Publications of Katharina V. Koelle

Papers Published

  1. Sobel Leonard, A; Weissman, DB; Greenbaum, B; Ghedin, E; Koelle, K, Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus, edited by Lyles, DS, Journal of virology, vol. 91 no. 14 (July, 2017), pp. e00171-17-e00171-17
  2. Sobel Leonard, A; McClain, MT; Smith, GJD; Wentworth, DE; Halpin, RA; Lin, X; Ransier, A; Stockwell, TB; Das, SR; Gilbert, AS; Lambkin-Williams, R; Ginsburg, GS; Woods, CW; Koelle, K; Illingworth, CJR, The effective rate of influenza reassortment is limited during human infection., PLoS pathogens, vol. 13 no. 2 (February, 2017), pp. e1006203
  3. Sobel Leonard, A; McClain, MT; Smith, GJD; Wentworth, DE; Halpin, RA; Lin, X; Ransier, A; Stockwell, TB; Das, SR; Gilbert, AS; Lambkin-Williams, R; Ginsburg, GS; Woods, CW; Koelle, K, Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification., Journal of virology, vol. 90 no. 24 (December, 2016), pp. 11247-11258
  4. Flasche, S; Jit, M; Rodríguez-Barraquer, I; Coudeville, L; Recker, M; Koelle, K; Milne, G; Hladish, TJ; Perkins, TA; Cummings, DAT; Dorigatti, I; Laydon, DJ; España, G; Kelso, J; Longini, I; Lourenco, J; Pearson, CAB; Reiner, RC; Mier-Y-Terán-Romero, L; Vannice, K; Ferguson, N, 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., edited by von Seidlein, L, PLoS medicine, vol. 13 no. 11 (November, 2016), pp. e1002181
  5. Ben-Shachar, R; Schmidler, S; Koelle, K, Drivers of Inter-individual Variation in Dengue Viral Load Dynamics., edited by Ferguson, NM, PLoS computational biology, vol. 12 no. 11 (November, 2016), pp. e1005194
  6. Koelle, K; Rasmussen, DA, The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans., eLife, vol. 4 (September, 2015), pp. e07361
  7. Ben-Shachar, R; Koelle, K, 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, vol. 12 no. 103 (February, 2015), pp. 20140886-20140886, ISSN 1742-5689
  8. Koelle, K; Rasmussen, DA, Influenza: Prediction is worth a shot., Nature, vol. 507 no. 7490 (March, 2014), pp. 47-48, ISSN 0028-0836
  9. Rasmussen, DA; Boni, MF; Koelle, K, Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam., Molecular Biology and Evolution, vol. 31 no. 2 (February, 2014), pp. 258-271, ISSN 0737-4038
  10. Yuan, H-Y; Koelle, K, The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis., Philosophical Transactions B, vol. 368 no. 1614 (March, 2013), pp. 20120204, ISSN 1471-2970
  11. Wu, S; Koelle, K; Rodrigo, A, Coalescent entanglement and the conditional dependence of the times to common ancestry of mutually exclusive pairs of individuals., Journal of Heredity, vol. 104 no. 1 (January, 2013), pp. 86-91
  12. Scholle, S.O., Ypma, R., Lloyd, A.L., Koelle, K., Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamicssubstitution rates, The American Naturalist, vol. 182 no. 4 (2013), pp. 494-513
  13. Scholle, SO; Ypma, RJF; Lloyd, AL; Koelle, K, Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics, American Naturalist, vol. 182 no. 4 (2013), pp. 494-513, ISSN 0003-0147
  14. Yuan, H-Y; Koelle, K, The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis., Philosophical Transactions B, vol. 368 no. 1614 (2013), pp. 20120204-
  15. Luo, S; Reed, M; Mattingly, JC; Koelle, K, The impact of host immune status on the within-host and population dynamics of antigenic immune escape., Journal of the Royal Society Interface, vol. 9 no. 75 (2012), pp. 2603-2613
  16. Koelle, WHO-VMIDVMGIK, Assessing the potential of a candidate dengue vaccine with mathematical modeling, PLoS Neglected Tropical Diseases, vol. 6 no. 3 (2012), pp. e1450
  17. Luo, S; Koelle, K, Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature, The American Naturalist, vol. 181 no. S58-S75 (2012)
  18. Arinaminpathy, N; Ratmann, O; Koelle, K; Epstein, SL; Price, GE; Viboud, C; Miller, MA; Grenfell, BT, Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza, Proceedings of the National Academy of Sciences of USA, vol. 109 no. 8 (2012), pp. 3173-3177, ISSN 0027-8424
  19. Koelle, K; Rasmussen, DA, Rates of coalescence for common epidemiological models at equilibrium, Journal of the Royal Society Interface, vol. 9 no. 70 (2012), pp. 997-1007, ISSN 1742-5689
  20. Ratmann, O; Donker, G; Meijer, A; Fraser, C; Koelle, K, Phylodynamic inference and model assessment with Approximate Bayesian Computation: influenza as a case study, PLoS Computational Biology, vol. 8 no. 12 (2012), pp. e1002835
  21. Volz, EM; Koelle, K; Bedford, T, Viral phylodynamics, PLoS Computational Biology, vol. 9 no. 3 (2013), pp. e1002947
  22. Meyers, LA; Kerr, B; Koelle, K, Network perspectives on infectious disease dynamics, Interdisciplinary Perspectives on Infectious Diseases, vol. 2011 no. 146765 (2011), pp. 2, ISSN 1687-708X
  23. Rasmussen, DA; Ratmann, O; Koelle, K, Inference for nonlinear epidemiological models using genealogies and time series, PLoS computational biology, vol. 7 no. 8 (2011), pp. e1002136, ISSN 1553-734X
