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Picture of Alexei Dr Alexei Drummond
Senior Lecturer in Bioinformatics

Room 585, Building 303S
Department of Computer Science
University of Auckland
Auckland, New Zealand

+64 9 3737599 ext 88298
alexei AT cs.auckland.ac.nz


Below are a couple of areas that my research is currently focused on. For more detailed information about specific projects related to these research topics please contact me directly.

Virus Evolution and Molecular Epidemiology

An area that I have published in for the last few years is developing and testing software and probabilistic models to understand virus evolution. Most of these models have been assessed through computationally-intensive Bayesian statistical methods such Markov chain Monte Carlo. I would like to continue research in this area, with a particular focus on full genome analyses and scaling software up to much larger data sets. There are a number of important open questions both on the computer science and biology sides of this research.

Genome evolution

A primary area I would like to target in the future is empirically-driven research into evolutionary models of genomic variation within and between species. In particular I would like to bring genomic data to bear on current statistical models of sequence evolution and population genetics. Initially I would like to focus on bacterial genomes because of their relatively small size (~million bytes) and the large numbers of publicly available genomes that have already been sequenced to date.

Model comparison, model averaging and model selection

I am interested in the development of general software tools for doing model comparison, model averaging and model selection. In particular I am interested in models of sequence evolution and coalescent-based models of population genetics. In this context Bayesian inference (reversible-jump MCMC) and maximum-likelihood-based model comparison strategies such as AIC are both promising avenues of enquiry.

Bioinformatic software development

Through industry connections with Biomatters Ltd, I am interested in the development of high-level software platforms for bioinformatic research. These interests include:
Funding for PhD and MSc projects in these areas is available through the BEST scholarship program run by Biomatters.


Simulation Models of Prebiotic Evolution of Genetic Coding

Common to all life on Earth are the mechanisms of genetic encoding, in which specific trinucleotide sequences in DNA and RNA map to specific amino acids in synthesized proteins. Sidney Markowitz's thesis project investigates feasible models of the evolution of genetic encoding from an initially random population of genomes and proteins. The focus of the research is on developing an abstract framework that does not make explicit the molecular details of replication or translation while demonstrating a plausible mechanism of self-organisation.

Last modified: August 6, 2007