SELECTED PUBLICATIONS

* Corresponding author

• Lu Y, Oliva M, Pierce BL, Liu J* and Chen LS*. (2024) Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits. Nature Communications, 15, Article number: 2383. PMID: 38493154 PMCID: PMC10944527.
• Yang F*, Chen LS*, Oveisgharan S, Darbar D and Bennett DA. (2024) Integrating Mendelian Randomization with causal mediation analysis for characterizing direct and indirect exposure-to-outcome effects. Annals of Applied Statistics, 18(3): 2656-2677.
• Lu Y, Xu K, Maydanchik N, Kang B, Pierce BL, Yang F* and Chen LS*. (2024) An integrative multi-context Mendelian randomization method for identifying risk genes across human tissues. The American Journal of Human Genetics, 111, 1736–1749.
• Oliva M*, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS*, Pierce BL*. (2023) DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nature Genetics, 55, 112–122. PMID: 36510025
• Cheng Q, Zhang X, Chen LS*, Liu J* (2022) Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology. Nature Communications, 13: 6490. PMID: 36310177. PMCID: PMC9618026.
• Gleason KJ, Yang F*, Chen LS*. (2021) A robust two-sample transcriptome-wide Mendelian Randomization method integrating GWAS with multi-tissue eQTL summary statistics. Genetic Epidemiology, 45(4):353-371.
*The Best Paper in Genetic Epidemiology Award for the Year 2021.
• Yang F*, Gleason KJ, Wang J, The GTEx consortium, Duan J, He X, Pierce BP, Chen LS* (2021) CCmed: Cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits. Bioinformatics, 37(17):2513-2520.
• Gleason KJ, Yang F, Pierce BL, He X, Chen LS* (2020) Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits. Genome Biology, 21: Article 236. PMID: 32912334
• Demanelis K, Jasmine F, Chen LS, Chernoff M, Tong L, Delgado D, Zhang C, Shinkle J, Sabarinathan M, Lin H, Ramirez E, Oliva M, Kim-Hellmuth S, Stranger BE, Lai TP, Aviv A, Ardlie K, Aguet F, Ahsan H, GTEx Consortium, Doherty JA, Kibriya M, Pierce BL. (2020) Determinants of telomere length across human tissues. Science, 369, eaaz6876. PMID: 32913074
• Song X, Ji J, Yang F, Gleason KJ, Martignetti JA, Chen LS*, Wang P*. (2019) Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape of human ovarian cancer via a multi-omics integrative analysis. Molecular & Cellular Proteomics, 18(8 suppl 1):S52-S65.
• Ma WP, Chen LS, Ozbek U, Han SW, Lin C, Paulovich AG, Zhong H, Wang P. (2019) Integrative proteo-genomic analysis to construct CNA-protein regulatory map in breast tumors. Molecular & Cellular Proteomics, 18(8 suppl 1):S66-S81.
• Wang J, Wang P, Hedeker D, Chen LS* (2019) Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness. Biostatistics,20(4):648-665. PMID: 29939200.
• Pierce BL, Tong L, Argos M, Jasmine F, Zaman R, Islam T, Rahman M, Baron JA, Kibriya MG, Chen LS, Ahsan H (2018) Co-occurring eQTLs and mQTLs: evidence for shared causal variants and shared causal mechanisms. Nature Communications, 9: 804.
• Wang J, Liu Q, Pierce BL, Huo D, Olopade OI, Ahsan H, Chen LS* (2018). A meta-analysis approach with filtering for identifying gene-level gene-environment interactions. Genetic Epidemiology, 42(5), 434-446.
• Yang F, Wang J, The GTEx consortium, Pierce BL, Chen LS* (2017). Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Research, 27: 1859-1871..
• Chen LS, Wang J, Wang X, Wang P (2017). A mixed-effects model for incomplete data with batch-level abundance-dependent missing-data mechanism. Annals of Applied Statistics., 11(1), 114-138.
• Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS* (2016). Imputing gene expression in uncollected tissues within and beyond GTEx. The American Journal of Human Genetics, 98(4), 697-708.
• Liu Q, Chen LS*, Nicolae DL, Pierce BL (2016). A unified set-based test with adaptive filtering for gene-environment interaction analyses in association studies. Biometrics, 72(2):629-638.
• Chen LS, Prentice BL, Wang P (2014). A penalized EM algorithm for multivariate Gaussian data with non-ignorable missing data. Biometrics, 70(2):312-322.
• Pierce BL, Tong T, Chen LS , Rahaman R, Argos M, Jasmine F, Roy S, Paul-Brutus R, Westra HJ, Franke L, Esko T, Zaman R, Islam T, Rahman M, Baron JA, Kibriya MG, Ahsan H (2014) Mediation analysis demonstrates that trans-eQTLs are often explained by cis-Mediation: A genome-wide analysis among 1,800 South Asians. PLoS Genetics, 10(12):e1004818.
• Liu Q, Nicolae DL, Chen LS* (2013) Marbled inflation from population structure in gene-based association studies with rare variants. Genetic Epidemiology, 37(3): 282-292.
• Chen LS*, Hsu L, Gamazon E, Cox NJ, Nicolae DL (2012) An exponential combination procedure for set-based association test in sequencing studies. The American Journal of Human Genetics, 91(6): 977-986.
• Chen LS, Paul D, Prentice RL, Wang P (2011) A regularized Hotelling's T2 test for pathway analysis in proteomics studies. Journal of the American Statistical Association, 106(496): 1345-1360.
• Chen LS, Hutter CM, Potter JD, Liu Y, Prentice RL, Peters U, Hsu L (2010) Insights into colon cancer etiology using a regularized approach to gene set analysis of GWAS data. The American Journal of Human Genetics,86(6): 860-871.
• Chen LS and Storey JD (2008) Eigen-R2 for dissecting the variation of high-dimensional studies. Bioinformatics, 24 (19): 2260-2262.
• Chen LS, Emmert-Streib F, Storey JD (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8: R219.
• Chen LS and Storey JD (2006) Relaxed significance criteria for linkage analysis. Genetics, 173: 2371-2381.