Hinkley, Trevor

ETH Zürich
Trevor Hinkley
Institut f. Integrative Biologie
CHN H 78
Universitätstrasse 16
8092 Zürich

Phone: +41 44 632 76 23
E-Mail: 

Research

Fuzzy Modularity

Traditional modular decompoitions in systems biology focus on deriving a crisp result, partitioning elements of the system entirely into one module. Whilst this is a viable strategy for artificial systems, which tend to be deesigned with crisp modularity as an objective, biological systems show a much greater degree of "cross-talk" between modules. I am therefore constructing a fuzzy graphical clustering algorithm, called xanabalph, based on objective function minimization and fuzzy cluster merging to apply to biological networks.

Viral Fitness Prediction

Using an astounding data-set of over 60,000 HIV-1 sequences and measured fitnesses, I have applied an algorithm based on kernel ridge regression to produce fitness landscapes for this virus under 16 different environments. It is hoped that these fitness landscapes will shed new light on evolutionary questions in general and questions related to the evolution of drug resistance in HIV specifically.

Publications

• Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum (2007)
• The Evolutionary Systems Biology of HIV Drug Resistance (In press)