Publications

A full list of publications can be found at Google Scholar.

(\(^*\)First authors with equal contribution; \(^\dagger\)senior authors with equal contribution or serving as co-corresponding authors.)

1. Wang A\(^*\), Tian P\(^*\), Zhang YD. (2024) TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference. Bioinformatics, Volume 40, Issue 8, August 2024, btae502. [link] [code]

2. Lai D, Lim D, Lu J, Wang H, Huang T, Zhang YD. (2024) Risk of myocarditis after three doses of COVID-19 mRNA vaccines in the United States, 2020–2022: A self-controlled case series study. J Evid Based Med. 2024;17:65–77. [link]

3. Xiong Z, Thach T, Zhang YD\(^\dagger\), Sham PC\(^\dagger\). Improved estimation of functional enrichment in SNP heritability using feasible generalized least squares, Human Genetics and Genomics Advances, Volume 5, Issue 2, 2024, 100272. [link] [code]

4. Li X, Sham P, Zhang YD. (2024) A Bayesian fine-mapping model using a continuous global-local shrinkage prior with applications in prostate cancer analysis. The American Journal of Human Genetics. [link] [code]

   2023

5. Wang W, Jin H, Zhang YD and Yin G (2023) Two-dimensional calibration-free odds design for phase I drug-combination trials. Front. Oncol. 13:1294258. [link]

6. Wang X, Wang H, Yin G, Zhang YD. Network-based drug repurposing for the treatment of COVID-19 patients in different clinical stages. Heliyon, 2023;9(3): e14059. [link]

7. Liu Z\(^*\), Qin Y\(^*\), Wu T, Tubbs J, Baum L, Mak T, Li M\(^\dagger\), Zhang YD\(^\dagger\), Sham PC\(^\dagger\). Reciprocal causation mixture model for robust Mendelian randomization analysis using genome-scale summary data. Nat Commun, 14, 1131 (2023). [link]

   2022

8. Tian P, Hu Y, Liu Z\(^\dagger\), Zhang YD\(^\dagger\). Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures. BMC Bioinformatics 23, 478 (2022). [link][code]

9. Wang H, Wang X, Li T, Lai D, Zhang YD. Adverse effect signature extraction and prediction for drugs treating COVID-19. Front. Genet. 13:1019940. doi: 10.3389/fgene.2022.1019940 (2022) [link]

10. Gan D, Yin G, Zhang YD. The GR2D2 estimator for the precision matrices, Briefings in Bioinformatics, 2022; bbac426. [link] [code]

11. Tian P, Chan TH, Wang Y-F, Yang W, Yin G, Zhang YD. Multiethnic polygenic risk prediction in diverse populations through transfer learning. Frontiers in Genetics, 19 August 2022 Sec. Statistical Genetics and Methodology. [link] [code]

12. Su W, He B, Zhang YD, Yin G. C-index regression for recurrent event data, Contemporary Clinical Trials, Volume 118, 2022, 106787, ISSN 1551-7144. [link]

13. Lai D, Zhang YD, Lu J. Venous Thromboembolism following Two Doses of COVID-19 mRNA Vaccines in the US Population, 2020–2022. Vaccines. 2022; 10(8):1317. [link]

14. Lai D, Cai Y, Chan TH, Gan D, Hurson AN, Zhang YD. How to organise travel restrictions in the new future: lessons from the COVID-19 response in Hong Kong and Singapore. BMJ Global Health. 2022 Feb 1;7(2):e006975. [link]

    2020

15. Zhang YD, Naughton BP, Bondell HD, Reich BJ. Bayesian regression using a prior on the model fit: The R2-D2 shrinkage prior. Journal of the American Statistical Association. 2020 Nov 5:1-3. [link][code]

16. Meisner A, Kundu P, Zhang YD, Lan LV, Kim S, Ghandwani D, Choudhury PP, Berndt SI, Freedman ND, Garcia-Closas M, Chatterjee N. Combined utility of 25 disease and risk factor polygenic risk scores for stratifying risk of all-cause mortality. The American Journal of Human Genetics. 2020 Sep 3;107(3):418-31. [link]

17. Hong X, Zhang B, Liang L, Zhang Y, Ji Y, Wang G, … & Wang X. Postpartum plasma metabolomic profile among women with preeclampsia and preterm delivery: implications for long-term health. BMC medicine. 2020 18(1), 1-12. [link]

18. Zhang YD, Hurson AN, Zhang H, …, Chatterjee N\(^\dagger\), Garcia-Closas M\(^\dagger\).
    Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers. Nature communications. 2020 Jul 3;11(1):1-3. [link] [code]

19. Tubbs JD, Zhang YD, Sham PC. Intermediate confounding in trio relationships: The importance of complete data in effect size estimation. Genetic Epidemiology. 2020 Jun;44(4):395-9. [link]

20. Pal Choudhury P\(^*\), Wilcox AN\(^*\), Brook MN, Zhang Y, Ahearn T, Orr N, Coulson P, Schoemaker MJ, Jones ME, Gail MH, Swerdlow AJ, Chatterjee N\(^\dagger\), Garcia-Closas M\(^\dagger\). Comparative validation of breast cancer risk prediction models and projections for future risk stratification. JNCI: Journal of the National Cancer Institute. 2020 Mar 1;112(3):278-85. [link]

21. Ji Y, Azuine RE, Zhang Y, Hou W, Hong X, Wang G, Riley A, Pearson C, Zuckerman B, Wang X. Association of cord plasma biomarkers of in utero acetaminophen exposure with risk of attention-deficit/hyperactivity disorder and autism spectrum disorder in childhood. JAMA psychiatry. 2020 Feb 1;77(2):180-9.[link]

    2018

22. Zhang Y, Qi G, Park JH, Chatterjee N. Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits. Nature Genetics. 2018 Sep;50(9): 1318-1326. [link] [code]

23. Zhang Y, Bondell HD. Variable selection via penalized credible regions with Dirichlet–Laplace global-local shrinkage priors. Bayesian Analysis. 2018;13(3):823-44. [link]