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I am interested in parasite genomics and the biology of genome evolution. How do genomes evolve? Can we trace gene order, identify and determine the fate of horizontally transferred genes (as well as any existing endogenous orthologs) and identify genes that are phylogenetically restricted? The answers to these questions are important because of the insight they provide into parasite biology and the identification of potential drug targets. My research focuses on, but is not limited to, Apicomplexan parasites. The Apicomplexa are ideal for phylogenomic studies for several reasons:
- All of the estimated 5000 species of Apicomplexa are believed to be parasitic
- The Apicomplexa have a rich evolutionary history that includes endosymbiotic events and extensive gene transfer
- There are currently 14 genome sequencing projects underway (2 are complete) and numerous EST and GSS projects for prominent members of this phylum including numerous Plasmodium species (the causative agent of malaria), Theileria, Babesia, Eimeria, Toxoplasma and Cryptosporidium.
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Our approach is to apply molecular, computational and phylogenetic tools to the analysis of parasite genomes. Projects include the development of tools for data mining, comparative genomics and assessing the phylogenetic distribution of genes. We utilize standard molecular biology techniques as well as powerful multi-processor Linux clusters on the computational side. I welcome students interested in working on the bench, at the computer, or both.
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NIH/Massachusetts Institute of Technology HHSN26620040001C - Cryptosporidium parvum EST's(PI)
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NIH R01 AI068908 - Genome Evolution, Innovation and Host adaptation in the Apicomplexa (PI)
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NIH R01 AI065246 - Informatics Analysis of Cryptosporidium gene Expression (Co-PI)
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NIH R01 AI058515 - PlasmoDB (Co-PI)
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NIH D43 TW007012 - Informatics training for Brazilian vector and parasitic diseases (PI)
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NIH Contract # HHSN26600400037C - Integrated databases for Apicomplexan Pathogens (Co-PI)
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USDA CSREES 0624492 - Genome sequencing and comparative analysis of coronaviruses (Co-PI)
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Building a Trypanosoma cruzi genome resource: Integrating diverse genomic data sets to facilitate basic research, AHA, 0330338N
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Pattern finding and phylogenetic restriction in Trypanosoma cruzi, PhRMA Foundation
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Perkinsus marinus EST project, NOAA - MD Sea Grant SA7528068-I (Co-investigator)
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