Mitch Day

My main research focus is on applications of Sequencing-by-Hybridization (SBH) to microbial community analysis. SBH is a classic computational biology problem that seeks to re-assemble a sequence given its k-tuple list (partial or complete list of possible sub-strings). The re-assembly problem is challenging in itself. When faced with the error-prone nature of low-stringency hybridization of short (7-12 bp) nucleic acid probes, it becomes quite difficult and remains an open problem in computational biology.

There are applications of SBH that stop short of reconstructing full sequence. Collectively, we refer to these applications as Oligonucleotide Fingerprinting by Hybridization (OF-Hyb). OF-Hyb methods rely on a binary fingerprint generated by serial hybridization of short probes, but the probes are selected according to various criteria depending upon the research question at hand.

I focus on probe design methods for applying OF-Hyb to microbial community analysis using two approaches, in silico and in vitro. For my in silico projects, I'm looking for correlation between probes selected by certain algorithms and accepted microbial phylogenies. For the in vitro project, I will apply a probe set to isolates from an Antarctic salt pond to generate a community fingerprint. The advantage of this approach is the ability to separate, identify and characterize a large number of samples with less effort and expense. Isolates that show a desired fingerprint can be subjected to more detailed analysis using established methods.