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Danyu Lin’s publications on Google Scholar

In Press

Lin, DY, Xu Y, Gu Y, Zeng D, Sunny S, Moore Z. Durability of Bivalent Boosters against Omicron Subvariants. N Engl J Med.

Lin DY, Gu Y, Xu Y, Zeng D, Wheeler B, Young H, Sunny SK, Moore Z. Effects of Vaccination and Previous Infection on Omicron Infections in Children. N Engl J Med. PMCID: 9511630.

Yang H, Lin DY, Li Q (2021). An efficient greedy search algorithm for high-dimensional linear discriminant analysis. Statistica Sinica.

Wong KY, Zeng D, Lin DY: Variable selection for multiple types of high-dimensional features with missing data. Statistica Sinica.

Xu Y, Zeng D, Lin DY: Marginal proportional hazards models for multivariate interval-censored data. Biometrika.


Kidd J, Raulerson CK, Mohlke KL, Lin DY. Meditation analysis of multiple mediators with incomplete omics data. Vol. 47,1 (2023): 61-77. Genetic Epidemiology.

Wang X, Zein J, Ji X, Lin DY: Impact of vaccination, prior infection and therapy on Omicron Infection and mortality. The Journal of Infectious Diseases. Vol. 227,8 (2023): 970-976.

Young KL, Fisher V, Deng X, Brody JA, Graff M, Lim E, Lin BM, Xu H, Amin N, An P, Aslibekyan S, Fohner AE, Hidalgo B, Lenzini P, Kraaij R, Medina-Gomez C, Prokić I, Rivadeneira F, Sitlani C, Tao R, van Rooij J, Zhang D, Broome JG, Buth EJ, Heavner BD, Jain D, Smith AV, Barnes K, Boorgula MP, Chavan S, Darbar D, De Andrade M, Guo X, Haessler J, Irvin MR, Kalyani RR, Kardia SLR, Kooperberg C, Kim W, Mathias RA, McDonald ML, Mitchell BD, Peyser PA, Regan EA, Redline S, Reiner AP, Rich SS, Rotter JI, Smith JA, Weiss S, Wiggins KL, Yanek LR, Arnett D, Heard-Costa NL, Leal S, Lin D, McKnight B, Province M, van Duijn CM, North KE, Cupples LA, Liu CT: Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants. HGG Advances 4: 100163, 2023. PMCID: PMC9772568.


Lin DY, Zeng D, Gu Y, Krause P, Fleming TR. Reliably assessing duration of protection for COVID-19 vaccines. The Journal of Infectious Diseases. Vol. 226,11 (2022): 1863-1866. PMCID: 9383791.

Lin DY, Zeng D. Maximum likelihood estimation of semiparametric regression models with interval-censored data. In Emerging Topics in Modeling Interval-Censored Survival Data, eds. J Sun & D. G. Chen, pp. 107-122. Springer.

Lin DY. Response to the Letter to the Editor by Ladhani et al on “More on Omicron Infections in Children”. N Engl J Med 2022; 387:1911-1912.

Lin DY, Gu Y, Zeng D, Janes HE, Gilbert PB (2021): Evaluating vaccine efficacy against SARS-CoV-2 infection. Clinical Infectious Diseases. 74: 544-552, 2022. PMCID: PMC8057249.

Wong KY, Zeng D, Lin DY. Semiparametric latent-class models for multivariate longitudinal and survival data. The Annals of Statistics. 50: 487-510, 2022. PMCID: PMC9269993.

Quintanilha JCF, Wang J, Sibley AB, Xu W, Espin-Garcia 0, Jiang C, Etheridge AS, Ratain MJ, Lenz HJ, Bertagnolli M, Kindler HL, Dickler MN, Venook A, Liu G, Owzar K, Lin DY, Innocenti F: Genome-wide association studies of survival in 1,520 cancer patients treated with bevacizumab-containing regimens. The International Journal of Cancer. 150: 279-289, 2022. PMCID: PMC8627468.

Quintanilha JCF, Racioppi A, Wang J, Ethridge A, Denning S, Peña C, Skol A, Crona D, Lin DY, Innocenti F: PIK3R5 genetic predictors of hypertension induced by VEGF-pathway inhibitors. The Pharmacogenomics Journal. 22: 82-88, 2022. PMCID: PMC8799524.

Lin DY, Baden LR, El Sahly HM Essink B, Neuzil KM, Corey L, Miller J, for the COVE Study Group:  Durability of protection against symptomatic COVID-19 among participants of the mRNA-1273 SARS-CoV-2 vaccine trial. JAMA Network Open 5: e2215984, 2022. PMCID: PMC9178430.

Lin DY, Gu Y, Wheeler B, Young H, Holloway S, Sunny SK, Moore Z, Zeng D (2021). Effectiveness of Covid-19 vaccines over 9 months in North Carolina. New England Journal of Medicine 386: 933-941, 2022. PMCID: PMC8781317.

Highland HM, Wojcik GL, Graff M, Nishimura KK, Hodonsky CJ, Baldassari AR, Cheng I, Gignoux CR, Tao R, Li Y, Boerwinkle E, Fornage M, Haessler J, Hindorff LA, Hu Y, Justice AE, Lin BM, Lin DY, Stram DO, Haiman CA, Kooperberg C, Le Marchand L, Matise TC, Kenny EE, Carlson CS, Stahl EA, Avery CL, North KE, Ambite JL, Buyske S, Loos RJ, Peters U, Young KL, Bien SA, Huckins LM: Predicted gene expression in ancestrally diverse populations leads to discovery of novel susceptibility loci for lifestyle and cardiometabolic traits. The American Journal of Human Genetics 109: 669-679, 2022. PMCID: PMC9069067.

Wang R, Lin DY, Jiang Y: EPIC: inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing. PLOS Genetics 18: e1010251, 2022. PMCID: PMC9242467.

Wang J, Zeng D, Lin DY: Semiparametric single-index models for optimal treatment regimens with censored outcomes. Lifetime Data Analysis 28: 744-763, 2022.

Lin DY, Gu Y, Xu Y, Zeng D, Wheeler B, Young H, Sunny SK, Moore Z: Effects of vaccination and previous infection on omicron infections in children. New England Journal of Medicine 387: 1141-1143, 2022.

Lin DY, Gu Y, Xu Y, Wheeler B, Young H, Sunny SK, Moore Z, Zeng D: Association of primary and booster vaccination and prior infection with SARS-CoV-2 infection and severe COVID-19 outcomes. Journal of the American Medical Association 328: 1415-1426, 2022. PMCID: PMC9513711


Lin DY, Gu Y, Wheeler B, Young H, Holloway S, Sunny SK, Moore Z, Zeng D (2021). Effectiveness of Covid-19 vaccines over 9 months in North Carolina. New England Journal of Medicine. 386: 933-941, 2022. PMCID: PMC8781317.

Raffield LM, Howard AG, Graff M, Lin DY, Cheng S, Demerath E, Ndumele C, Palta P, Rebholz C, Seidelmann S, Yu B, Gordon-Larsen P, North KE, Avery C: Obesity duration, severity, and distribution trajectories and cardiovascular disease risk in the Atherosclerosis Risk in Communities Study. Journal of the American Heart Association 10: e019946, 2021. PMCID: PMC9075238.

Lin DY, Zeng D, Gilbert PB: Evaluating the long-term efficacy of Coronavirus Disease 2019 (COVID-19) vaccines. Clinical Infectious Diseases. 73: 1927-1939, 2021. PMCID: PMC7989522.

Zeng D, Lin DY (2020): Maximum likelihood estimation for semiparametric regression models with panel count data. Biometrika. 108: 947-963, 2021. NIHMSID: NIHMS1672870.

Lin DY, Zeng D, Eron JJ: Evaluating the efficacy of therapies in COVID-19 patients. Clinical Infectious Diseases 72: 1093-1100, 2021. PMCID: PMC7454372.

Hu Y, Bien SA, Nishimura KK, Haessler J, Hodonsky CJ, Baldassari AR, Highland HM, Wang Z, Preuss M, Sitlani CM, Wojcik GL, Tao R, Graff M, Huckins LM, Sun Q, Chen MH, Mousas A, Auer PL, Lettre G, Tang W, Qi L, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin DY, Reiner AP, North KE, Loos RJF, Raffield LM, Peters U, Avery CL, Kooperberg C: Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study. BMC Genomics 22: 432, 2021. PMCID: PMC8191001.

