Publications

Publications authored by members of the research group

Publications and preprints from our research group in Edinburgh:

• L Lansch-Justen, M El Karoui, HK Alexander (2023). Estimating mutation rates under heterogeneous stress responses. Preprint on bioRxiv (doi:10.1101/2023.09.05.555499) 
• HK Alexander (2023). Quantifying stochastic establishment of mutants in microbial adaptation. Microbiology 169:001365. Available open access

Selected publications by Helen Alexander from previous academic positions:

• HK Alexander, RC MacLean (2020). Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells. Proceedings of the National Academy of Sciences USA 117:19455-19464.

  • available open access from publisher
  • data and code deposited in Dryad
• MA Greischar, HK Alexander, F Bashey, AI Bento, A Bhattacharya, M Bushman, LM Childs, DR Daversa, T Day, CL Faust, ME Gallagher, S Gandon, CK Glidden, FW Halliday, KA Hanley, T Kamiya, AF Read, P Schwabl, AR Sweeny, AT Tate, RN Thompson, N Wale, HJ Wearing, PJ Yeh, N Mideo (2020). Evolutionary consequences of feedbacks between within-host competition and disease control. Evolution, Medicine, and Public Health [2020] pp. 30-34.
  • available open access from publisher
• L Sun*, HK Alexander*, B Bogos, DJ Kiviet, M Ackermann, S Bonhoeffer (2018). Effective polyploidy causes phenotypic delay and influences bacterial evolvability. PLoS Biology 16:e2004644. *Joint first authors.
  • available open access from publisher
  • data and code deposited in Dryad
• HK Alexander*, S 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. †Student advisee.
  • available open access from publisher
• P Nagaraja*, HK 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.
  • available open access from publisher
• HK Alexander, A Lambert, T Stadler (2016). Quantifying age-dependent extinction from species phylogenies. Systematic Biology 65:35-50.
  • available open access from publisher
  • inference methods available within R package ‘TreePar: Estimating birth and death rates based on phylogenies’
• HK Alexander, G Martin, OY Martin, S Bonhoeffer (2014). Evolutionary rescue: linking theory for conservation and medicine. Evolutionary Applications 7:1161-1179.
  • available open access from publisher
• A Lambert, HK Alexander, T Stadler (2014). Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics. Journal of Theoretical Biology 352:60-70.
  • available from publisher - not open access; please contact us if you require a copy
• HK Alexander (2013). Conditional distributions and waiting times in multi-type branching processes. Advances in Applied Probability45:692-718.
  • available on JSTOR
• HK Alexander, S Bonhoeffer (2012). Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics 4:187-202.
  • available open access from publisher
• HK Alexander, LM Wahl (2011). Self-tolerance and autoimmunity in a regulatory T cell model. Bulletin of Mathematical Biology 73:33-71.
  • available from publisher - not open access; please contact us if you require a copy
• HK Alexander, T Day (2010). Risk factors for the evolutionary emergence of pathogens. Journal of the Royal Society Interface 7:1455-1474.
  • available open access from publisher
• HK Alexander, LM Wahl (2008). Fixation probabilities depend on life history: fecundity, generation time and survival in a burst-death model. Evolution 62:1600-1608.
  • available open access from publisher