Our Research

We are 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. Our 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 genome sequences available for more than a dozen species and hundreds of new genome and strain sequencing projects are underway in addition to numerous RNA-Seq, and ChIP-Seq projects for prominent members of this phylum including numerous Plasmodium species (the causative agent of malaria), Theileria, Babesia, Eimeria, Sarcocystis, Toxoplasma and Cryptosporidium.

 

Our approach is to apply molecular, computational and phylogenetic tools to the analysis of parasite genomes. Projects include the development of tools for data integration, data mining, comparative genomics and assessing the phylogenetic distribution of genes. We utilize standard molecular biology techniques as well as powerful high-performance computing approaches. We welcome students interested in working on the bench, at the computer, or both.

Apicomplexans Genome Evolution

Figure A
Figure A
Figure B
Figure B
Figure C
Figure C
Figure A
Figure D

 
We study the phylogenetic distribution of genes (Figure A), the evolution of gene families, like the ApiAP2 transcription factors (Figure B) and the conservation of synteny among closely related species yet the amazing lack of synteny throughout the phylum (Figures C and D).

Data Integration - How can we make sense of all the data?

Figure E
Figure E
  

 

Half of the research group is dedicated to the Eukaryotic Pathogen, Vector & Host Informatics Resources Center, VEuPathDB.org (Figure E). We, WS Annotations Group, also work on the development of ontology terms and web service to enhance parasitology research and the automation of work flows, for example by making Galaxy Web Service aware (Figure F).

Figure F
Figure F

Gene Regulation in Cryptosporidium

Figure A
Figure G
 

Which genes are coordinately regulated during the first 72 hours of the in vitro life cycle? (Figure G) and do coordinately regulated genes contain shared motifs? (Figures H-I). Which of these motifs are shared with other apicomplexan species?

 

Figure A
Figure H
Figure A
Figure I

 

The Mitochondrial Genome of Toxoplasma gondii

Figure M
Figure L
 
The mitochondrial genome of this species appears to be different from other apicomplexan species in that it exists in many different permutations and >10,000 fragments of the mitochondrial genome have also been inserted into the nuclear genome (Figure L).