Katia Koelle

Principal Investigator





Martin MA, VanInsberghe D, Koelle K. (2021). Insights from SARS-CoV-2 sequences. Science (New York, N.Y.), 371(6528)

Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. (2021). Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. PLoS pathogens, 17(2)

Vieira MC, Donato CM, Arevalo P, Rimmelzwaan GF, Wood T, Lopez L, Huang QS, Dhanasekaran V, Koelle K, Cobey S. (2021). Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases. Nature communications, 12(1)

Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED Jr., Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. (2020). CpG-creating mutations are costly in many human viruses. Evolutionary ecology, 34(3)

Gallagher ME, Sieben AJ, Nelson KN, Kraay ANM, Orenstein WA, Lopman B, Handel A, Koelle K. (2020). Indirect benefits are a crucial consideration when evaluating SARS-CoV-2 vaccine candidates. Nature medicine

Steele MK, Wikswo ME, Hall AJ, Koelle K, Handel A, Levy K, Waller LA, Lopman BA. (2020). Characterizing Norovirus Transmission from Outbreak Data, United States. Emerging infectious diseases, 26(8)

Vera Cruz D, Nelson CS, Tran D, Barry PA, Kaur A, Koelle K, Permar SR. (2020). Intrahost cytomegalovirus population genetics following antibody pretreatment in a monkey model of congenital transmission. PLoS pathogens, 16(2)

Gallagher ME, Sieben AJ, Nelson KN, Kraay ANM, Lopman B, Handel A, Koelle K. (2020). Considering indirect benefits is critical when evaluating SARS-CoV-2 vaccine candidates. medRxiv : the preprint server for health sciences

Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. (2020). Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nature communications, 11(1)

Miller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A. (2020). Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nature communications, 11(1)

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)

Li ZT, Zarnitsyna VI, Lowen AC, Weissman D, Koelle K, Kohlmeier JE, Antia R. (2019). Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?. Journal of virology, 93(6)

Craig R, Kunkel E, Crowcroft NS, Fitzpatrick MC, de Melker H, Althouse BM, Merkel T, Scarpino SV, Koelle K, Friedman L, Arnold C, Bolotin S. (2020). Asymptomatic Infection and Transmission of Pertussis in Households: A Systematic Review. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 70(1)

Koelle K, Farrell AP, Brooke CB, Ke R. (2019). Within-host infectious disease models accommodating cellular coinfection, with an application to influenza. Virus evolution, 5(2)

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)

Nelson CS, Vera Cruz D, Su M, Xie G, Vandergrift N, Pass RF, Forman M, Diener-West M, Koelle K, Arav-Boger R, Permar SR. (2019). Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees. Journal of virology, 93(5)

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)

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, Illingworth CJ. (2017). The effective rate of influenza reassortment is limited during human infection. PLoS pathogens, 13(2)

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)

Flasche S, Jit M, Rodríguez-Barraquer I, Coudeville L, Recker M, Koelle K, Milne G, Hladish TJ, Perkins TA, Cummings DA, Dorigatti I, Laydon DJ, España G, Kelso J, Longini I, Lourenco J, Pearson CA, Reiner RC, Mier-Y-Terán-Romero L, Vannice K, Ferguson N. (2016). The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengvaxia): A Model Comparison Study. PLoS medicine, 13(11)

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

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)

Koelle K, Rasmussen DA. (2015). The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans. Elife, (4)

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

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)

Rasmussen DA, Volz EM, Koelle K. (2014). Phylodynamic inference for structured epidemiological models. PLoS computational biology, 10(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, (181 Suppl 1)

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)

Volz EM, Koelle K, Bedford T. (2013). Viral phylodynamics. PLoS computational biology, 9(3)

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)

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)

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)

Beatty M, Boni MF, Brown S, Buathong R, Burke D, Coudeville L, Cummings DA, Edelman R, Farrar J, Focks DA, Gomes MG, Guignard A, Halstead S, Hombach J, Knerer G, Koelle K, Lam FC, Lang J, Longini I, Medlock J, Namgyal P, Powell M, Recker M, Rohani P, Standaert B, Struchiner C, Teyssou R, Wearing H. (2012). Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS neglected tropical diseases, 6(3)

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)

Arinaminpathy N, Ratmann O, Koelle K, Epstein SL, Price GE, Viboud C, Miller MA, Grenfell BT. (2012). Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza. Proceedings of the National Academy of Sciences of the United States of America, 109(8)

Meyers LA, Kerr B, Koelle K. (2012). Network perspectives on infectious disease dynamics. Interdisciplinary perspectives on infectious diseases, (2011)

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)

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

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)

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. (2006). Serotype cycles in cholera dynamics. Proceedings. Biological sciences, 273(1603)

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)

Buckee CO, Koelle K, Mustard MJ, Gupta S. (2004). The effects of host contact network structure on pathogen diversity and strain structure. Proceedings of the National Academy of Sciences of the United States of America, 101(29)

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)

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