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.)
Lai D, Wang H, Gu T, Wu S, Liu D, Sham PC, Zhang YD. TransferTWAS: A transfer learning framework for cross-tissue transcriptome-wide association study . The American Journal of Human Genetics. 2025 June 30. [link] [code]
Chan TH, Zhang DY, Yin G, Yu L. Feature Preserving Shrinkage on Bayesian Neural Networks via the R2D2 Prior. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2025 May 23. [link]
Wang H, Li X, Li T, Li Z, Sham PC, Zhang YD. MAAT: a new nonparametric Bayesian framework for incorporating multiple functional annotations in transcriptome-wide association studies. Genome Biology. 2025 Feb 4;26:21. [link] [code]
2024 Wang A\(^*\), Tian P\(^*\), Zhang YD. TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference. Bioinformatics. 2024 Aug;40(8):btae502. [link] [code]
Lai D, Lim D, Lu J, Wang H, Huang T, Zhang YD. Risk of myocarditis after three doses of COVID‐19 mRNA vaccines in the United States, 2020–2022: A self‐controlled case series study. Journal of Evidence‐Based Medicine. 2024 Mar;17(1):65-77. [link]
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. 2024 Apr 11;5(2). [link] [code]
Li X, Sham P, Zhang YD. A Bayesian fine-mapping model using a continuous global-local shrinkage prior with applications in prostate cancer analysis. The American Journal of Human Genetics. 2024 Feb 1;111(2):213-26. [link] [code]
2023 Wang W, Jin H, Zhang YD, Yin G. Two-dimensional calibration-free odds design for phase I drug-combination trials. Frontiers in Oncology. 2023 Nov 29;13:1294258. [link]
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 Mar 1;9(3). [link]
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. Nature Communications. 2023 Feb 28;14(1):1131. [link]
2022 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. 2022 Nov 14;23(1):478. [link] [code]
Wang H, Wang X, Li T, Lai D, Zhang YD. Adverse effect signature extraction and prediction for drugs treating COVID-19. Frontiers in Genetics. 2022 Nov 4;13:1019940. [link]
Gan D, Yin G, Zhang YD. The GR2D2 estimator for the precision matrices. Briefings in Bioinformatics. 2022 Nov;23(6):bbac426. [link] [code]
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. 2022 Aug 19;13:906965. [link] [code]
Su W, He B, Zhang YD, Yin G. C-index regression for recurrent event data. Contemporary Clinical Trials. 2022 Jul 1;118:106787. [link]
Lai D, Zhang YD, Lu J. Venous thromboembolism following two doses of COVID-19 mRNA vaccines in the US population, 2020–2022. Vaccines. 2022 Aug 15;10(8):1317. [link]
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 28;7(2). [link]
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. 2022 Apr 3;117(538):862-74. [link] [code]
2020 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]
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 Dec;18:1-2. [link]
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):3353. [link] [code]
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]
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]
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 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):1318-26. [link] [code]
Zhang Y, Bondell HD. Zhang Y, Bondell HD. Variable selection via penalized credible regions with Dirichlet–Laplace global-local shrinkage priors. Bayesian Analysis. 2018 Sep;13(3): 823-844. [link]