San Diego State University Mathematics Research Experience for Undergraduates and Teachers

2007 Projects:

Phage Contig Spectra Analysis (biomathematics)
Project Director: Peter Salamon

Phages are viruses that predate on bacteria. The study of phage communities has recently been made possible using metagenomic techniques, i.e. techniques that work from shotgun sequencing of the DNA fragments extracted from environmental samples such as seawater, soils, feces, etc. Al- though there are about 1031 phage particles on earth, most of them are unknown and no techniques are available for studying them in culture. Contigs are contiguous DNA fragments that overlap and give the primary source of information about the structure (e.g. rank-abundance relationships) of a phage community. The SDSU Phagemath Research Group has developed a suite of models to analyze the sequence of numbers of contigs of various sizes observed from an environment, the so-called contigs spectrum. This research group includes faculty from the department of math- ematics and statistics, faculty from the department of biology, as well as a large group of graduate and undergraduate students. PHACCS, an online tool for the analysis of PHAge Communities from Contig Spectra, is based on this suite of models. The online implementation was written by several masters students; it is available for use by anyone on the web and gets regularly utilized all over the world. In fact, our server hosting the software is unable to keep up with the demand. Since their publication last year, the models have been further developed. The algorithms have been sped up and better adapted to the much larger sizes of available datasets that have grown a thousand fold due to better and cheaper sequencing technology. The proposed project is for a team of REU students to investigate and implement these improvements to the community structure models available in PHACCS. The improvements include alternative summing techniques for populations with very many genotypes, automated model selection building in statistical tests for model selection and more complicated models employing additional parameters.

Internet Survey Weighting Schemes (statistics)
Project Director: Kristin Duncan

This project will study ways to help account for population members who do not have internet access when conducting internet surveys. Weighting schemes will be formulated and evaluated to determine how well they improve the accuracy of estimates based on survey data. The study will use data from the computer and internet supplement of the U.S. Census Bureau's Current Population Survey. More details may be found here.