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University of Wisconsin–Madison

Genome Annotation

We develop computational methods to functionally annotate the human genome. Through integration of high-throughput transciptomic and epigenomic data from a variety of tissue and cell types, we predict context-specific functional non-coding DNA elements.

GenoCanyon

An unsupervised learning framework to predict functional DNA elements in the human genome.

GenoSkyline

Predict tissue-specific functional regions in the human genome through integration of data from Roadmap Epigenomics Project.

GenoSkyline-Plus

A substantial upgrade of GenoSkyline, available for all 127 tissue and cell types from Roadmap Epigenomics Project.

GWAS and sequencing downstream analysis

We develop statistical frameworks to better analyze genetic data and dissect the genetic architecture of complex traits and diseases. In particular, we focus on applications of integrative genome annotations in downstream analyses of GWAS and sequencing-based association studies.

GenoWAP

Functional SNP reprioritization through integrative analysis of GWAS summary statistics and functional annotations.

GNOVA

Powerful and annotation-stratified genetic covariance estimation using GWAS summary statistics

Genetic risk prediction

We also develop novel statistical methods to improve the accuracy of genetic risk prediction. In particular, we achieve better prediction accuracy through explicitly modeling external information such as linkage disequilibrium, functional annotations, and pleiotropy.

AnnoPred

An empirical Bayesian framework that uses integrative functional annotations to improve risk prediction accuracy.