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.
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.
I am leading and aiding in the assembly of chromosome-scale,
haplotype-phased reference genomes for a diversity of threatened and
elusive marine animals including deep sea fishes and marine mammals.
This work combines long-read and HiC reads, as well as the development
of new software to evaluate accurate phasing and assembly.
Laboratory experiments are a hallmark of my scientific approach. I
frequently employ common garden experiments, multigenerational studies,
and quantitative genetic breeding designs under
environmentally-manipulated seawater systems. These experiments allow me
understand how global change stressors reshape phenotypes, regulation of
the genome, and evolutionary processes.
My research on orgnismal physiology has frequently included
phenotyping of fitness-correlating traits (survival and reproduction)
and performance traits in ectotherms (upper thermal tolerance, growth
rate, biomineralization, development, and metamorphosis). Fo
Integrating environmental and biological data requires statistical analyses go beyond multiple regression, evaluating specific and mechanistic hypotheses constructed from directional relationships among variables. My work in organismal physiology and multiomics employs structural equation modeling to do just this. Using causal inference with structural equations, I evaluate how environmental variation spurs changes in epigenomic variables, gene expression, and phenotypes while controlling for confounding factors that otherwise cause spurious correlation. The goal of this approach is to identify networks and modules of gene regulatory processes that predict plastic responses to the environment.