Heterogeneous rates of duplication, loss and transposition of genes

Date

Tuesday, November 24

Place

Informatics East, Room 130

Time

1:00 p.m.

The School of Informatics and Computing will be holding a Dissertation Proposal Colloquium by Mira Han.

As part of the dissertation process, our Ph.D. Informatics students are required to present their proposed dissertation topic in a public colloquium. There will be question and answer time after the presentation.

A surprising discovery from the whole genome sequencing of various mammalian genomes is that the divergence in the structure of two genomes is greater than the total sequence divergence between the homologous genes in the genomes. Thus the variation in genome structure appears to have a significant role complementary to that of sequence divergence in explaining the phenotypic difference across species. However, the studies on the large-scale structural variation are still at an initial stage, compared to the fifty years of research accumulated on sequence variation. My thesis proposes to study the rate of large-scale structural genetic change. We will focus on the genetic changes in the genome that are measured in units of genes instead of amino acids or nucleotides. The variables we are studying are the presence, multiplicity, and arrangement of genes in the genome, and the processes we are examining are operations that change these variables i.e. duplication, loss, and transposition. The study will carefully encode the variation we see between different genomes into manageable pieces of information, build a set of probabilistic models that describe the processes that may generate the variation we observe, and statistically evaluate different models with the empirical data from several genomes of Drosophila, yeast, and mammals. By doing so, we aim to understand the tempo of structural change, and find trends that pertain to specific lineages or patterns associated with specific gene families.