My work utilizes high-throughput sequencing approaches to explore broad patterns in microbial eukaryote assemblages (biodiversity and biogeography, functional roles for microbial taxa, and the relationship between species and environmental parameters), with an emphasis on benthic marine habitats. I am particularly interested in the integration of different data types (metagenomics, marker gene amplicons, and metatranscriptomics), and assessing data processing tools using a combination of environmental and simulated datasets. Biological questions thus drive the development and refinement of computational analysis focused on eukaryotes. My specific research questions include:
- How do different OTU pickers affect the biological interpretation of rRNA amplicon data derived from eukaryotic taxa, where genomes contain multiple rRNA gene copies and intragenomic variation across these rRNA sequences?
- What new and novel biological insights can be gained through the development of innovative, exploratory data visualization tools?
- How can we link disparate types of eukaryotic –omic data to better inform our understanding of ecosystem function?
- How can we improve taxonomic assignments and increase our confidence in species presence/abundance for high-throughput environmental sequence data? (e.g. through tree placement, more robust mathematical/statistical approaches)