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Transposable Elements -

Most research in our lab revolves around transposable elements (TEs). These DNA sequences have the ability to move around and/or make copies of themselves within the genomes they occupy. For example, around 10 percent of the human genome is made up of copies of an ~300bp sequence called Alu. Most eukaryotic genomes harbor these elements and we consider it our job to investigate what impact these elements have had on those genomes (not to mention the inverse - the impact genomic conditions have had on the evolution of the TEs) We're also interested in using transposable elements to elucidate evolutionary patterns and processes.

Crocodilian Genomics -

Crocodilians are an ancient group of reptiles of tremendous ecological, social, and evolutionary importance. As one of the major extant reptilian clades, a basic grasp of the structure and function of their genomes is essential to understanding amniote evolution as well as protecting reptile diversity. We have sequenced and assembled the genomes of three crocodilians with the help of colleagues at universities around the world.  We are continuing our research into crocodilian evolution by studying small RNA regulation in alligators and crocodiles.

Bat TE Dynamics -

Our laboratory was fortunate to be the first to find evidence of unprecedented transposable element activity in a particular family of bats and this field has developed as one of our major research efforts. Briefly, all mammals studied to date appear to be the nearly exclusive playground of one class of TEs, the retrotransposons. Other researchers had determined that the second class of elements, DNA transposons, had not had a significant impact on mammalian genomes for the last 40 million years or so.  Myotis lucifugus (the little brown bat) however, has exhibited the opposite trend. For the past 35-40 million years, retrotransposon activity has decreased and DNA transposons have experienced a dramatic resurgence in activity. We are interested in several questions related to this activity including why the taxonomic limits of the activityand the impacts of this activity on genomic function and taxonomic diversity of these bats. 

Small RNAs and TE control -

Even though a small number of TE insertions have consequences, the unrestricted proliferation of TEs can have profound, and mostly deleterious, biological effects.  Consequently, the question of how organisms control TE mobilization has attracted high interest. In the last decade substantial progress has been made in addressing this question. Experimental data suggest that small noncoding RNAs play a central role in protecting the genome from TE-related damage.  Specifically, Piwi-interacting RNAs (piRNAs) are emerging as a key component in defending animal genomes against TE proliferation. In addition to small RNAs defending the genome from TEs, small RNAs are also generated by the TEs themselves.  For example, we have recently identified a massive number of miRNAs (small RNAs involved in gene regulation) that are derived from TEs in bats, dogs and horses.  Finally, we are working to identify patterns of TE control by small RNAs in a variety of insects to elucidate patterns of evolutionary conservation in a diverse and ancient clade.

Mammalian Phylogenomics -

Their primary advantage of modern phylogenomic approaches is the ability to provide vast amounts of sequence data for comparative analysis. Unfortunately, these approaches have thus far seen their application limited to relatively broad taxonomic groups such with very little attention paid to more closely related groups such as those within a single genus. This research, funded by the National Science Foundation, will integrate phylogenomic approaches with TE based systematic inference to revolutionize phylogenetic analysis of large species groups. We are employing TE-based phylogenetic inference to determine the phylogeny of several mammals.