selected publications
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academic article
- Modeling the therapeutic potential of defective interfering particles in the presence of immunity. Virus Evolution. 8. 2022
- The coalescent with replication-independent mutations. PeerJ. 10. 2022
- A White Noise Approach to Evolutionary Ecology. Journal of Theoretical Biology. 521:110660. 2021
- The Timing and Nature of Behavioural Responses Affect the Course of an Epidemic. Bulletin of Mathematical Biology. 82:14. 2020
- Spatial structure undermines parasite suppression by gene drive cargo.. PeerJ. 7:e7921. 2019
- Paul Joyce and the infinite alleles model. Theoretical Population Biology. 122:43163. 2018
- Phage-Bacterial Dynamics with Spatial Structure: Self Organization around Phage Sinks Can Promote Increased Cell Densities.. Antibiotics (Basel, Switzerland). 7. 2018
- Evolution and the duration of a doomed population. Evolutionary Applications. 10.0:471.0-484.0. 2017
- A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis. PLOS Computational Biology. 12. 2016
- Opinion strength influences the spatial dynamics of opinion formation. Journal of Mathematical Sociology. 40:207-218. 2016
- Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ. 4. 2016
- Models for the directed evolution of bacterial allelopathy: bacteriophage lysins. PeerJ. 3. 2015
- Fitness benefits of low infectivity in a spatially structured population of bacteriophages. Proceedings of the Royal Society B: Biological Sciences. 281. 2014
- Invasion of E. coli biofilms by antibiotic resistance plasmids. Plasmid. 70:110-119. 2013
- The impact of humans on the evolution and mobilization of the environmental antibiotic resistome. Emerging Infectious Diseases. 19. 2013
- On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations. Journal of Theoretical Biology. 294:144-152. 2013
- Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage phi X174. Bmc Evolutionary Biology. 13. 2013
- Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface. Applied and Environmental Microbiology. 77. 2011
- Accounting for mating pair formation in plasmid population dynamics. Journal of Theoretical Biology. 262:711-719. 2010
- Dual reporter system for in situ detection of plasmid transfer under aerobic and anaerobic conditions.. Applied and Environmental Microbiology. 76:4553-4556. 2010
- Space, Time, and Host Evolution Facilitate Coexistence of Competing Bacteriophages: Theory and Experiment. American Naturalist. 173:E121-E138. 2009
- Application of ecological network theory to the human microbiome.. Interdisciplinary Perspectives on Infectious Diseases. 2008. 2008
- Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. The ISME (International Society for Microbial Ecology) Journal. 2:1024-1039. 2008
- Analyzing animal movements using Brownian bridges. Ecology. 88:2354-2363. 2007
- Modelling the spatial dynamics of plasmid transfer and persistence.. Microbiology. 153:2803-2816. 2007
- Small-world mcmc and convergence to multi-modal distributions: From slow mixing to fast mixing. Annals of Applied Probability. 17:284-304. 2007
- Markov Chain Monte Carlo in small worlds. Statistics and Computing. 16:193-202. 2006
- Spatial self-organization in a cyclic resource-species model. Journal of Theoretical Biology. 241:14-25. 2006
- On the Meaning and Existence of an Effective Population Size. Genetics. 169:1061-1070. 2005
- Spatial invasion by a mutant pathogen. Journal of Theoretical Biology. 236:335-348. 2005
- Spatial models: Stochastic and deterministic. Mathematical and Computer Modelling. 40:393-409. 2004
- The coalescent process in a population with stochastically varying size. Journal of Applied Probability. 40:33-48. 2003
- When can one detect overdominant selection in the infinite-alleles model?. Annals of Applied Probability. 13:181-212. 2003
- Gaussian limits associated with the Poisson-Dirichlet distribution and the Ewens sampling formula. Annals of Applied Probability. 12:101-124. 2002
- Coalescent theory for seed bank models. Journal of Applied Probability. 38:285-300. 2001
- A spatial model of range-dependent succession. Journal of Applied Probability. 37:1044-1060. 2000
- The two-stage contact process. Annals of Applied Probability. 9:331-351. 1999
- Ancestral processes with selection. Theoretical Population Biology. 51:210-237. 1997
- The genealogy of samples in models with selection. Genetics. 145:519-534. 1997
- Representations for continuous additive functionals of super-Brownian and super-stable processes. Statistics and Probability Letters. 34:211-223. 1997
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chapter
- Modeling Phage Plaque Growth. Bacteriophage Ecology. Cambridge University Press. 415-438. 2008