Jin C, Chen M, Lin DY, Sun W: Cell-type-aware analysis of RNA-seq data. Nature Computational Science 1: 253-261, 2021. PMCID: PMC8697413.

Lin BM, Grinde KE, Brody JA, Breeze CE, Raffield LM, Mychaleckyj JC, Thornton TA, Perry JA, Baier LJ, Fuentes LL, Guo X, Heavner BD, Hanson RL, Hung YJ, Qian H, Hsiung CA, Hwang SJ, Irvin MR, Jain D, Kelly TN, Kobes S, Lange L, Lash JP, Li Y, Liu X, Mi X, Musani SK, Papanicolaou GJ, Parsa A, Reiner AP, Salimi S, Sheu WHH, Shuldiner AR, Taylor KD, Smith AV, Smith JA, Tin A, Vaidya D, Wallace RB, Yamamoto K, Sakaue S, Matsuda K, Kamatani Y, Momozawa Y, Yanek LR, Young BA, Zhao W, Okada Y, Abecasis G, Psaty BM, Arnett DK, Boerwinkle E, Cai J, Chen IYD, Correa A, Cupples LA, He J, Kardia SLR, Kooperberg C, Mathias RA, Mitchell BD, Nickerson DA, Turner ST, Ramachandran VS, Rotter JI, Levy D, Kramer HJ, Köttgen A, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Kidney Working Group, Rich SS, Lin DY, Browning SR, Franceschini N: Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. EBIOMed 63: 103157, 2021. PMCID: PMC7804602.


McCabe SD, Lin DY, Love ML: Consistency and overfitting of multi-omics methods on experimental data. Briefings in Bioinformatics 21: 1277-1284, 2020. PMCID: PMC7373174.

Tao R, Zeng D, Lin DY: Optimal designs of two-phase studies. Journal of the American Statistical Association 115: 1946-1959, 2020. PMCID: PMC7954143.

Zeng D, Pan Z, Lin DY: Design and analysis of bridging studies with prior probabilities on the null and alternative hypotheses. Biometrics 76: 224-234, 2020. PMCID: PMC7983026.

Diao G, Lin DY: Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies. BMC Genetics 21: 1-11, 2020. PMCID: PMC7487716.

Hodonsky CJ, Baldassari AR, Bien SA, Raffield LM, Highland HM, Sitlani C, Wojcik GL, Tao R, Graff M, Tang W, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin DY, Reiner AP, North KE, Loos RJF, Kooperberg CL, Avery CL: Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics. BMC Genomics 21: 228, 2020. PMCID: PMC7071748.

Lin DY, Zeng D, Couper D: A general framework for integrative analysis of incomplete multi-omics data. Genetic Epidemiology 44: 646-664, 2020. PMCID: PMC7951090.

Wang R, Lin DY, Jiang Y: SCOPE: a normalization and copy number estimation method for single-cell DNA sequencing. Cell Systems 10: 445-452.e6, 2020. PMCID: PMC7250054.


Wong KY, Zeng D, Lin DY: Robust score tests with missing data in genomics studies. Journal of the American Statistical Association 114: 1778-1786, 2019. PMC6951249

Little PL, Lin DY, Sun W: Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time. Genome Medicine 11: 37, 2019. PMCID: PMC6540540.

Palace J, Lin DY, Zeng D, Majed M, Elsone L, Hamid S, Messina S, Misu T, Sagen J, Whittam D, Yoshiki T, Leite MI, Weinshenker B, Cabre P, Jacob A, Nakashima I, Fujihara K, Pittock SJ: Outcome prediction models in AQP4-IgG positive neuromyelitis optica spectrum disorders. Brain 142: 1310-1323, 2019. PMCID: PMC6487334

Deng Q, Bai X, Liu D, Roy D, Ying Z, Lin DY: Power and sample size for dose-finding studies with survival endpoints under model uncertainty. Biometrics 75: 308-314, 2019. PMCID: PMC6411454.

Gao F, Zeng D, Couper D, Lin DY: Semiparametric Regression Analysis of Multiple Right- and Interval-Censored Events, Journal of the American Statistical Association 114: 1232-1240, 2019. NIHMS995827.

Raulerson CK, Ko A, Kidd JC, Currin KW, Brotman SM, Cannon ME, Wu Y, Spracklen CN, Jackson AU, Stringham HM, Welch RP, Fuchsberger C, Locke AE, Narisu N, Lusis  AJ, Civelek M, Furey TS, Kuusisto J, Collins FS, Boehnke M, Scott LJ, Lin DY, Love MI, Laakso M, Pajukanta P, Mohlke KL: Adipose tissue gene expression associations reveal hundreds of candidate genes for cardiometabolic traits. The American Journal of Human Genetics 105: 773-787, 2019.

Wojcik GL*, Graff M*, Nishimura KK*, Tao R*, Haessler J*, Gignoux CR*, Highland HM*, Patel YM*, Sorokin EP, Avery CL, Belbin GM, Bien SA, Cheng I, Cullina S, Hodonsky CJ, Hu Y, Huckins LM, Jeff J, Justice AE, Kocarnik JM, Lim U, Lin BM, Lu Y, Nelson SC, Park SSL, Poisner H, Preuss MH, Richard MA, Schurmann C, Setiawan VW, Vahi K, Vishnu A, Verbanck M, Walker R, Young KL, Zubair N, Acuna-Alonso V, Ambite JL, Barnes KC, Boerwinkle E, Bottinger E, Bustamante CD, Caberto C, Canizales-Quinteroes S, Conomos MP, Deelman E, Do R, Doheny K, Fernandez-Rhodes L, Fornage M, Heiss G, Henn B, Hindorff LA, Jackson RD, Hailu B, Laurie CA, Laurie CC, Li Y, Lin DY, Moreno-Estrada A, Nadkarni G, Norman P, Pooler LC, Reiner AP, Romm J, Sabati C, Sandoval K, Sheng X, Stahl EA, Stram DO, Thornton TA, Wassel CL, Wilkens LR, Winkler CA, Yoneyama S, Buyske S, Haiman C, Kooperberg C, Le Marchand L, Loos RJF, Matise TC, North KE, Peters U, Kenny EE, Carlson CS: The PAGE study: how genetic diversity improves our understanding of the architecture of complex traits. Nature 570: 514-518, 2019. *shared first authorship (Dr. Tao is Dr. Lin’s Ph.D. student.).

Gao F, Zeng D, Lin DY: Semiparametric regression analysis of interval-censored data with informative dropout. Biometrics 74: 1213-1222, 2019. PMCID: PMC6309250.

Wong KY, Fan C, Tanioka M, Parker JS, Nobel AB, Zeng D, Lin DY, Perou CM: I-BOOST: an integrative boosting approach for predicting survival time with multiple genomics platforms. Genome Biology 20:52, 2019. PMCID: PMC6404283.

Lin DY: A simple and accurate method to determine genomewide significance for association tests in sequencing studies. Genetic Epidemiology 43: 365-372, 2019. PMCID: PMC6520182.

Lin BM, Nadkarni GN, Tao R, Graff M, Fornage M, Buyske S, Matise TC, Highland H, Wilkens LR, Carlson CS, Park SL, Setiawan VW, Ambite JL, Heiss G, Boerwinkle E, Lin DY, Morris AP, Loos RJF, Kooperberg C, North K, Wassel C, Franceschini N: Genetics of chronic kidney disease stages across ancestries: The PAGE study. Frontiers in Genetics. 10: 494, doi: 10.3389/fgene.2019.00494, 2019. PMCID: PMC6544117.


Hodonsky CJ, Schurmann C, Schick UM, Kocarnik J, Tao R, van Rooij FJA, Wassel C, Buyske S, Fornage M, Hindorff LA, Floyd JS, Ganesh SK, Lin DY, North KE, Reiner AP, Loos RJF, Kooperberg C, Avery CL: Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE Study. American Journal of Hematology, 93: 1061-1073, 2018.

Lin DY: Discussion of the paper by R. L. Prentice and Y. Huang: Optimal designs and efficient inference for biomarker studiesStatistical Theory and Related Fields, 2,: 21–22, 2018.

