I am interested in the process and mechanisms of evolution. I study this primarily in fungi using comparative, computational, and experimental tools. We utilize genome and RNA sequencing, sequence analysis, molecular evolution, and phylogenetics, and molecular biology tools to explore the functions of genes or genomic regions identified by analyses to be involved in processes we study.
Our current NSF projects include ExFAB and Herptile Microbiomes and continued work on Ping/mPing Transposon dynamics in Rice and support of a project on Magnaporthe. Our NIH projects include A. fumigatus and C lusitaniae research.
Most of our work is focused in the zygomycete and zoosporic chytrid fungi (fungi that move!). We also have collaborative projects and interests in Aspergillus, Fusarium, Coccidioides, and Clavispora lusitaniae. The lab is increasingly moving towards questions that relate to symbioses with new projects on fungal-bacteria antagonism and on the biological symbioses that occur among fungi, algae, bacteria in desert Biological crusts. I also have a new interest in extremophile fungi and working on projects to understand the halophilic Hortaea werneckii and endolithic Antarctic fungi through genome sequencing and laboratory experiments.
I am involved in several fungal genome projects including co-leading the 1000 fungal genomes project with the JGI and the ZyGoLife project.
My interests are also in the evolution of multicellular forms and regulation of development in fungi. I think understanding how differential gene regulation is established can help learn more about the mechanisms of cell type differentiation. We are also studying the cell wall to understand how innovations in the cell wall and dimorphism impact interactions between pathogenic fungi and hosts they infect. These different projects seek to provide new insight into the big picture of how the complexity of life evolved and how host and pathogen interactions co-evolved.
To address this work we also need tools to sift and mine the gigantic datasets that genomics can produce. In the past I focused on building tools for comparative and computational analyses of genomes including work on the BioPerl and Gbrowse projects and the development of open source software for bioinformatics and life sciences research through the Open Bioinformatics Foundation.
Disclosures
I am a paid consultant for Michroma.
I was briefly part of the Scientific Advisory Board of Sincarne (company is on pause as of 2023).
I have served as a paid consultant in the past for Zymergen, Trace Genomics, Triton Algae, and Indigo Ag.