Dr Helen Alexander

Research Interests

I am a theoretical biologist, adding an experimental dimension to my work during my current postdoc. In my past and ongoing research I have developed mathematical (especially stochastic) models of population dynamic and evolutionary processes, mainly of microbial populations and infectious disease spread. At Oxford in Prof. Craig MacLean's lab, my primary project is to investigate the stochastic population dynamics of antibiotic-resistant bacterial cells, using the bacterium Pseudomonas aeruginosa. Specifically, I am quantifying the probability that rare antibiotic-resistant cells grow into large populations, and testing how various environmental factors influence this probability.

Key topics: bacterial and viral population dynamics, evolutionary rescue, drug resistance, mutation rates, phylodynamics, evolutionary epidemiology, stochastic models, maximum likelihood inference

Selected Publications

L. Sun*, H. K. Alexander*, B. Bogos, D. J. Kiviet, M. Ackermann, S. Bonhoeffer (2018). "Effective polyploidy causes phenotypic delay and influences bacterial evolvability". PLoS Biology 16:e2004644. (* joint first authors)

H. K. Alexander*, S. I. Mayer*, S. Bonhoeffer (2017). "Population heterogeneity in mutation rate increases the frequency of higher-order mutants and reduces long-term mutational load". Molecular Biology and Evolution 34:419-436. (* joint first authors)

P. Nagaraja*, H. K. Alexander*, S. Bonhoeffer, N. Dixit (2016). "Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1". Epidemics 14:11-25. (* joint first authors)

H. K. Alexander, A. Lambert, T. Stadler (2016). "Quantifying age-dependent extinction from species phylogenies". Systematic Biology 65:35-50.

H. K. Alexander, G. Martin, O. Y. Martin, S. Bonhoeffer (2014). "Evolutionary rescue: linking theory for conservation and medicine". Evolutionary Applications 7:1161-1179.

H. K. Alexander (2013). "Conditional distributions and waiting times in multi-type branching processes". Advances in Applied Probability 45:692-718.

H. K. Alexander, S. Bonhoeffer (2012). "Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics". Epidemics 4:187-202.

H. K. Alexander, L. M. Wahl (2011). "Self-tolerance and autoimmunity in a regulatory T cell model". Bulletin of Mathematical Biology 73:33-71.

H. K. Alexander, T. Day (2010). "Risk factors for the evolutionary emergence of pathogens". Journal of the Royal Society Interface 7:1455-1474.

H. K. Alexander, L. M. Wahl (2008). "Fixation probabilities depend on life history: fecundity, generation time and survival in a burst-death model". Evolution 62:1600-1608.



List of site pages