Wong KY, Zeng D, Lin DY: Efficient Estimation for Semiparametric Structural Equation Models With Censored Data, Journal of the American Statistical Association, 113: 893-905, 2018.

Engeda JC, Holliday KM, Hardy ST, Chakladar S, Lin DY, Talavera GA, Howard BV, Daviglus ML, Pirzada A, Schreiner PJ, Zeng D, Avery CL: Transitions from ideal to intermediate cholesterol levels may vary by cholesterol metric. Scientific Reports, 8: 2782, 2018. PMCID: PMC5807429.

Zeng D, Pan J, Hu K, Chi E, Lin DY: Improving the power to establish clinical similarity in a phase 3 efficacy trial by incorporating prior evidence of analytical and pharmacokinetic similarityJournal of Biopharmaceutical Statistics, 28: 320-332, 2018. PMCID: PMC5909990.

Gong J, Nishimura K, Fernandez-Rhodes L, Haessler J, Bien S, Graff M, Lim U, Lu Y, Gross M, Fornage M, Yoneyama S, Isasi C, Buzkova´ P, Daviglus ML, Lin DY, Tao R, Goodloe R, Bush W, Farber-Eger E, Boston J, Dilks H, Ehret G, Gu C, Lewis C, Nguyen KD, Cooper R, Leppert M, Irvin M, Bottinger E, Wilkens L, Haiman C, Park L, Monroe K, Cheng I, Stram D, Carlson C, Jackson R, Kuller L, Houston D, Kooperberg C, Buyske S, Hindorff L, Crawford D, Loos R, Le Marchand L, Matise T, North K, Peters U: Trans-Ethnic Analysis of Metabochip Data Identifies Two New Loci Associated with BMIInternational Journal of Obesity, 42: 384-390, 2018. PMCID: PMC5876082.

Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin DY: The association between copy number aberration, DNA methylation and gene expression in tumor samplesNucleic Acids Rsearch,46: 3009-3018, 2018. PMCID: PMC5887505.


Tao R, Zeng D, Lin DY: Efficient semiparametric inference under two-phase sampling, with applications to genetic association studies. Journal of the American Statistical Association, 112: 1468-1476, 2017. NIHMSID: NIHMS855879.

Gao F, Zeng D, Lin DY: Semiparametric estimation of the accelerated failure time model with partly interval-censored data. Biometrics, 73: 1161-1168, 2017.

Avery CL, Wassel CL, Richard MA, Highland HM, Bien S, Zubair N, Soliman EZ, Fornage M, Bielinski SJ, Tao R, Seyerle AA, Shah SJ, Lloyd-Jones DM, Buyske S, Rotter JI, Post WS, Rich SS, Hindorff LA, Jeff JM, Shohet RV, Sotoodehnia N, Lin DY, Whitsel EA, Peters U, Haiman CA, Crawford DC, Kooperberg C, North KE: Fine mapping of QT interval regions in global populations refines previously identified QT interval loci and identifies signals unique to African and Hispanic descent populations. Heart Rhythm, 14 :572-580, 2017. PMCID: PMC5448160.

Mao L, Lin DY: Efficient estimation of semiparametric transformation models for the cumulative incidence of competing risks. Journal of the Royal Statistical Society, Series B, 79: 573-587, 2017. PMCID: PMC5319638.

Hardy ST, Holliday KM, Chakladar S, Engeda JC, Allen NB, Heiss G, Lloyd-Jones DM, Schreiner PJ, Shay CM, Lin DY, Zeng D, Avery CL: Heterogeneity in blood pressure transitions over the life course: Age-specific emergence of racial/ethnic and sex disparities in the United States. Journal of the American Medical Association Cardiology, 2: 653-661, 2017. PMCID: PMC5634332

Tang ZZ, Bunn P, Tao R, Liu Z, Lin DY: PreMeta: a tool to facilitate meta-analysis of rare-variant associations. BMC Genomics, 18: 160, 2017. PMCID: PMC5310051.

Holliday KM, Lin DY, Chakladar S, Castañeda SF, Daviglus ML Evenson KR, Marquez DX, Qi Q, Shay CM, Sotres-Alvarez D, Vidot DC, Zeng D, Avery CL: Targeting physical activity interventions for adults: When should intervention occur? Preventive Medicine, 97: 13-18, 2017. PMCID: PMC5337155.

Mao L, Lin DY, Zeng D: Semiparametric regression analysis of interval-censored competing risks data. Biometrics, 73: 857-865, 2017. PMCID: PMC5561531.

Zeng D, Gao F, Lin DY: Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data. Biometrika, 104: 505-525, 2017. PMCID: PMC5787874.



He Q, Zhang HH, Avery CL, Lin DY: Sparse meta-analysis with high-dimensional data. Biostatistics, 17: 205-220, 2016. PMCID: PMC4834947.

Mao Lu, Lin DY: Semiparametric regression for the weighted composite endpoint of recurrent and terminal events. Biostatistics, 17: 390-403, 2016. PMCID: PMC4804115.

Yu B,Pulit SL, Hwang SJ, Brody JA, Amin N, Auer PL, Bis JC, Boerwinkle E, Burke GL, Chakravarti A, Correa A, Dreisbach AW, Ehret GB, Franceschini N, Lin DY, Metcalf GA, Musani SK, Muzny D, Palmas W, Raffel L, Reiner A, Rice K, Rotter JI, Veeraraghavan N, Wilson JG, Fox E, Guo X, North KE, Gibbs RA, van Duijn CM, Psaty BM, Levy D, Newton-Cheh C, Morrison AC, on behalf of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium and the National Heart, Lung, and Blood Institute GO Exome Sequencing Project (ESP): Rare exome sequence variants in CLCN6 reduce blood pressure levels and hypertension risk. Circulation: Cardiovascular Genetics, 9: 64-70, 2016. PMCID: PMC4771070.

Zeng D, Mao L, Lin DY: Maximum likelihood estimation for semiparametric transformation models with interval-censored data. Biometrika, 103: 253-271, 2016. PMCID: PMC4890294.

Kan M, Auer PL, Wang GT, Bucasas KL, Hooker S, Rodriguez A, Li B, Ellis J, Cupples LA, Chen YDI, Dupuis J, Fox C, Gross MD, Smith JD, Heard-Costa N, Meigs JB, Pankow JS, Rotter JI, Siscovick D, Wilson JG, Shendure J, Jackson R, Peters U, Whitsel E, Zhong H, Lin DY, Hsu L, Franceschini N, Carlson C, Abecasis G, Gabriel S, Bamshad MJ, Altshuler D, Nickerson DA, North KE, Lange LA, Reiner AP, NHLBI-Exome Sequencing Project, Leal SM: Rare variant associations with waist-to-hip ratio in European-American and African-American women from the NHLBI-Exome Sequencing Project. European Journal of Human Genetics, 24: 1181-1187, 2016. PMCID: PMC4970686

Lin DY, Gong J, Gallo P, Bunn PH, Couper D: Simultaneous inference on treatment effects in survival studies with factorial designs. Biometrics, 72: 1078-1085, 2016. PMCID: PMC5026867.

Lin DY, Dai L, Cheng G, Sailer MO: On confidence intervals for the hazard ratio in randomized clinical trials. Biometrics, 75: 1098-1102, 2016. PMCID: PMC5085885.

Zubair N, Graff M, Luis Ambite J, Bush WS, Kichaev G, Lu Y, Manichaikul A, Sheu WH, Absher D, Assimes TL, Bielinski SJ, Bottinger EP, Buzkova P, Chuang LM, Chung RH, Cochran B, Dumitrescu L, Gottesman O, Haessler JW, Haiman C, Heiss G, Hsiung CA, Hung YJ, Hwu CM, Juang JJ, Le Marchand L, Lee IT, Lee WJ, Lin LA, Lin D, Lin SY, Mackey RH, Martin LW, Pasaniuc B, Peters U, Predazzi I, Quertermous T, Reiner AP, Robinson J, Rotter JI, Ryckman KK, Schreiner PJ, Stahl E, Tao R, Tsai MY, Waite LL, Wang TD, Buyske S, Ida Chen YD, Cheng I, Crawford DC, Loos RJF, Rich SS, Fornage M, North KE, Kooperberg C, Carty CL: Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Human Molecular Genetics, 25 :5500-5512, 2016.

