My goal is to leave this world with a legacy of discoveries for fellow scientists using non-standard approaches to address biological problems. With the multitude of bioinformatics pipelines that have been standardized, significant details can be overlooked. To add to the problem, the rapid evolution of sequencing technology, an unprecedented amount of data is being generated faster than can be analyzed. Rather than reinventing the wheel, I prefer to adjust standardized pipelines for each species and situation, to reveal more biological insight.
I started my career as a graduate student in Dr. James Birchler’s lab with a project focusing on the utility of extraneous chromosome vectors in maize for gene expression. I used the natural mechanisms of B chromosome inheritance to accumulate different sizes of minichromosomes in individual plants. After reaching multiple numbers, I examined chromosome pairing and segregation, vector expression, and fortuitously discovered a heritable endoreduplicating chromosome. While many studies were published, a great many phenomena associated with repetitive DNA were observed that could not be explained. Thus, my interest was spurred to investigate the role of repetitive DNA in the genome. With this insight, I wrote a grant with Jonathan Wendel to identify and characterize centromeres in allopolyploid and diploid cotton species using microscopy and bioinformatics. Using ChIP-seq with the centromeric histone, I learned a great deal about repetitive DNA, the lack of distinction between genes and transposons, and created numerous pipelines to identify centromeric sequences. By collaborating with a previous mentor, Kai Wang, we identified the diploid progenitor centromere repeats and their subsequent expansion/contraction in allopolyploids.
My second postdoc entailed characterizing the soybean cyst nematode genome and creating a genomics web portal for breeders to utilize. To identify targets for breeding SCN resistance in soybean I applied my knowledge of repetitive DNA to cluster and identify effector genes associated with repetitive elements and tandem dulications in the genome. My current position as an associate scientist in the Genome Informatics Facility has allowed me to work with a multitude of projects, including a continuation of the above. Currently my work is focused on GWAS and genome characterization in a number of wild and cultured abalone species, in attempt to identify factors pertinent to aquaculture.