Current Research

rRNA

Goal 1 – Ascertain microRNA molecular origins to facilitate target prediction.
Computationally predicting miRNA targets. Active transposable elements (TEs) regularly integrate into inter- and intragenic regions. Since numerous miRNAs have now been identified as being formed from TEs, and miRNAs target mRNAs through complementarity, logic dictates that a miRNA regulates transcripts baring copies of its progenitor TE. In our lab, student researchers are trained to actively search characterized and novel genomes alike for functional miRNA targets. Students identify putative miRNA::target mRNA relationships through using a unique computational strategy which limits miRNA target searches to transcripts containing that miRNA’s progenitor TE.

Goal 2 - Identify novel genomic repeat and microRNA compositions 
Another focus of our lab is de novo genome sequencing using the departmental Ion Torrent Next Gen sequencer as well as training students in the retrieval of sequences from publicly available datasets. Following sequence acquisition, students are trained how to annotate these using web-based applications, and how to use alignment software to identify genomic hairpins, putative miRNAs, and novel repeats.

Goal 3 – Characterize novel prokaryotic and eukaryotic small RNAs.
I wholly believe that life arose from small RNA interactions. I further believe that life and all cellular activity are still coordinated by small, noncoding RNA biology. Unfortunately due to their small size, the vast majority of small, noncoding RNAs remain undescribed. Another focus of my laboratory is the sequencing of small RNA populations from a variety of prokaryotic and eukaryotic species.

Goal 4 - Characterize miRNA misregulations with casual roles in oncogenesis.
Utilizing many of the tools described above, my students also computationally examine additional putative (potentially causal) microRNA interactions through exploring publicly available small RNA libraries derived from specific oncologies.