Avery CL, Holliday KM, Chakladar S, Engeda JC, Hardy ST, Reis JP, Schreiner PJ, Shay CM, Daviglus ML, Heiss G, Lin DY, Zeng D: Disparities in early transitions to obesity in contemporary multi-ethnic U.S. populations. PLOS ONE 11: e0158025, 2016. PMCID: PMC4922630.


The Network and Pathway Analysis Subgroup of the Psychiatric Genomics Consortium: Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nature Neuroscience, 18: 199-209, 2015. PMCID: PMC4378867.

Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium: Genetic differences in the immediate transcriptome response to stress predict risk-related brain function and psychiatric disorders. Neuron 86: 1189-1202, 2015. PMC4490780.

Psychiatric Genomics Consortium and Rheumatoid Arthritis Consortium International: New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. International Journal of Epidemiology 44: 1706-1721, 2015. PMC4881824.

Tao R, Zeng D, Franceschini N, North KE, Boerwinkle E, Lin DY: Analysis of sequence data under multivariate trait-dependent sampling. Journal of the American Statistical Association, 110:560-572, 2015. PMCID: PMC4565625.

Tang ZZ, Lin DY: Meta-analysis for discovering rare-variant associations: statistical methods and software programs. American Journal of Human Genetics, 97: 35-53, 2015. PMCID: PMC4571037.

Zeng D, Lin DY: On random-effects meta-analysis, Biometrika, 102: 281-294, 2015. PMCID: PMC4681410.

Nyante SJ, Gammon MD, Kaufman JS, Bensen JT, Lin DY, Barnholtz-Sloan JS, Hu Y, He Q, Luo J, Millikan RC (2015): Genetic variation in estrogen and progesterone pathway genes and breast cancer risk: an exploration of tumor subtype-specific effects, Cancer Causes & Control, 26: 121-31, 2015. PMCID: PMC4291841

Hu YJ, Li Y, Auer PL, Lin DY (2015): Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations, Proceedings of the National Academy of Sciences, 112: 1019-1024. PMCID: PMC4313847


Franceschini N, Hu Y, Reiner AP, Buyske S, Nalls M, Yanek LR, Li Y, Hindorff LA, Cole SA, Howard BV, Andrews JS, Carty CL, Sethupathy P, Martin LW, Lin DY, Johnson KC, Becker LC, North KE, Dehghan A, Bis JC, Liu Y, Greenland P, Manson J, Maeda N, Garcia M, Harris TB, Becker DM, O’Donnell C, Heiss G, Kooperberg C, Boerwinkle E: Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study, Plos One, 9(12):e113203. doi: 10.1371/journal.pone.0113203, 2014. PMCID: PMC4277270.

Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang ZZ, Bizon C, Lange EM, Smith JD, Turner EH, Jun G, Kang HM, Peloso G, Auer P, Li KP, Flannick H, Zhang J, Fuchsberger C, Gaulton K, Lindgren C, Locke A, Manning A, Sim X, Rivas MA, Holmen OL, Gottesman O, Lu Y, Ruderfer D, Stahl EA, Duan Q, Li Y, Durda P, Jiao S, Isaacs A, Hofman A, Bis JC, Correa A, Griswold ME, Jakobsdottir J, Smith AV, Schreiner PJ, Feitosa MF, Zhang Q, Huffman JE, Crosby J, Wassel CL, Do R, Franceschini N, Martin LW, Robinson JG, Assimes TL, Crosslin DR, Rosenthal EA, Tsai M, Rieder MJ, Farlow DN, Folsom AR, Lumley T, Fox ER, Carlson CS, Peters U, Jackson RD, van Duijn CM, Uitterlinden AG, Levy D, Rotter JI, Taylor Jr HA, Gudnason V, Siscovick DS, Fornage M, Borecki IB, Hayward C, Rudan I, Chen YE, Bottinger EP, Loos RJF, Sætrom P, Hveem K, Boehnke M, Groop L, McCarthy M, Meitinger T, Ballantyne CM, Gabriel SB, O’Donnell CJ, Post WS, North KE, Reiner AP, Boerwinkle E, Psaty MB, Altshuler D, Kathiresan S, Lin DY, et al, on behalf of the NHLBI Exome Sequencing Project (2014): Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. American Journal of Human Genetics, 94: 233-245. PMCID: PMC3928660

Zeng D, Lin DY (2014): Efficient estimation of semiparametric transformation models for two-phase cohort studies. Journal of the American Statistical Association, 109: 371-383, 2014. PMCID: PMC3960088.

Stitziel, NO, Won, HH, Morrison, AC, Peloso, GM, Do, R, Lange, LA, Fontanillas, P, Gupta, N, Duga, S, Goel, A, Farrall, M, Saleheen, D, Ferrario, P, König, I, Asselta, R, Merlini, P, Marziliano, N, Notarangelo, MF, Schick, U, Auer, P, Assimes, TL, Reilly, M, Wilensky, R, Rader, DJ, Hovingh, GK, Meitinger, T, Kessler, T, Kastrati, A, Laugwitz, KL, Siscovick, D, Rotter, JI, Hazen, S, Tracy, R, Cresci, S, Spertus, J, Jackson, R, Schwartz, SM, Natarajan, P, Crosby, J, Muzny, D, Ballantyne, C, Rich, SS, O’Donnell, CJ, Abecasis, G, Sunyaev, S, Nickerson, DA, Buring, JE, Ridker, PM, Chasman, DI, Austin, E, Ye, Z, Kullo, IJ, Weeke, PE, Shaffer, CM, Bastarache, LA, Denny, JC, Roden, DM, Palmer, C, Deloukas, P, Lin, DY, et al, on behalf of The Myocardial Infarction Genetics Consortium (2014): Inactivating mutations in NPC1L1 and protection from coronary heart disease, New England Journal of Medicine, 371: 2072-82, 2014. PMCID: PMC4335708.

Tang ZZ, Lin DY (2014): Meta-analysis of sequencing studies with heterogeneous genetic associationsGenetic Epidemiology, 38: 389-401, 2014. PMCID: PMC4157393.

Crosby, J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA, Lu Y, Tang ZZ, Zhang H, Hindy G, Masca N, Stirrups K, Kanoni S, Do R, Jun G, Hu Y, Kang HM, Xue C, Goel A, Farrall M, Duga S, Merlini PA, Asselta R, Girelli D, Martinelli N, Yin W, Reilly D, Speliotes E, Fox C, Hveem K, Holem O, Nikpay M, NHLBI Exome Sequencing Project, Farlow DN, Assimes TL, Franceschini N, Robinson J, North KE, Martin LW, DePristo M, Gupta N, Escher SA, Jansson JH, Van Zuydam N, Palmer CNA, Wareham N, Koch W, Meitinger T, Peters A, Lieb W, Erbel R, Konig IR, Kruppa J, Degenhardt F, Gottesman O, Bottinger EP, O’Donnell CJ, Psaty BM, Ballantyne CM, Abecasis G, Ordovas JM, Melander O, Watkins H, Orho-Melander M, Ardissino D, Loos RJF, McPherson R, Willer CJ, Erdmann J, Hall AS, Samani NJ, Deloukas P, Schunkert H, Wilson JG, Kooperberg C, Rich SS, Tracy RP, Lin DY, et al (2014): Loss-of-function mutations in APOC3, triglycerides, and coronary disease. New England Journal of Medicine, 371: 22-31. PMCID: PMC4180269.

Lin DY, Tao R, Kalsbeek WD, Zeng D, Gonzalez II, F, Fernandez-Rhodes L, Graff M, Koch GG, North KE, Heiss G (2014): Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos, American Journal of Human Genetics, 95: 675-88, 2014. PMC4259979.

Hu YJ, Lin DY, Sun W, Zeng D (2014): A likelihood-based framework for association analysis of allele-specific copy numbers, Journal of the American Statistical Association, 109: 1533-1545, 2014. PMCID: PMC4315366.

Lin DY (2014): Survival analysis with incomplete genetic data. Lifetime Data Analysis, 20: 16-22, 2014. PMCID: PMC3806886.


Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, et al (2013): Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.  Nature Genetics, 45: 501-512, 2013. PMCID: PMC3973018.

Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium (Sullivan PF, Daly MJ, Ripke S, Lewis CM, Lin DY, et al) (2013): A mega-analysis of genome-wide association studies for major depressive disorder. Molecular Psychiatry, 18: 497-511, 2013, PMCID: PMC3837431.

