I am interested in the process and mechanisms of evolution. I study this primarily in fungi using comparative, computational, and experimental tools. We utilize genomic tools like high throughput sequencing, computational tools for 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.
We are currently focused on projects that include the filamentous mold Neurospora crassa, early diverging chytrid fungi including the frog killing chytrid fungus Batrachochytrium dendrobatidis, and the fungal cell wall. I have also worked on human pathogenic fungi such as Coccidioides and Cryptococcus neoformans and am generally interested in the mechanisms of fungal pathogenesis and the evolution of these factors.
I am involved in several fungal genome projects including co-leading the 1000 fungal genomes project with the JGI.
In the broader scope I am interested 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. I have 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.
The lab is also focused on the development of databases for fungal genome data to make the genome and functional information more available. I also blog about interesting findings in fungal, microbial, and genome research and share protocols and coordinate projects through a wiki site.
I also help maintain the Mycological Society of America website.
At UCR I teach in different years a selection of these courses.
- Bio5C – Introductory Evolution & Ecology
- Bio20 – Dynamic Genomes
- Bio119 – Introduction to Genomics & Bioinformatics
- Microbiology 124 – Microbial Pathogenesis
- Microbiology 211 – Microbial Ecology
- Microbiology 202 – Microbial Pathogenesis and Physiology
- Genetics 240B – Tools for Bioinformatics and Genome Analysis
- Genetics 220 – Computational Analysis of High Throughput Biological Data
I have regularly taught at the CSHL Programming for Biology, at Woods Hole Marine Biological Lab in the Molecular Mycology summer course, and in the past several tutorials on BioPerl and related tools.
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