computer science


Shawn Martin
My research interests have revolved around the use of computational techniques to analyze and understand large, high-dimensional scientific datasets, mostly in bioinformatics, cheminformatics, and computational biology.

My most recent interest is at the intersection of dimension reduction, computational algebraic geometry, and computational topology. My application interest is molecular biology. I believe there is a lot to be gained by combining statistical approaches (such as dimension reduction) with approaches using structural information. In particular, our recent analysis of cyclo-octane manifolds showed that a structure that was previously assumed to be a 2 dimensional manifold had a very complicated structure, and was in fact not a manifold at all. This opens up a whole new and previously unconsidered avenue of research. How can you use computational topology to improve dimension reduction? How can you perform dimension reduction on algebraic varieties?

In the past I have been involved in various other projects, including: inferring genetic networks from time series gene expression measurements; predicting protein interactions from sequence; extrapolating protein networks from protein complexes; predicting protein structure from sequence; designing novel homopolymers with specific properties; designing novel peptide rings to inhibit blood clotting; understanding the genetic basis of leukemia; computing the underlying dimension of image datasets; and identifying superconducting materials.

Postal Address

Department of Computer Science
University of Otago
PO Box 56
Dunedin 9054
New Zealand

Courier Address

Department of Computer Science
University of Otago
Owheo Building
133 Union Street East
Dunedin 9016
New Zealand

Phone, Fax, Email

Phone: +64 3 479-7950
Fax: +64 3 479-8529