, Hughes JP, Brown E. Estimating PrEP efficacy for HIV prevention among participants with a threshold level of drug concentration. American Journal of Epidemiology 2013; 177(3):256-263. PubMed Link
Dai JY, Kooperberg C, LeBlanc M, Prentice RL. Two-stage testing procedures with independent filtering for genome-wide gene-environment interaction. Biometrika 2012; 99(4):929-944. PubMed Link
Dai JY, Logsdon B, Huang Y, Hsu L, Reiner A, Prentice R, Kooperberg C. Simultaneously testing for marginal genetic association and gene-environment interaction. American Journal of Epidemiology 2012;176:164-173. PubMed Link
Dai JY, Gilbert PB, Masse BR. Partially hidden Markov model for time-varying principal stratification in HIV prevention trials. Journal of American Statistical Association 2012;107:52-65. PubMed Link
Lumley T, Shaw PA, Dai JY. Connections between Survey Calibration Estimators and Semiparametric Models for Incomplete Data. International Statistical Review 2011; 79(2):200-20. PubMed Link
Dai JY, LeBlanc M, Smith NL, Psaty B, Kooperberg C. SHARE: an adaptive algorithm to select the most informative set of SNPs for candidate genetic association. Biostatistics 2009; 10(4):680-93. PubMed Link
Dai JY, LeBlanc M, Kooperberg C. Semiparametric estimation exploiting covariate independence in two-phase randomized trials. Biometrics 2009; 65(1):178-87. PubMed Link
Dai JY, Ruczinski I, LeBlanc M, Kooperberg C. Imputation methods to improve inference in SNP association studies. Genetic Epidemiology 2006; 30(8):690-702. PubMed Link