  24. Koelle, K; Ratmann, O; Rasmussen, DA; Pasour, V; Mattingly, J, A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses, Proceedings of the Royal Society of London: Biological Sciences, vol. 278 no. 1725 (2011), pp. 3723-3730, ISSN 0962-8452
  25. Koelle, K; Khatri, P; Kamradt, M; Kepler, TB, 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, vol. 7 no. 50 (September, 2010), pp. 1257-1274
  26. Koelle, K., Khatri, P., Kamradt, M., Kepler, T., 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 (2010)
  27. Koelle, K; Kamradt, M; Pascual, M, Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: Influenza as a case study, Epidemics: the journal of infectious disease dynamics, vol. 1 no. 2 (2009), pp. 129-137, ISSN 1755-4365
  28. Koelle, K, The impact of climate on the disease dynamics of cholera, Clinical Microbiology and Infection, vol. 15 no. s1 (2009), pp. 29-31, ISSN 1198-743X
  29. Koelle, K, The impact of climate on the disease dynamics of cholera, Clinical Microbiology and Infection, vol. 15 no. SUPPL. 1 (2009), pp. 29-31, ISSN 1198-743X
  30. Nagao, Y; Koelle, K, Decreases in dengue transmission may act to increase the incidence of dengue hemorrhagic fever, Proceedings of the National Academy of Sciences of USA, vol. 105 no. 6 (2008), pp. 2238-2243, ISSN 0027-8424
  31. Cobey, S; Koelle, K, Capturing escape in infectious disease dynamics, Trends in Ecology & Evolution, vol. 23 no. 10 (2008), pp. 572-577, ISSN 0169-5347
  32. Pascual, M; Cazelles, B; Bouma, MJ; Chaves, LF; Koelle, K, Shifting patterns: Malaria dynamics and rainfall variability in an African highland, Proceedings of the Royal Society of London: Biological Sciences, vol. 275 no. 1631 (2008), pp. 123-132, ISSN 0962-8452
  33. Finkelman, BS; Viboud, C; Koelle, K; Ferrari, MJ; Bharti, N; Grenfell, BT, Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: Viral coexistence and latitudinal gradients, PloS one, vol. 2 no. 12 (2007), pp. e1296, ISSN 1932-6203
  34. Pascual, M; Koelle, K; Dobson, A, Hyperinfectivity in Cholera: A New Mechanism for an Old Epidemiological Model?, PLoS Medicine, vol. 3 no. 6 (2006), pp. e280, ISSN 1549-1277
  35. Koelle, K; Pascual, M; Yunus, M, Serotype cycles in cholera dynamics, Proceedings of the Royal Society of London: Biological Sciences, vol. 273 no. 1603 (2006), pp. 2879-2886, ISSN 0962-8452
  36. Koelle, K; Cobey, S; Grenfell, B; Pascual, M, Epochal evolution shapes the phylodynamics of interpandemic influenza a (H3N2) in humans, Science, vol. 314 no. 5807 (2006), pp. 1898-1903, ISSN 0036-8075
  37. Pascual, M; Koelle, K; Dobson, AP, Hyperinfectivity in cholera: A new mechanism for an old epidemiological model? [2], PLoS medicine, vol. 3 no. 6 (2006), pp. 0931-0933, ISSN 1549-1277
  38. Koelle, K; Vandermeer, J, Dispersal-induced desynchronization: From metapopulations to metacommunities, Ecology Letters, vol. 8 no. 2 (2005), pp. 167-175, ISSN 1461-023X
  39. Koelle, K; Pascual, M; Yunus, M, Pathogen adaptation to seasonal forcing and climate change, Proceedings of the Royal Society of London: Biological Sciences, vol. 272 no. 1566 (2005), pp. 971-977, ISSN 0962-8452
  40. Koelle, K; Rodó, X; Pascual, M; Yunus, M; Mostafa, G, Refractory periods and climate forcing in cholera dynamics, Nature, vol. 436 no. 7051 (2005), pp. 696-700
  41. Koelle, K; Pascual, M, Disentangling extrinsic from intrinsic factors in disease dynamics: A nonlinear time series approach with an application to cholera, American Naturalist, vol. 163 no. 6 (2004), pp. 901-913, ISSN 0003-0147
  42. Buckee, CO; Koelle, K; Mustard, MJ; Gupta, S, 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, vol. 101 no. 29 (2004), pp. 10839-10844
  43. Blower, SM; Koelle, K; Kirschner, DE; Mills, J, Live attenuated HIV vaccines: Predicting the tradeoff between efficacy and safety, Proceedings of the National Academy of Sciences of USA, vol. 98 no. 6 (2001), pp. 3618-3623, ISSN 0027-8424
  44. Blower, S; Koelle, K; Lietman, T, Antibiotic resistance - To treat... [1], Nature Medicine, vol. 5 no. 4 (1999), pp. 358-, ISSN 1078-8956

Papers Accepted

  1. Rasmussen, DA; Volz, EM; Koelle, K, Phylodynamic inference for structured epidemiological models., edited by Kosakovsky Pond, SL, PLoS computational biology, vol. 10 no. 4 (2014), pp. e1003570

Book Chapter

  1. R. Savit, K. Koelle, W. Treynor, R. Gonzalez, Man and Superman: Human Limitations, Innovation, and Emergence in Resource Competition, in Collectives and the Design of Complex Systems, edited by Tumer, K. & Wolpert, D. (2004), Springer-Verlag, New York, NY
  2. S.M. Blower, K. Koelle, J. Mills, Health policy modeling: epidemic control, HIV vaccines and risky behavior, in Quantitative Evaluation of HIV Prevention Programs, edited by E. H. Kaplan & R. Brookmeyer (2002), Yale University Press, New Haven, CT