Cross-Disorder Group of the Psychiatric Genomics Consortium (2013): Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics, 45: 984-994, 2013. PMCID: PMC3800159.

Lin DY (2013): Transformation models. In Handbook of Survival Analysis. J. P. Klein, H. C. van Houwelingen, J. G. Ibrahim, T. H. Scheike, eds., 2013. Chapman and Hall.

Lin DY: (2013) An overview of Ross Prentice’s contributions to statistical science. Statistics in Biosciences, 5: 224-231, 2013. PMCID: PMC3821774.

Tang ZZ, Lin DY (2013): MASS: meta-analysis of score statistics for sequencing studies. Bioinformatics, 29:1803-1805, 2013. PMCID: PMC3702254.

Lin DY, Zeng D, Tang, ZZ on behalf of the NHLBI GO Exome Sequencing Project (2013): Quantitative trait analysis in sequencing studies with trait-dependent sampling. Proceedings of the National Academy of Sciences, 110:12247-12252, 2013. PMCID: PMC3725118.

Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY (2013): Meta-analysis of gene-level associations for rare variants based on single-variant statistics. The American Journal of Human Genetics, 93:236-248, 2013. PMCID: PMC3738834.

He Q, Avery CL, Lin DY (2013): A general framework for association tests with multivariate traits in large-scale genomics studiesGenetic Epidemiology, 37: 759-767. PMCID: PMC3926135


Chen L, Lin DY, Zeng D (2012). Predictive accuracy of covariates for event times. Biometrika, 99:615-630. PMCID: PMC3635702.

Avery CL, Sethupathy P, Buyske S, He Q, Lin DY, et al. (2012). Fine-mapping and initial characterization of QT interval loci in African Americans. PLoS Genetics, 8(8):e1002870. doi:10.1371/journal.pgen.1002870. PMCID: PMC3415454.

Chen L, Lin DY, Zeng D (2012). Checking semiparametric transformation models with censored data. Biostatistics, 13:18-31. PMCID: PMC3276276.


Ripke S, Sanders AR, Kendler KS, Levinson DF, Sklar P, Holmans PA, Lin DY, et al; The Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (2011). Genome-wide association study identifies five new schizophrenia loci. Nature Genetics, 43:969-976. PMCID: PMC3303194.

Sklar P, Ripke S, Scott LJ, Andreassen OA, Cichon S, Craddock N, Edenberg HJ, Nurnberger JI Jr, Rietschel M, Blackwood D, Corvin A, Flickinger M, Guan W, Mattingsdal M, McQuillin A, Kwan P, Wienker TF, Daly M, Dudbridge F, Holmans PA, Lin D, et al; The Psychiatric GWAS Consortium Bipolar Disorder Working Group (2011). Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nature Genetics, 43:977-983. PMCID: PMC3637176.

Avery CL, He QC, North KE, Ambite JL, Boerwinkle E, Fornage M, Hindorff LA, Kooperberg C, Meigs JB, Pankow JS, Pendergrass SA, Psaty BM, Ritchie MD, Rotter JI, Taylor KD, Wilkens LR, Heiss G, Lin DY (2011). A phenomics-based strategy identifies loci on APOC1, BRAP, and PLCG1 associated with metabolic syndrome phenotype domains. PLoS Genetics, 7:e1002322. PMCID: PMC3192835.

Nyante SJ, Gammon MD, Kaufman JS, Bensen JT, Lin DY, Barnholtz-Sloan JS, Hu YJ, He QC, Luo JC, Millikan RC (2011). Common genetic variation in adiponectin, leptin, and leptin receptor and association with breast cancer subtypes. Breast Cancer Research and Treatment, 129:593-606. PMCID: PMC3355661.

Franceschini N, Carty C, Bužková P, Reiner A, Garrett T, Lin Y, Vöckler JS, Hindorff LA, Cole SA, Boerwinkle E, Lin DY, et al. (2011). Association of genetic variants and incident coronary heart disease in multi-ethnic cohorts: The PAGE study. Circulation: Cardiovascular Genetics, 4:661-672. PMCID: PMC3293207.

Lin DY, Zeng D (2011). Correcting for population stratification in genome-wide association studies. Journal of the American Statistical Association, 106:997-1008. PMCID: PMC3314247.

Lin DY, Tang ZZ (2011). A general framework for detecting disease associations with rare variants in sequencing studies. The American Journal of Human Genetics, 89:354-367. PMCID: PMC3169821.

He Q, Lin DY (2011). A variable selection method for genome-wide association studies. Bioinformatics, 27:1-8. PMCID: PMC3025714.

Liu Y, Blackwood DH, Caesar S, de Geus EJC, Farmer A, Ferreira MAR, Ferrier IN, Fraser C, Gordon-Smith K, Green EK, Grozeva D, Gurling HM, Hamshere ML, Heutink P, Holmans PA, Hoogendijk WJ, Hottenga JJ, Jones L, Jones IR, Kirov G, Lin DY, et al. (2011). Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder. Molecular Psychiatry, 16:2-4. PMCID: PMC3883627.


Hu YJ, Lin DY (2010). Analysis of untyped SNPs: Maximum likelihood and imputation methods. Genetic Epidemiology, 34:803-815. PMCID: PMC3030127.

Hu YJ, Lin DY, Zeng D (2010). A general framework for studying genetic effects and gene–environment interactions with missing data. Biostatistics, 11:583-598. PMCID: PMC3294269.

Zeng D, Lin DY.(2010). A general asymptotic theory for maximum likelihood estimation in semiparametric regression models with censored data. Statistica Sinica, 20:871-910. PMCID: PMC2888521.

Lin DY, Zeng D (2010). Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data. Genetic Epidemiology, 34:60-66. PMCID: PMC3878085.

Diao G, Lin DY (2010). Variance-components methods for linkage and association analysis of ordinal traits in general pedigrees. Genetic Epidemiology, 34:232-237. PMCID: PMC3003595.

Lin DY, Zeng D (2010). On the relative efficiency of using summary statistics versus individual level data in meta-analysis. Biometrika, 97:321-332. PMCID: PMC3412575.

Tobacco and Genetics Consortium (2010). Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nature Genetics, 42:441-447. PMCID: PMC2914600.

Chen L, Lin DY, Zeng D (2010). Attributable fraction functions for censored time to event data. Biometrika, 97:713-726. PMCID: PMC3744602.


Zeng D, Lin DY (2009). Semiparametric transformation models with random effects for joint analysis of recurrent and terminal events. Biometrics, 65:746-752. PMCID: PMC3030128.

Sullivan P, de Geus E, Willeen G, James MR, Smit JH, Zandbelt T, Arolt V, Baune BT, Blackwood D, Cichon S, Coventry WL, Dohke M, Farmer A, Fava M, Gordon SD, He Q, Heath A, Heutink P, Holsboer F, Hoogendijk WJ, Hottenga JJ, Hu Y, Kohli M, Lin DY, et al. (2009). Genomewide association for major depressive disorder: a possible role for the presynaptic protein piccoloMolecular Psychiatry, 14:359-375. PMCID: PMC2717726.

Lin DY, Zeng D (2009). Proper analysis of secondary phenotype data in case-control association studies. Genetic Epidemiology, 33:256-265. PMCID: PMC2684820.

Lin DY, Sullivan PF (2009). Meta-analysis of genome-wide association studies with overlapping subjects. The American Journal of Human Genetics, 85:862-872. PMCID: PMC2790578.

Joubert BR, Diao G, Lin DY, North KE, Franceschini N: Longitudinal age-dependent effect on systolic blood pressure. BMC Proceedings, 3: S87, 2009. PMCID: PMC2795990.

Yan Y, Hu YJ, North KE, Franceschini N, Lin DY: Evaluation of population impact of candidate polymorphisms for coronary heart disease in the Framingham offspring study. BMC Proceedings, 3: S118, 2009. PMCID: PMC2795890.


Lin DY (2008): Genetic association analysisEncyclopedia of Clinical Trials.  D’Agostino, L. Sullivan, J. Massaro, eds., 2008.  John Wiley & Sons.

