Holder Laboratory
Research
Biological
Applications in Optimization
Allen Holder, Ph.D.
Associate Professor
Department of Mathematics
Mathematics and computation are increasingly important to biological
studies. In particular, many biological structures are assumed to be
(nearly) optimized, which allows us to dovetail the mathematical
methods of optimization with the computational questions that are being
posed in biology. One of two such problems is proposed for this
project. The first possibility lies in
the study of E. coli's
metabolic network through what is called Flux Balance Analysis
(FBA). The premise behind this research is that a cell's
enzymatic state maximizes growth within the confines of its
environmental. The second possibility is to address the problem of
haplotype inference by pure
parsimony, which asks us to construct the minimal amount of genetic
diversification needed to explain the current population.
The project will start with an introduction to both problems, and the
one that is selected will depend on the participant's interest. Both
problems are well-suited to undergraduate research, and there is a
strong possibility that the work will lead to peer-reviewed
publication. The ideal candidate will have strong interests in both
mathematics and computer science, together with a willingness to learn
about the biological application.
