Research

Pest, Pathogen Vector, and Parasite Genomics

As genome sequencing technologies have matured, it is now possible to generate high-quality genome assemblies and functional genomics data in virtually all organisms, including non-model pest, pathogen vector and parasitic organisms. Our lab is currently contributing to genome projects and functional genomics analyses in insect pests (the red palm weevil Rhynchophorus ferrugineus), pathogen vectors (kissing bugs in the genus Rhodnius), and parasites (the rat tapeworm Hymenolepis diminuta).

Genome Evolution

Whole genome sequence data offers an unparalleled resource for the evolutionary analysis of biological sequences, and allows new analyses of regions and types of mutations that were not available in the pre-genomic era. Our lab uses diverse comparative sequence analysis methods to understand the patterns, rates, and forces of genome evolution within and between species with an emphasis on non-protein-coding regions of the genome. Currently, our work in this area focuses on understanding the evolution of transposable elements (TEs) in insect and yeast genomes.

Genome Bioinformatics

As much of post-genomic biological research (including our own) relies upon high quality genome annotations, our lab is actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences. In the past, we have worked on improving annotation of non-protein-coding regions of the genome including conserved noncoding sequences (CNSs), cis-regulatory modules (CRMs), transcription factor binding sites (TFBSs), transposable elements (TEs) and noncoding RNA (ncRNA) genes. Current projects in this area include developing computational methods for the prediction of polymorphic TE insertions using short- (McClintock) and long-read (TELR) high-throughput whole genome sequence data.