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For an up-to-date list of publications through PubMed, click here.

2016

Sobel Leonard, A., McClain, M., Smith, G. Wentworth, D. Halpin, R., Lin, X., Ransier, A., Stockwell, T., Das, S., Gilbert, A., Lambkin-Williams, R., Ginsburg, G., Woods, C., Koelle, K., and C. Illingworth (submitted). Limited effective reassortment shapes influenza evolution in a human host.

Flasche, S.*, Jit, M., Rodriguez-Barrauer*, I., Coudeville*, L., Recker*, M., Koelle*, K., Milne*, G., Hladish*, T., Perkins*, A., Dorigatti, I., Cummings, D., Espana, G., Kelso, J., Longini, I., Lorenco, J., Pearson, C., Reiner, R.C., and N. Ferguson. (in press, PLoS Medicine) The long term safety, public health impact, and cost effectiveness of routine vaccination with Dengvaxia®: a model comparison study. *authors contributed equally.

Ben-Shachar, R., Schmidler, S.C., and K. Koelle (in press, PLoS Computational Biology). Drivers of inter-individual variation in dengue viral load dynamics.

Sobel Leonard, A., McClain, M., Smith, G. Wentworth, D. Halpin, R., Lin, X., Ransier, A., Stockwell, T., Das, S., Gilbert, A., Lambkin-Williams, R., Ginsburg, G., Woods, C., and K. Koelle (in press, J. of Virology). Deep sequencing of influenza A virus from a human challenge study reveals a large founder population size and rapid intrahost viral evolution. doi: 10.1128/JVI.01657-16. Journal of Virology Spotlight

Flasche, S.*, Jit, M., Rodriguez-Barrauer*, I., Coudeville*, L., Recker*, M., Koelle*, K., Milne*, G., Hladish*, T., Perkins*, A., Dorigatti, I., Cummings, D., Espana, G., Kelso, J., Longini, I., Lorenco, J., Pearson, C., Reiner, R.C., and N. Ferguson. (2016) Comparative modelling of dengue vaccine public health impact. Report to the Strategic Advisory Groups of Experts (SAGE) on Immunization.  *authors contributed equally.

2015

Koelle, K. and D.A. Rasmussen (2015). The effects of a deleterious mutation load on patterns of influenza A/H3N2’s antigenic evolution in humans. eLife. doi: 10.7554/eLife.07361

Ben-Shachar, R. and K. Koelle. Minimal within-host dengue models highlight the specific roles of the immune response to primary and secondary dengue infections. (2015) Journal of the Royal Society,  Interface. 12 (105). doi:

2014

Koelle, K. and D.A. Rasmussen. Influenza: prediction is worth a shot. (2014) Nature. 507 (7490), pp. 47-48. doi:10.1038/nature13054

Rasmussen, D.A., Volz, E., and K. Koelle (2014). Phylodynamic inference for structured epidemiological models. PLoS Computational Biology. 10(4), p. e1003570. doi: 10.1371/journal.pcbi.1003570

Rasmussen, D.A., Boni, M., and K. Koelle (2014). Reconciling phylodynamics with epidemiology: The case of dengue virus in southern Vietnam. Molecular Biology and Evolution. doi: 10.1093/molbev/mst203

2013

Scholle, S.O., Ypma, R., Lloyd, A.L., and K. Koelle (2013). Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics. The American Naturalist. 182(4), pp.494-513. doi: 10.1086/672000

Yuan, H. and K. Koelle (2013). The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis. Philosophical Transactions of the Royal Society, B. 368 (1614): p. 20120204. doi: 10.1098/rstb.2012.0204. PDF

Luo, S. and K. Koelle (2013). Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature. The American Naturalist.181, pp. S58-S75. doi: 10.1086/669952. PDF

Volz, E.M., Koelle, K., and T. Bedford (2013). Viral phylodynamics. PLoS Computational Biology. 9(3): e1002947. doi: 10.1371/journal.pcbi.1002947. PDF

Wu, S., Koelle, K., and A. Rodrigo (2013). Coalescent entanglement: conditional dependence of the times-to-common-ancestry of mutually exclusive pairs of individuals. Journal of Heredity. 104 (1): 86-91. doi: 10.1093/jhered/ess074. PDF

2012

Ratmann, O., Donker, G., Meijer, A., Fraser, C., and K. Koelle (2012). Phylodynamic inference and model assessment with Approximate Bayesian Computation: influenza as a case study. PLoS Computational Biology. 8(12):e1002835. doi: 10.1371/journal.pcbi.1002835. PDF

Luo, S., Reed, M., Mattingly, J., Koelle, K. (2012) The impact of host immune status on the within-host and population dynamics of antigenic immune escape. Journal of the Royal Society,  Interface. 9, pp. 2603-2613. PDF

Arinaminpathy, N., Ratmann, O., Koelle, K., Epstein, S.L., Price, G.E., Viboud, C., Miller, M., Grenfell, B. (2012) Impact of cross-protective vaccines on the epidemiological and evolutionary dynamics of influenza. PNAS 109(8), pp. 3173-3177. PDF

