John Quackenbush

Abstract In analyzing gene regulatory network models, a common question is how members of a particular set of genes are connected. For example, one might want to explore network relationship between a set of differentially expressed genes, a gene set previously reported in the literature, or elements of one or more pathways.

Abstract Complex traits are determined by many loci---mostly regulatory elements---that, through combinatorial interactions, can affect multiple traits. Such high levels of epistasis and pleiotropy have been proposed in the omnigenic model and may explain why such a large part of complex trait heritability is usually missed by genome-wide association studies while raising questions about the possibility for such traits to evolve in response to environmental constraints.

Abstract Single Nucleotide Polymorphisms (SNPs) associated with traits typically explain a small part of the trait genetic heritability---with the remainder thought to be distributed throughout the genome. Such SNPs are likely to alter expression levels of biologically relevant genes. Expression Quantitative Trait Locus (eQTL) networks analysis has helped to functionally characterize such variants.