Jake Byrnes
About me:
I am currently a graduate student at the University of Chicago in the Department of Ecology and Evolution. I am finishing my Ph.D., working with my advisor Dr. Wen-Hsiung Li. I am a very serious person (see above picture).
My science:
I began my PhD working on questions of large scale genome evolution in yeast. The evolutionary lineage leading to S. cerevisiae (brewer’s yeast) underwent a whole genome duplication approximately 100 million years ago. Following this duplication event, the yeast genome lost approximately 90% of the duplicate genes causing massive reorganization. Taking advantage of the abundance of yeast genomic data, I examined how this reorganization took place and what effects it had on gene expression.
More recently, I have completed an M.S. degree in Statistics. I have shifted my research emphasis to the development of statistical tools to solve evolutionary genetics questions. My first project of this type involved the development of a hidden Markov model to identify gene conversion events between duplicates genes using sequence divergence data. The model is sensitive to the reduction in sequence divergence due to conversion events. I hope to apply this model to gain a better understanding of the evolutionary consequences of concerted evolution.
One of my current projects involves the development of a general comparative method for identifying both expression variation and copy number variation using tiling microarray data. Briefly, I have developed a hidden Markov model for which the observations are probewise p-values. This way the user can apply whatever comparative statistical test (t-test, f-test, etc.) is appropriate to the data individually for each probe of the array. The HMM is then used to identify regions with an over-abundance of either high or low p-values (depending on the effect of interest) against a background of roughly uniform p-values for regions in which the null hypothesis holds. This model is likely to be useful for numerous questions. For example, I am currently collaborating with Dr. Justin Borevitz and Dr. Xu Zhang to examine alternative splicing patterns from two closely related lines of A. thaliana using this model.
