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.