Hunter Fraser

Hunter B. Fraser is a Professor of Biology at Stanford University, where he leads a research laboratory focused on evolutionary genomics and quantitative genetics. He is a member of Stanford Bio-X, Stanford's interdisciplinary biosciences institute, the Maternal & Child Health Research Institute (MCHRI), the Stanford Cancer Institute, and the Wu Tsai Neurosciences Institute. His research focuses on developing new experimental and computational methods to study the evolution of gene expression and complex traits. As an undergraduate, he participated in the Santa Fe Institute's Undergraduate Complexity Research (UCR) program in 1999, where he received his first introduction to computational biology.

Career

Following his doctorate, Fraser undertook postdoctoral research at Stanford University, working on the relationship between genetic variation and gene regulation across species. During this period, he was supported by the Merck/MIT Computational Systems Biology Initiative Postdoctoral Fellowship (2006) and the Life Science Research Foundation Postdoctoral Fellowship (2007). His long-term goal is to understand the genetic basis of complex traits well enough to introduce them into new species via genome editing.

Model organisms used by the lab span a broad evolutionary range, including yeast (Saccharomyces cerevisiae), Drosophila species, primates, sticklebacks, and cichlids, enabling comparative analyses across widely diverged lineages.

An extension of this technology, CRISPEY-BAR (BARcoded Cas9 Retron Precise Parallel Editing via homology), was subsequently developed to map gene-by-environment (GxE) interactions of naturally occurring genetic polymorphisms at single-nucleotide resolution.

Epigenetics and DNA methylation

The lab has made significant contributions to mapping genetic variants associated with DNA methylation, an epigenetic modification that plays a key role in gene regulation. Fraser developed a novel pooling-based approach to map methylation quantitative trait loci (meQTLs) at genome-wide scale with allele-specific resolution, a major improvement over prior microarray-based methods limited to less than two percent of the genome.

Human evolution and primate genomics

The Fraser lab has used cell fusion techniques to study the cis-regulatory differences between humans and other primates. A notable study published in Nature Genetics used human–chimpanzee fused cells to reveal cis-regulatory divergence underlying skeletal differences between the two species. A parallel study used primate cell fusions to disentangle gene regulatory divergence in neurodevelopment.

Natural selection and adaptive evolution

An influential early contribution from Fraser's lab introduced a statistical test for detecting lineage-specific selection on gene expression, and applied it to genome-wide yeast expression data to show that hundreds of gene expression levels had been subject to lineage-specific selection.

Teaching

At Stanford, Fraser teaches the course The Science and Ethics of Personalized Genomic Medicine (BIO 4N), offered in the Winter quarter.