Research

We aim to isolate and culture the most abundant, and as yet unknown, protists on earth. Once in culture, we will characterize their cell biology, ultrastructure, life history, behavior and interspecies interactions using time-lapse and fluorescence microscopy techniques, accompanied by single-cell sequencing. In this process, we hope to establish these protists as new model systems whose biology and ecosystem relevance can be studied intensively in the lab.

We begin with hypotheses, based on our lab studies, regarding the potential ecological roles of the abundant protists we study. Armed with the their gene catalogs from genome and transcriptome sequencing, we apply the bioinformatic methods we developed to investigate the patterns in their gene expression in global-scale metatranscriptomic sequencing databases. As examples, these hypotheses may relate to their ecological roles, in terms of species interactions, or their responses to changes in environmental conditions.

We develop new computational methods to study the genes and genomes of diverse eukaryotes in order to reconstruct the evolutionary history of gene families, protein domains and the biological processes they drive.

In addition, because only a tiny fraction of protist species are available in culture, we anticipate that the sequence resources we generate for newly isolated protists will be informative for studies of eukaryotic diversity and the evolution of gene content and function.

As we work, we design the output of our research projects to be reusable. We make our data, code and wet lab protocols available to the research community. We also lead (EukProt) or participate in (UniEuk) projects to collect and organize eukaryotic sequence data and taxonomy, in order to standardize and streamline their use for all researchers.

Please see our Resources page for more information.