Researchers in our laboratory are encouraged to develop their own line of inquiry and to collaborate with other laboratory members across different disciplines. The general description below is intended to provide some general guidance to potential PhD student candidates and postdocs about what lines of research is already taking place in the lab.
Empirical fitness landscapes
We are fundamentally interested in how genotypes manifest on the phenotypic level. We are working to close the gap between data availability and theoretical interpretation of the data in how it shapes our understanding the nature of fitness landscapes. We have a number of different projects in the lab that aim to produce a large volume of such fitness landscape data, in which for a large number of genotypes we measure some phenotype. These projects target three types of questions: 1) descriptive of the nature of the genotype to phenotype relationships 2) using the fitness landscape to test specific hypotheses in the field of molecular evolution and 3) using these data to improve specific protein functions. Perspective PhD students and Postdocs would be welcome to design their own large scale fitness landscape projects for their own purpose.
Theory and analysis of fitness landscapes
The wealth of available experimental and sequence data, from our lab and publicly available, often requires new computational and conceptual approaches to analyze. We have several projects in the lab that develop the theory of how to analyze fitness landscape data, frequently utilizing novel machine learning and AI tools. Sometimes, these approaches rely on a mathematical way of thinking.
Molecular evolution and bioinformatics
We have a general interest in understanding molecular evolution, and frequently engage in projects that aim to understand what governs the rate of molecular evolution, either across different gene families or with a focus on particularly interesting genes. Sometimes we develop our own tools for this analysis, but the use of already established computational tools to ask evolutionary questions is more typical.
Comparative genomics
Our laboratory has a strong interest in understanding the evolution using a variety of omics approaches, with a strong focus on genomics and transcriptomics. Fungal and avian genomics is of particular focus by some of our lab members, combining obtaining our own omics data with using data that is publicly available.
Plant synthetic biology
In collaboration with our colleagues from the UK and funded by the ASPIRE program of JSPS we are developing plant synthetic with a focus to develop sentinel plans utilizing luciferase reporter assays. While our work currently is focused on development of the luciferase systems, we are taking this as an opportunity to develop plants as a model system in the laboratory.
Ecology of endangered avian species
We participate in a global network focusing on two species of the East Asian-Australian Flyaway. The first one is the Spoon-billed sandpiper and the second is the Kentish plover. For both species we are interested in combining field work with a genomics-based approaches to understand their recent evolution and demographic history with the aim to establish and guide policy and conservation efforts through the EAAF.