Publications

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A
Dahl, A., Guillemot, V., Mefford, J., Aschard, H. & Zaitlen, N. Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives. Genetics 211, 1179-1189 (2019).
Raffield, L. M. et al. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet 106, 112-120 (2020).
Park, D. S. et al. An ancestry-based approach for detecting interactions. Genet Epidemiol 42, 49-63 (2018).
DeBoever, C. et al. Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases. Am J Hum Genet 106, 611-622 (2020).
B
Wang, Q. et al. A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. Nat Neurosci 22, 691-699 (2019).
Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179-189 (2020).
C
Gottlieb, A. et al. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans. Genome Med 9, 98 (2017).
Hu, Y. et al. A common loss-of-function variant is associated with lower vitamin B concentration in African Americans. Blood 131, 2859-2863 (2018).
Caggiano, C. et al. Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 12, 2717 (2021).
Aschard, H. et al. Covariate selection for association screening in multiphenotype genetic studies. Nat Genet 49, 1789-1795 (2017).
Sakaue, S. et al. A cross-population atlas of genetic associations for 220 human phenotypes. Nat Genet 53, 1415-1424 (2021).
Keys, K. L. et al. On the cross-population generalizability of gene expression prediction models. PLoS Genet 16, e1008927 (2020).
McAllister, K. et al. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol 186, 753-761 (2017).
D
Verbanck, M., Chen, C. - Y., Neale, B. & Do, R. Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases. Nat Genet 50, 693-698 (2018).
Stern, A. J., Speidel, L., Zaitlen, N. A. & Nielsen, R. Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies. Am J Hum Genet 108, 219-239 (2021).
Li, X. et al. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nat Genet 52, 969-983 (2020).
E
Zaitlen, N. et al. The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium. Genetics 205, 375-383 (2017).
Chen, H. et al. Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies. Am J Hum Genet 104, 260-274 (2019).
Zhong, X. et al. Electronic health record phenotypes associated with genetically regulated expression of CFTR and application to cystic fibrosis. Genet Med 22, 1191-1200 (2020).
Nayar, K. et al. Elevated Polygenic Burden for Autism Spectrum Disorder Is Associated With the Broad Autism Phenotype in Mothers of Individuals With Autism Spectrum Disorder. Biol Psychiatry 89, 476-485 (2021).
Goleva, S. B., Lake, A. M., Torstenson, E. S., Haas, K. F. & Davis, L. K. Epidemiology of Functional Seizures Among Adults Treated at a University Hospital. JAMA Netw Open 3, e2027920 (2020).
Seplyarskiy, V. B. et al. Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations. Nat Genet 51, 36-41 (2019).
Cassa, C. A. et al. Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nat Genet 49, 806-810 (2017).
Kousi, M. et al. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nat Genet 52, 1145-1150 (2020).
F
Qian, J. et al. A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank. PLoS Genet 16, e1009141 (2020).
Venkataraman, G. Ram et al. FasTag: Automatic text classification of unstructured medical narratives. PLoS One 15, e0234647 (2020).
Westra, H. - J. et al. Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes. Nat Genet 50, 1366-1374 (2018).
Gazal, S. et al. Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations. Nat Genet 50, 1600-1607 (2018).
Regier, A. A. et al. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun 9, 4038 (2018).
Slowikowski, K., Wei, K., Brenner, M. B. & Raychaudhuri, S. Functional genomics of stromal cells in chronic inflammatory diseases. Curr Opin Rheumatol 30, 65-71 (2018).
G
Rochtus, A. et al. Genetic diagnoses in epilepsy: The impact of dynamic exome analysis in a pediatric cohort. Epilepsia 61, 249-258 (2020).
Belbin, G. M., Nieves-Colón, M. A., Kenny, E. E., Moreno-Estrada, A. & Gignoux, C. R. Genetic diversity in populations across Latin America: implications for population and medical genetic studies. Curr Opin Genet Dev 53, 98-104 (2018).
Battle, A., Brown, C. D., Engelhardt, B. E. & Montgomery, S. B. Genetic effects on gene expression across human tissues. Nature 550, 204-213 (2017).
Belbin, G. Morven et al. Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system. Elife 6, (2017).
He, L., Zhbannikov, I., Arbeev, K. G., Yashin, A. I. & Kulminski, A. M. A genetic stochastic process model for genome-wide joint analysis of biomarker dynamics and disease susceptibility with longitudinal data. Genet Epidemiol 41, 620-635 (2017).
Sinnott-Armstrong, N. et al. Genetics of 35 blood and urine biomarkers in the UK Biobank. Nat Genet 53, 185-194 (2021).
Amar, D., Sinnott-Armstrong, N., Ashley, E. A. & Rivas, M. A. Graphical analysis for phenome-wide causal discovery in genotyped population-scale biobanks. Nat Commun 12, 350 (2021).
H
Martin, A. R. et al. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. Am J Hum Genet 100, 635-649 (2017).
I
Dietlein, F. et al. Identification of cancer driver genes based on nucleotide context. Nat Genet 52, 208-218 (2020).
Bonder, M. Jan et al. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet 53, 313-321 (2021).
Frésard, L. et al. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nat Med 25, 911-919 (2019).
Liu, B. & Montgomery, S. B. Identifying causal variants and genes using functional genomics in specialized cell types and contexts. Hum Genet 139, 95-102 (2020).
Li, X. et al. The impact of rare variation on gene expression across tissues. Nature 550, 239-243 (2017).
Kichaev, G. et al. Improved methods for multi-trait fine mapping of pleiotropic risk loci. Bioinformatics 33, 248-255 (2017).
Amariuta, T. et al. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet 52, 1346-1354 (2020).
Wojcik, G. L. et al. Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies. G3 (Bethesda) 8, 3255-3267 (2018).
Ritchie, M. D. et al. Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. Am J Epidemiol 186, 771-777 (2017).
L
Ritz, B. R. et al. Lessons Learned From Past Gene-Environment Interaction Successes. Am J Epidemiol 186, 778-786 (2017).
Fonseka, C. Y., Rao, D. A. & Raychaudhuri, S. Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis. Curr Opin Immunol 49, 27-36 (2017).
Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat Genet 49, 600-605 (2017).

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