Scott Clark

My current research interests are in metagenomics and its applications. Metagenomics is the analysis of genetic sequence information from communities, rather than single organisms. A common analogy is sifting through many scrambled jigsaw puzzles and trying to coax out useful information.
Last summer I worked at Los Alamos (LANL) developing fast local alignment algorithms for these metagenomic datasets. Because of the size and uncertainty involved in sampling sequences from communities instead of single organisms, different and new methods need to be developed to make the field approachable. I am continuing to work with the metagenomics group there on these algorithms and their applications.

This summer I am going to work at the Joint Genome Institute at LBL. I will be working with a group on metagenomic assembly. This is the reassembling of genomes from communities after they have been chopped up to be sequenced. It is an extremely difficult problem computationally and I will be working with them developing quick, easily parallelizable methods and modeling the uncertainty that they introduce to the system.

I am also working on a project dealing with speeding up and simplifying boolean satisfiability problems using random, redundant data and another project adding optimal learning techniques to my metagenomic algorithms to increase efficiency.

Kunes KC, Clark SC, et. al. Left handed beta helix models for mammalian prion fibrils. Prion. 2008 Apr;2(2):81-90. Epub 2008 Apr 23.