Sullivan PF, Lin DY, Tzeng J-Y, van den Oord E, Wanger M, Wright F.A Zou F, Lee S, Perkins D, Stroup TS, Lieberman J, Close SL, Liu W, Downing AM (2008). Genomewide association for schizophrenia in the CATIE study. Molecular Psychiatry, 13:570-584. PMCID: PMC3910086.

Zeng D, Lin DY (2008). Efficient resampling methods for non-smooth estimating functions. Biostatistics, 9:355-363. PMCID: PMC2673016.

Johnson BA, Lin DY, Zeng Z (2008). Penalized estimating functions and variable selection in semiparametric regression models. Journal of the American Statistical Association, 103:672-680. PMCID: PMC2850080.

Marchenko YV, Carroll RJ, Lin DY, Amos CI (2008). Semiparametric analysis of case-control genetic data in the presence of environmental factors. The Stata Journal, 8:305-333.

Lin DY, Hu Y (2008). Reply to Marchini and Howie. The American Journal of Human Genetics, 83:539-540.

Zeng D, Lin DY, Lin X (2008). Semiparametric Transformation Models with Random Effects for Clustered Failure Time Data. Statistica Sinica, 18:355-377. PMCID: PMC2756664.

Lin DY, Hu Y, Huang BE (2008). Simple and Efficient Analysis of Disease Association with Missing Genotype Data. The American Journal of Human Genetics, 82:444-452. PMCID: PMC2427170.


Lin DY, Huang BE (2007). The use of inferred haplotypes in downstream analysis – Reply to P. Kraft and D.O. Stram. The American Journal of Human Genetics, 81:865-866.

Zeng D, Lin DY (2007). Discussion of P. Diggle, D. Farewell and R. Henderson, “Analysis of Longitudinal Data with Drop-out: Objectives, Assumptions and a Proposal. Journal of the Royal Statistical Society, (Series c), 56:544-545.

Zeng D, Lin DY (2007). Efficient Estimation for the Accelerated Failure Time Model. Journal of the American Statistical Association, 102:1387-1396.

Huang BE, Amos CI, Lin DY (2007). Detecting Haplotype Effects in Genomewide Association Studies. Genetic Epidemiology, 31:803-812.

Zeng D, Lin DY (2007). Semiparametric Transformation Models with Random Effects for Recurrent Events. Journal of the American Statistical Association, 102:167-180.

Elston RC, Lin DY, Zheng G (2007). Multistage Sampling for Genetic Studies. Annual Review of Genomics and Human Genetics, 8:327-342.

Gijbels I, Lin DY, Ying Z (2007). Non- and semi-parametric analysis of failure time data with missing failure indicators. IMS Lecture Notes – Monograph Series, 54:203-223.

Lin DY (2007). On the Breslow estimator. Lifetime Data Analysis, 13:471–480.

Zeng D, Lin DY (2007). Maximum likelihood estimation in semiparametric regression models with censored data (with discussion). Journal of the Royal Statistical Society, (Series B), 69(4):507-564.

Lin DY, Huang BE (2007). The use of inferred haplotypes in downstream analyses. The American Journal of Human Genetics, 80:577-579. PMCID: PMC1821109

Huang BE, Lin DY (2007). Efficient association mapping of quantitative trait loci with selective genotyping. The American Journal of Human Genetics, 80: 567-576.


Lin DY (2006). A note on permutation tests in multistage association scans – Reply to Dubridge. The American Journal of Human Genetics, 78:1096.

Lange LA, Carlson CD, Hindorff LA, Lange EM, Walston J, Durda JP, Cushman M, Bis JC, Zeng D, Lin DY, Kuller LH, Nickerson DA, Psaty BM, Tracy RP, Reiner AP (2006). Association of polymorphisms in the CRP gene with circulating c-reactive protein levels and cardiovascular events. The Journal of the American Medical Association, 296:2703-2711.

Diao G, Lin DY (2006). Semiparametric Variance-Component Models for Linkage and Association Analyses of Censored Trait Data. Genetic Epidemiology, 30(7):570-581.

Zeng D, Lin DY, Avery CL, North KE, Bray MS (2006). Efficient semiparametric estimation of haplotype-disease associations in case-cohort and nested case-control studies. Biostatistics, 7(3):486-502.

Lin DY (2006). Evaluating statistical significance in two-stage genomewide association studies. The American Journal of Human Genetics, 78:505-509.

Diao G, Lin DY (2006). Improving the power of association tests for quantitative traits in family studies. Genetic Epidemiology, 30(4):301-313.

Lin DY, Zeng D (2006). Likelihood-based inference on haplotype effects in genetic association studies (with discussion). Journal of the American Statistical Association, 101:89-118.

Zeng D, Lin DY (2006). Efficient estimation of semiparametric transformation models for counting processes. Biometrika, 93:627-640.

Jin Z, Lin DY, Ying Z (2006). On least-squares regression with censored data. Biometrika, 93(1):147-161.

Jin Z, Lin DY, Ying Z (2006). Rank regression methods for multivariate failure time data based on marginal linear models. The Scandinavian Journal of Statistics, 33:1-23.


Diao G, Lin DY (2005). A powerful and robust method for mapping quantitative trait loci in general pedigrees. The American Journal of Human Genetics, 77:97-111.

Lin DY (2005). An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics, 21:781-787.

Whitsel EA, Boyko EJ, Rautaharju PM, Raghunathan TE, Lin DY, Pearce RM, Weinmann SA, Siscovick DS (2005). Electrocardiographic QT interval prolongation and risk of primary cardiac arrest in diabetic patients. Diabetes Care, 28:2045-2047.

Zeng D, Lin DY (2005). Estimating haplotype-disease associations with pooled genotype data. Genetic Epidemiology, 28:70-82.

Pan Z, Lin DY (2005). Goodness-of-fit methods for generalized linear mixed models. Biometrics, 61:1000-1009.

Zeng D, Lin DY, Yin G (2005). Maximum likelihood estimation for the proportional odds model with random effects. Journal of the American Statistical Association, 100:470-483.

Lin DY, Zeng D, Millikan R (2005). Maximum likelihood estimation of haplotype effects and haplotype-environment interactions in association studies. Genetic Epidemiology, 29:299-312.

Arbogast P, Lin DY (2005). Model-checking techniques for stratified case-control studies. Statistics in Medicine, 24(2):229-247.

Lin DY (2005). On rapid simulation of P-values. The American Journal of Human Genetics, 77:513-514.

Willan AR, Lin DY, Manca A (2005). Regression methods for cost-effectiveness analysis with censored data. Statistics in Medicine, 24:131-145.

Diao G, Lin DY (2005). Semiparametric methods for mapping quantitative trait loci with censored data. Biometrics, 61:1000-1009.


Zou F, Fine JP, Hu J, Lin DY (2004). An efficient resampling method for assessing genomewide statistical significance in mapping quantitative trait loci. Genetics, 168:2307-2316.

Lin DY, Zou F (2004). Assessing genomewide statistical significance in linkage studies. Genetic Epidemiology, 27:202-214.

Arbogast P, Lin DY (2004). Goodness-of-fit methods for matched case-control studies. The Canadian Journal of Statistics, 32:373-386.

Lin DY (2004). Haplotype-based association analysis in cohort studies of unrelated individuals. Genetic Epidemiology, 26:255-264.

Kulich M, Lin DY (2004). Improving the efficiency of relative-risk estimation in case-cohort studies. Journal of the American Statistical Association, 99:832-844.

Diao G, Lin DY, Zou F (2004). Mapping quantitative trait loci with censored observations. Genetics, 168:1689-1698.

Lin DY, Heagerty P. Proceedings of the Second Seattle Symposium in Biostatistics: Analysis of Correlated Data., (2004), Springer-Verlag.

Combes B, Luketic VA, Peters MG, Zetterman RK, Garcia-Tsao G, Munoz SJ, Lin DY, Flye N, Carithers RL (2004). Prolonged follow-up of patients in the U.S. multicenter trial of ursodeoxycholic acid for primary biliary cirrhosis. American Journal of Gastroenterology, 99:264-268.

Hu C, Lin DY (2004). Semiparametric failure time regression with replicates of mismeasured covariates. Journal of the American Statistical Association, 99:105-118.


Rea TD, Siscovick DS, Psaty BM, Pearce RM, Raghunathan TE, Whitsel EA, Cobb LA, Weinmann S, Anderson GD, Arbogast P, Lin DY (2003). Digoxin therapy and the risk of primary cardiac arrest in patients with congestive heart failure – Effect of mild-moderate renal impairment. Journal of Clinical Epidemiology, 56:646-650.

