Publications

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2021
Caggiano, C. et al. Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 12, 2717 (2021).
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).
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).
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).
Ji, Y. et al. Incorporating European GWAS findings improve polygenic risk prediction accuracy of breast cancer among East Asians. Genet Epidemiol (2021). doi:10.1002/gepi.22382
Sun, R. et al. Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genet Epidemiol 45, 99-114 (2021).
Contreras, M. G. et al. Native American Ancestry and Air Pollution Interact to Impact Bronchodilator Response in Puerto Rican Children with Asthma. Ethn Dis 31, 77-88 (2021).
Naseri, A., Shi, J., Lin, X., Zhang, S. & Zhi, D. RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID. PLoS Genet 17, e1009315 (2021).
Naseri, A., Shi, J., Lin, X., Zhang, S. & Zhi, D. RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID. PLoS Genet 17, e1009315 (2021).
Tsetsos, F. et al. Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl Psychiatry 11, 56 (2021).
Tsetsos, F. et al. Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl Psychiatry 11, 56 (2021).
Tsetsos, F. et al. Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl Psychiatry 11, 56 (2021).
Hu, S. et al. Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut 70, 285-296 (2021).
2020
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).
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).
Keys, K. L. et al. On the cross-population generalizability of gene expression prediction models. PLoS Genet 16, e1008927 (2020).
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).
Mefford, J. et al. Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models. J Comput Biol 27, 599-612 (2020).
Mefford, J. et al. Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models. J Comput Biol 27, 599-612 (2020).
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).
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).
Venkataraman, G. Ram et al. FasTag: Automatic text classification of unstructured medical narratives. PLoS One 15, e0234647 (2020).
C Y Mak, A. et al. Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand and Gene-By-Air-Pollution Interaction. Genetics 215, 869-886 (2020).
C Y Mak, A. et al. Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand and Gene-By-Air-Pollution Interaction. Genetics 215, 869-886 (2020).
Rau, C. D. et al. Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for "polygenic epistasis". PLoS Genet 16, e1009165 (2020).
Dahl, A. et al. A Robust Method Uncovers Significant Context-Specific Heritability in Diverse Complex Traits. Am J Hum Genet 106, 71-91 (2020).
Liu, D. et al. A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Genes for Pancreatic Cancer Risk. Cancer Res 80, 4346-4354 (2020).
Liu, D. et al. A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Genes for Pancreatic Cancer Risk. Cancer Res 80, 4346-4354 (2020).
Ferraro, N. M. et al. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science 369, (2020).
Ferraro, N. M. et al. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science 369, (2020).
Sajuthi, S. P. et al. Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium. Nat Commun 11, 5139 (2020).
Sajuthi, S. P. et al. Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium. bioRxiv (2020). doi:10.1101/2020.04.09.034454
Zhou, D. et al. A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. Nat Genet 52, 1239-1246 (2020).
Zhou, D. et al. A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. Nat Genet 52, 1239-1246 (2020).
Werling, D. M. et al. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. Cell Rep 31, 107489 (2020).
Werling, D. M. et al. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. Cell Rep 31, 107489 (2020).
2019
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).
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).
Yang, H. et al. De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. Bioinformatics 35, 1453-1460 (2019).
Yang, H. et al. De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. Bioinformatics 35, 1453-1460 (2019).
Dennis, J. et al. Diagnostic Algorithms to Study Post-Concussion Syndrome Using Electronic Health Records: Validating a Method to Capture an Important Patient Population. J Neurotrauma 36, 2167-2177 (2019).
Saito, Y. et al. Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. Neuron 101, 707-720.e5 (2019).
Uricchio, L. H., Kitano, H. C., Gusev, A. & Zaitlen, N. A. An evolutionary compass for detecting signals of polygenic selection and mutational bias. Evol Lett 3, 69-79 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Xu, M. et al. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 51, 1131-1136 (2019).
Unlu, G. et al. GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish. Am J Hum Genet 104, 503-519 (2019).

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