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Katia Koelle

Principle Investigator

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Papers

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K. (2019). Correction for Sobel Leonard et al., "Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus". Journal of virology, 93(17)

Ben-Shachar R, Koelle K. (2018). Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context. Nature communications, 9(1)

Gallagher ME, Brooke CB, Ke R, Koelle K. (2018). Causes and Consequences of Spatial Within-Host Viral Spread. Viruses, 10(11)

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K. (2017). Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus. Journal of virology, 91(14)

Raghwani J, Thompson RN, Koelle K. (2017). Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution. Virus evolution, 3(2)

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K. (2016). Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification. Journal of virology, 90(24)

Ben-Shachar R, Schmidler S, Koelle K. (2016). Drivers of Inter-individual Variation in Dengue Viral Load Dynamics. PLoS computational biology, 12(11)

Koelle K, Rasmussen DA. (2015). The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans. Elife

Ben-Shachar R, Koelle K. (2015). Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections. Journal of the Royal Society, Interface, 12(103)

Koelle K, Rasmussen DA. (2014). Influenza: Prediction is worth a shot. Nature, 507(7490)

Rasmussen DA, Boni MF, Koelle K. (2014). Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Molecular biology and evolution, 31(2)

Rasmussen DA, Volz EM, Koelle K. (2014). Phylodynamic inference for structured epidemiological models. PLoS computational biology, 10(4)

Yuan HY, Koelle K. (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 of London. Series B, Biological sciences, 368(1614)

Scholle SO, Ypma RJ, Lloyd AL, Koelle K. (2013). Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics. The American naturalist, 182(4)

Luo S, Koelle K. (2013). Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature. The American naturalist

Ratmann O, Donker G, Meijer A, Fraser C, Koelle K. (2012). Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study. PLoS computational biology, 8(12)

Meyers LA, Kerr B, Koelle K. (2012). Network perspectives on infectious disease dynamics. Interdisciplinary perspectives on infectious diseases

Luo S, Reed M, Mattingly JC, 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(75)

Koelle K, Rasmussen DA. (2012). Rates of coalescence for common epidemiological models at equilibrium. Journal of the Royal Society, Interface, 9(70)

Koelle K, Ratmann O, Rasmussen DA, Pasour V, Mattingly J. (2011). A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses. Proceedings. Biological sciences, 278(1725)

Rasmussen DA, Ratmann O, Koelle K. (2011). Inference for nonlinear epidemiological models using genealogies and time series. PLoS computational biology, 7(8)

Koelle K, Khatri P, Kamradt M, Kepler TB. (2010). A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. Journal of the Royal Society, Interface, 7(50)

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(2)

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 of the United States of America, 105(6)

Cobey S, Koelle K. (2008). Capturing escape in infectious disease dynamics. Trends in ecology & evolution, 23(10)

Koelle K, Pascual M, Yunus M. (2006). Serotype cycles in cholera dynamics. Proceedings. Biological sciences, 273(1603)

Koelle K, Cobey S, Grenfell B, Pascual M. (2006). Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science (New York, N.Y.), 314(5807)

Koelle K, Pascual M, Yunus M. (2005). Pathogen adaptation to seasonal forcing and climate change. Proceedings. Biological sciences, 272(1566)

Koelle K, Rodó X, Pascual M, Yunus M, Mostafa G. (2005). Refractory periods and climate forcing in cholera dynamics. Nature, 436(7051)

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)