Willan AR, Cook RJ, Chen E and Lin DY (2003). Incremental net benefit in randomized clinical trials with quality-adjusted survival. Statistics in Medicine, 22:353-362.

Jin Z, Lin DY, Wei LJ, Ying Z (2003). Rank-based inference for the accelerated failure time model. Biometrika, 90:341-353.

Lin DY (2003). Regression analysis of incomplete medical cost data. Statistics in Medicine, 22:1181-1200.

Ghosh D, Lin DY (2003). Semiparametric analysis of recurrent events data in the presence of dependent censoring. Biometrics, 59:877-885.

Lin DY, Ying Z (2003). Semiparametric regression analysis of longitudinal data with informative drop-outs. Biostatistics, 4:385-398.

Lin DY. “Survival analysis.” In: Advanced Medical Statistics. Y, Lu JQ, Fan, editors. World Scientific Publishing Company (2003).


Hu C and Lin DY (2002). Cox regression with covariate measurement error. The Scandinavian Journal of Statistics. 29:637-655.

Arbogast P, Lin DY, Schwartz SM and Siscovick DS (2002). Estimating incidence rates from population-based case-control studies in the presence of nonresponses. Biometrical Journal, 44:227-239.

Lemaitre RN, Siscovick DS, Psaty BM, Pearce RM, Raghunathan TE, Whitsel EA, Weinmann SA, Anderson GD, Lin DY (2002). Inhaled Beta-2 adrenergic receptor agonists and primary cardiac arrestAmerican Journal of Medicine, 113:711-716.

Gosh D and Lin DY (2002). Marginal regression models for recurrent and terminal events. Statistica Sinica, 12:663-688.

Lin DY, Wei LJ and Ying Z (2002). Model-checking techniques based on cumulative residuals. Biometrics, 58:1-12.

Willan AR, Lin DY, Cook RJ and Chen E (2002). Using inverse-weighting in cost-effectiveness analysis with censored data. Statistical Methods in Medical Research, 11:539-551.


Rea TD, Heckbert SR, Kaplan RC, Psaty BM, Smith NL, Lemaitre RN and Lin DY (2001). Body mass index and the risk of recurrent coronary events following acute myocardial infarction. American Journal of Cardiology, 88:467-472.

Willan AR and Lin DY (2001). Incremental net benefit in randomized clinical trials. Statistics in Medicine, 20:1563-1574.

Lin DY and Ying Z (2001). Nonparametric tests for the gap time distributions of serial events based on censored data. Biometrics, 57:369-375.

Heckbert SR, Kaplan RC, Starr JR, Psaty BM, Lin DY, Furberg CD, LaCroix AZ, Anderson GD, Weiss NS (2001). Risk of recurrent coronary events in relation to use and recent initiation of postmenopausal hormone therapy. Archives of Internal Medicine, 161:1709-1713.

Whitsel E, Raghunathan TE, Peane RM, Lin DY, Rautaharju PM, Lemaitre R, Siscovick DS (2001). RR interval variation, the QT interval index and risk of primary cardiac arrest among patients without clinically recognized heart disease. European Heart Journal, 22:165-173.

Lin DY and Ying Z (2001). Semiparametric and nonparametric regression analysis of longitudinal data (with discussion). Journal of the American Statistical Association, 96:103-126.

Lin DY, Wei LJ and Ying Z (2001). Semiparametric transformation models for point processes. Journal of the American Statistical Association, 96:620-628.


Kulich M, Lin DY (2000). Additive hazards regression for case-cohort studies. Biometrika, 87:73-88.

Kulich M, Lin DY (2000). Additive hazards regression with covariate measurement error. Journal of the American Statistical Association, 95:238-248.

Siscovick DS, Raghunathan TE, Lin DY, Weinmann S, Arbogast P, Lemaitre RV, Psaty BM, Alexander R, Cobb L (2000). Influenza vaccination and the risk of primary cardiac arrest. American Journal of Epidemiology, 152:674-677.

Lin DY (2000). Linear regression analysis of censored medical costs. Biostatistics, 1:35-47.

Lin DY. “Marginal models for multivariate survival data”. In: Encyclopedia of Biostatistics. P. Armitage, T. Colton, editors. John Wiley and Sons (2000).

Ghosh D, Lin DY (2000). Nonparametric analysis of recurrent events and death. Biometrics, 56:554-562.

Lin DY (2000). On fitting Cox’s proportional hazards models to survey data. Biometrika, 87:37-48.

Lin DY (2000). Proportional means regression for censored medical costs. Biometrics, 56:775-778.

Lin DY, Wei LJ, Yang I, Ying Z (2000). Semiparametric regression for the mean and rate functions of recurrent events. Journal of the Royal Statistical Society (Series B), 62:711-730.

Fleming TR, Lin DY (2000). Survival analysis in clinical trials: past developments and future directions. Biometrics, 56:971-983.


Lin DY, Yao Q, Ying Z. 1999. A general theory on stochastic curtailment for censored survival data. Journal of the American Statistical Association, 94:510-521.

Psaty BM, Koepsell TD, Lin DY, Weiss NS, Siscovick DS, Rosendaal FR, Pahor M, Furberg CD. 1999. Assessment and control for confounding by indication in observational studies. Journal of the American Geriatrics Society, 47:749-754.

Yip PSF, Zhou Y, Lin DY, Fang XZ. 1999. Estimation of population size based on additive hazards models for continuous-time recapture experiments. Biometrics, 55:904-908.

Lemaitre RN, Siscovick DS, Raghunathan TE, Weinmann S, Arbogast P, Lin DY. 1999. Leisure-time physical activity and the risk of primary cardiac arrest. Archives of Internal Medicine, 159:686-690.

Diehr P, Yanez D, Ash A, Hombrook M, Lin DY. 1999. Methods for analyzing health care utilization and costs. Annual Review of Public Health, 20:125-144.

Lin DY, Sun W, Ying Z. 1999. Nonparametric estimation of the gap time distributions for serial events with censored data. Biometrika, 86:59-70.

Etzioni RD, Feuer EJ, Sullivan SD, Lin DY, Hu C, Ramsey SD. 1999. On the use of survival analysis techniques to estimate medical care costs. Journal of Health Economics, 18:365-380.

Lin DY, Yip PSF. 1999. Parametric regression models for continuous-time removal and recapture studies. Journal of the Royal Statistical Society (Series B), 61:401-411.

Lin DY, Arbogast P, Siscovick DS, Lemaitre RN. 1999. Poisson regression with missing durations of exposure. Biometrics, 55:252-257.

Psaty BM, Weiss NS, Furberg CD, Koepsell TD, Siscovich DS, Rosendaal FR, Smith NL, Heckbert SR, Kaplan RC, Lin DY, Fleming TR, Wagner EH. 1999. Surrogated endpoints, clinical outcomes, and the drug approval process for antihypertensive medicine. Journal of the American Medical Association, 282:786-790.

Fisher LD, Lin DY. 1999. Time-dependent covariates in the Cox proportional hazards time-to-event regression analysis. Annual Review of Public Health, 20:145-157.


Lin DY, Wei LJ, Ying Z. 1998. Accelerated failure time models for counting processes. Biometrika, 85:605-618.

Lin DY, Oakes D, Ying Z. 1998. Additive hazards regression for current status data. Biometrika, 85:289-298.

Lin DY, Psaty BM, Kronmal RA. 1998. Assessing the sensitivity of regression results to unmeasured confounders in observational studies. Biometrics, 54:948-963.

Spiekerman CF, Lin DY. 1998. Marginal regression models for multivariate failure time data. Journal of the American Statistical Association, 93:1164-1175.

Albert JM, Ioannidis JPA, Reichelderfer P, Conway B, Coombs RW, Crane L, DeMasi R, Dixon DO, Flandre P, Hughes MD, Kalish L, Larntz K, Lin DY, et al.. 1998. Statistical issues for HIV surrogate markers: Point/counterpoint. Statistics in Medicine, 17:2435-2462.


Lin DY, Fleming TR. (Eds.) 1997. Proceedings of the First Seattle Symposium in Biostatistics: Survival Analysis.. Springer-Verlag.