WHO-VMI Dengue Vaccine Modeling Group (2012) Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS Neglected Tropical Diseases. 6(3), e1450. (The group consists of 28 experts in dengue epidemiology, clinical practice, immunology, virology, vaccinology, entomology, and mathematical modeling.) PDF

2011

Koelle, K., Rasmussen, D.A. (2011) Rates of coalescence for common epidemiological models at equilibrium. Journal of the Royal Society, Interface. 9(70), pp.997-1007. PDF

Rasmussen, D.A., Ratmann, O., Koelle, K. (2011) Inference for nonlinear epidemiological models using genealogies and time series. PLoS Computational Biology. 7 (8), e1002136. PDF | CODE

Koelle, K., Ratmann, O., Rasmussen, D.A., Pasour, V., Mattingly, J. (2011) A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses. Proceedings of the Royal Society, Series B. 278, pp. 3723-3730. PDF

2010

Koelle, K., Khatri, P., Kamradt, M., Kepler, T. (2010) A two-tiered model for studying the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. Journal of the Royal Society, Interface. 7, pp.1257-1274. PDF | CODE

2009

Koelle, K., Kamradt, M., Pascual, M. (2009) Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: influenza as a case study. Epidemics. 1, pp. 129-137. PDF

Koelle, K. (2009) The impact of climate on the disease dynamics of cholera. Clinical Microbiology and Infection. 15(s1), pp. 29-31. PDF

2008

Cobey, S., Koelle, K. (2008) Capturing escape in infectious disease dynamics. Trends in Ecology and Evolution. 23(10), pp.572-577. PDF

Nagao, Y., Koelle, K. (2008) Decreases in dengue transmission may act to increase the incidence of Dengue Hemorrhagic Fever. Proceedings of the National Academy of Sciences. 105(6), pp. 2238-2243. PDF

Pascual, M., Cazelles, B., Bouma, M., Chaves. L., Koelle, K. (2008) Shifting patterns: malaria dynamics and rainfall variability in an African highland Proceedings of the Royal Society, Series B, Biological Sciences. 275. pp.123-132. PDF

2007

Finkelman, B., Viboud, C., Koelle, K., Ferrari, M., Bharti, N., Grenfell, B. (2007) Global Patterns in Seasonal Activity of Influenza A/H3N2, A/H1N1, and B from 1997 to 2005: Viral Coexistence and Latitudinal Gradients. PLoS One. 2(12): e1296. PDF

2006

Koelle, K., Cobey, S., Grenfell, B., & Pascual, M. (2006) Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 314. pp. 1898-1903. PDF

Koelle, K., Pascual, M., Yunus, M. (2006) Serotype cycles in cholera dynamics. Proceedings of the Royal Society, Series B, Biological Sciences. 273. pp. 2879-2886. PDF

Pascual, M., Koelle, K., Dobson, A. (2006) Hyperinfectivity in Cholera: A New Mechanism for an Old Epidemiological Model? PLoS Medicine. 3 (6). p. e280. PDF

2005

Koelle, K., Rodó, X., Pascual, M., Yunus, M., & Mostafa, G. (2005) Refractory periods to climate forcing in cholera dynamics. Nature. 436. pp. 696-700. PDF

Koelle, K., Pascual, M., Yunus, M. (2005) Pathogen adaptation to seasonal forcing and climate change. Proceedings of the Royal Society, Series B, Biological Sciences.272. pp. 971-977. PDF

Koelle, K., Vandermeer, J. (2005) Dispersal-induced desynchronization: from metapopulations to metacommunities. Ecology Letters. 8(2). pp. 167-175. PDF

2004

Buckee, C., Koelle, K., Mustard, M., Gupta, S. (2004) The effects of host contact network structure on pathogen diversity and strain structure. Proceedings of the National Academy of Sciences. 101(29). pp.10839-10844. PDF

Koelle, K., Pascual, M. (2004) Disentangling extrinsic from intrinsic factors in disease dynamics: a nonlinear time series approach with an application to cholera. The American Naturalist 163(6), pp.901-913. PDF

Savit, R., Koelle, K., Treynor, W., Gonzalez, R. (2004) Man and Superman: Human Limitations, Innovation, and Emergence in Resource Competition in Collectives and the Design of Complex Systems, eds. Tumer, K. & Wolpert, D. (Springer-Verlag, New York, NY).

2002

Blower, S.M., Koelle, K., Mills, J. (2002) Health policy modeling: epidemic control, HIV vaccines and risky behavior in Quantitative Evaluation of HIV Prevention Programs, eds. Kaplan, E. H. & Brookmeyer, R. (Yale University Press, New Haven, CT).

2001

Blower, S.M., Koelle, K., Kirschner, D.E., Mills, J. (2001) Live attenuated HIV vaccines: Predicting the tradeoff between efficacy and safety. Proceedings of the National Academy of Sciences 98(6), pp. 3618-3623. PDF

1999

Blower, S.M., Koelle, K., Lietman, T. (1999) Antibiotic resistance- to treat… Nature Medicine 5(4), p. 358. PDF

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