Approaches and methods

Long-read sequencing

In my postdoctoral research, I’m leveraging long-read genomic and transcriptomic data to understand the causes and consequences of gene family expansion and contraction. Exploring a classical example of environmental adaptation, the evolution of antifreeze protein (AFP) genes in polar fishes, I’m using PacBio HiFi data to study structural genomic variation such as copy number variants, translocation, and inversion.

In shallow-water, cold-adapted lineages that experienced expansions in AFP copy number, I’m employing full-length long-read RNA-seq to confirm the expression of duplicated AFP genes and understand how gene family expansion has influenced their regulation.

In recent work led by undergraduate Owen Moosman, we have developed and applied tools to more accurately study structural variants in alignments of long reads to haplotype-aware data structures such as phased genomes and pangenomes.

Epigenomics

The role of epigenomic processes such as DNA methylation in driving changes in gene expression and phenotype is poorly understood. Part of this knowledge gap is attributed to (i) poor understanding of how different types of epigenomic modifications to DNA and chromatin interact and (ii) poor integration of epigenomic and transcriptomic data. I have integrated ATAC-seq with bisulfite sequencing and RNA-seq sampled from purple sea urchins exposed to experimental upwelling to investigate how chromatin accessibility influences associations between differential DNA methylation and expression in response to environmental stress.

To improve multiomic studies of DNA methylation and gene expression, I am currently codinge a structural equation modeling approach to test for changes in gene expression that are associated with environmentally-induced changes in DNA methylation. This project leverages whole genome bisulfite sequencing data and RNA-seq from urchin larvae spawned in a quantitative genetic breeding design.

Genome assembly

Section forthcoming br>

Experimental design

Laboratory experiments are a hallmark of my scientific approach. I frequently employ common garden experiments, multigenerational studies, and quantitative genetic breeding designs under highly-controlled environmental manipulation . These experiments allow me understand how global change stressors reshape the expression of genetic variation, epigenetic modifications, and regulation of the genome.

Physiological performance

Section forthcoming

Bayesian statistics

Section forthcoming