Lin DY, Ying Z. 1997. Additive hazards regression models for survival data. Proceedings of the First Seattle Symposium in Biostatistics: Survival Analysis. Springer-Verlag.

Deeg HJ, Lin DY, Leisenring W, Boeckh M, Anasetti C, Appelbaum FR, Chauncey TR, Doney K, Flowers M, Martin P, Nash R, Schoch G, Sullivan KM, Whitherspoon RP, Storb R. 1997. Cyclosporine or cyclosporine plus methylprednisolone for prophylaxis of graft-versus-host disease – a prospective randomized trial. Blood, 89:3880-3887.

Heckbert SR, Weiss NS, Koepsell TD, Lemaitre RN, Smith NL, Siscovick DS, Lin DY, Psaty BM. 1997. Duration of estrogen replacement therapy in relation to the risk of incident of myocardial infarction in postmenopausal women. Archives of Internal Medicine, 157:1330-1336.

Lin DY, Etzioni R, Feuer EJ, Wax Y. 1997. Estimating medical costs from incomplete follow-up data. Biometrics, 53:419-434.

Lin DY, Fleming TR, DeGruttola V. 1997. Estimating the proportion of treatment effect explained by a surrogate endpoint. Statistics in Medicine, 16:1515-1527.

Lin DY. 1997. Nonparametric inference for cumulative incidence functions in competing-risks studies. Statistics in Medicine, 16:901-910.

DeGruttola V, Fleming TR, Lin DY, Coombs R. 1997. Validating surrogate markers – Are we being naive?. Journal of Infectious Diseases, 175:237-246.

Schwartz SM, Siscovick DS, Longstreth WT, Psaty BM, Beverly RK, Raghunathan TE, Lin DY, Koepsell TD. 1997. Use of low-dose oral contraceptives and stroke in young women. Annals of Internal Medicine, 127:596-603.


Spiekerman CF, Lin DY. 1996. Checking the marginal Cox model for correlated failure time data. Biometrika, 83:143-156.

Lin DY, Robins JM, Wei LJ. 1996. Comparing two failure time distributions in the presence of dependent censoring. Biometrika, 83:381-393.

Lin DY, Shen L, Ying Z, Breslow NE. 1996. Group sequential designs for monitoring survival probabilities. Biometrics, 52:1033-1041.

Psaty BW, Siscovick DS, Weiss NS, Koepsell TD, Rosendaal FR, Lin DY, Hekbert SR, Wagner EM, Furberg CD. 1996. Hypertension and outcomes research: from clinical trials to clinical epidemiology. American Journal of Hypertension, 9:178-183.

Yip PSF, Huggins RM, Lin DY. 1996. Inference for capture-recapture experiments in continuous time with variable capture rates. Biometrika, 83:477-483.

Lin DY, Spiekerman CF. 1996. Model checking techniques for parametric regression with censored data. The Scandinavian Journal of Statistics, 23:157-177.


Combes B, Carithers RL, Maddrey WC, Lin DY, et al. 1995. A randomized, double-blind, placebo-controlled trial of ursodeoxycholic acid in primary biliary cirrhosis. Hepatology, 22:759-766.

Crawford SW, Pepe M, Lin DY, Benedetti F, Deeg HJ. 1995. Abnormalities of pulmonary function tests after marrow transplantation predict non-relapse mortality. American Journal of Respiratory Critical Care Medicine, 152:690-695.

Lin DY. 1995. Multivariate failure time data. In: PF Thall (Ed.), Recent Advances in Clinical Trial Design and Analysis Kluwer Academic Publishers.

Lin DY, Ying Z. 1995. Semiparametric analysis of general additive-multiplicative intensity models for counting processes. Annals of Statistics, 23:1712-1734.

Lin DY, Ying Z. 1995. Semiparametric inference for the accelerated life model with time-dependent covariates. Journal of Statistical Planning and Inference, 44:47-63.


Lin DY, Fleming TR, Wei LJ. 1994. Confidence bands for survival curves under the proportional hazards model. Biometrika, 81:73-81.

Lin DY. 1994. Cox regression analysis of multivariate failure time data: The marginal approach. Statistics in Medicine, 13:2233-2247.

Guo SW, Lin DY. 1994. Regression analysis of multivariate grouped survival data. Biometrics, 50:632-639.

Lin DY, Ying Z. 1994. Semiparametric analysis of the additive risk model. Biometrika, 81:61-71.


Lin DY, Ying Z. 1993. A simple nonparametric estimator of the bivariate survival function under univariate censoring. Biometrika, 80:573-581.

Lin DY, Wei LJ, Ying Z. 1993. Checking the Cox model with cumulative sums of martingale-based residuals. Biometrika, 80:557-572.

Lin DY, Ying Z. 1993. Cox regression with incomplete covariate measurements. Journal of the American Statistical Association, 88:1341-1349.

Lin DY, Fischl MJ, Schoenfeld DA. 1993. Evaluating the role of CD4-lymphocyte changes as surrogate endpoints in human immunodeficiency virus clinical trials. Statistics in Medicine, 12:835-842.

Lin DY. 1993. MULCOX2: A general computer program for the Cox regression analysis of multivariate failure time data. Computer Programs in Biomedicine, 40:279-294.

Koenig JQ, Larson TV, Hanley QS, Rebolledo V, Dumler K, Checkoway H, Wang SZ, Lin DY, Pierson WE. 1993. Pulmonary function changes in children associated with fine particulate matter. Environmental Research, 63:26-38.


Lin DY, Geyer CJ. 1992. Computational methods for semiparametric linear regression with censored data. Journal of Computational and Graphical Statistics, 1:77-90.

Lin DY, Wei LJ. 1992. Discussion of A Agresti, “A survey of exact inference for contingency tables”. Statistical Science, 7:166-167.

Lin DY. 1992. GOFCOX: A computer program for the goodness-of-fit analysis of the Cox regression model. Computer Programs in Biomedicine, 38:101-105.

Lin DY, Liu PY. 1992. Nonparametric sequential tests against ordered alternatives in multiple-armed clinical trials. Biometrika, 79:420-425.

Lin DY. 1992. Sequential log rank tests adjusting for covariates with the accelerated life model. Biometrika, 79:523-529.


Lin DY, Wei LJ, DeMets DL. 1991. Exact statistical inference for group sequential trials. Biometrics, 47:1399-1408.

Lin DY, Wei LJ. 1991. Global goodness-of-fit tests for the general Cox regression model. Statistica Sinica, 1:1-17.

Lin DY. 1991. Goodness-of-fit analysis for the Cox regression model based on a class of parameter estimators. Journal of the American Statistical Association, 86:725-728.

Lin DY. 1991. Nonparametric sequential testing in clinical trials with incomplete multivariate observations. Biometrika, 78:123-131.

Lin DY, Wei LJ. 1991. Repeated confidence intervals for a scale change in a sequential survival study. Biometrics, 47:289-294.


Wei LJ, Ying Z, Lin DY. 1990. Linear regression analysis of censored survival data based on rank tests. Biometrika, 77:845-851.

Lin DY. 1990. MULCOX: A computer program for the Cox regression analysis of multiple failure time variables. Computer Programs in Biomedicine, 32:125-135.

Wei LJ, Smythe RT, Lin DY, Park TS. 1990. Statistical inference with data-dependent treatment allocation rules. Journal of the American Statistical Association, 85:156-162.


Lin DY, Wei LJ. 1989. Discussion of C Jennison and BW Turnbull, “Interim analysis: the repeated confidence interval approach”. Journal of the Royal Statistical Society, 51:347-348.

Lin DY, Wei LJ. 1989. Discussion of JH Ware, “Investigating therapies of potentially great benefit: ECMO”. Statistical Science, 4:324-325.

Wei LJ, Lin DY, Weissfeld L. 1989. Regression analysis of multivariate incomplete failure time data by modeling marginal distributions. Journal of the American Statistical Association, 84:1065-1073.

Lin DY, Wei LJ. 1989. The robust inference for the Cox proportional hazards model. Journal of the American Statistical Association, 84:1074-1078.


Brown MB, Lin DY, Normolle DP, Herzog AR. Models for and the effect of nonresponse in a survey of the noninstitutionalized elderly.The 1988 Proceedings of the Section on Survey Research Methods of the American Statistical Association, (1988).