Publications

    2016

  1. Meaden, S., Metcalf, C.J.E., Koskella, B.T. 2016. The e ffects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur). Environmental Microbiology Reports. 10, 1758-2229.

  2. Fournier-Level, A., Perry, E.O., Wang, J., Braun, P.T., Migneault, A., Cooper, M.D., Metcalf, C.J.E., Schmitt,
    J. 2016. Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana. Proceedings of the National Academy of Sciences. 2, 201517456.

  3. Wesolowski, A, Mensah, K., Brook, C.A., Andrianja masy, M., Winter, A., Buckee, C.O., Raza ndratsimandresy,
    R., Tatem, A.J., Heraud, J-M., Metcalf, C.J.E. 2016. Introduction of Rubella-Containing-Vaccine to Madagascar: implications for roll-out across low-income countries. Journal of the Royal Society Interface. 13, 117.

  4. Metcalf, C.J.E., Farrar, J., Cutts, F.T., Basta, N., Graham, A.L., Lessler, J., Ferguson, N., Burke, D., Grenfell, B.T. 2016. Serological surveys: Generating key insight into the changing global landscape of infectious disease. Lancet. 16, 30164-7.

  5. Metcalf, C.J.E. 2016. Invisible trade-o ffs: van Noordwijk & de Jong and life history evolution. American Naturalist. 87 iii.

  6. Takahashi, S., Liao, Q., Van Boeckel, T.P., Xing, W., Sun, J., Hsiao, V.Y., Metcalf, C.J.E., Chang, Z., Liu, F., Zhang, J., Wu, J.T., Cowling, B.J., Leung, G.M., Farrar, J.J., van Doorn, H.R., Grenfell, B.T., Hongjie, Y. 2016. Hand, foot, and mouth disease in China: modelling epidemic dynamics of enterovirus serotypes and implications for vaccination. PLoS Medicine. 13, e1001958.

  7. Dalziel, B., Bjornstad, O.N., Van Panhuis, W.G., Burke, D.S., Metcalf, C.J.E., Grenfell, B.T. 2016. Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns. PloS Computational Biology. 12, 2.

  8. Bughardt, L., Metcalf, C.J.E. & Donohue, K. 2016. A cline in seed dormancy can conserve the environment
    experienced during reproduction across a range of Arabidopsis thaliana. American Journal of Botany. 103, 47-49.

  9. Metcalf, C.J.E., Graham, A.L., Martinez-Bakker, M., Childs, D.Z. 2016. Opportunities and challenges of Integral Projection Models for modeling infectious diseases and their dynamics. Journal of Animal Ecology. 83, 343-355.

  10. 2015

  11. Metcalf, C.J.E. , Ferrari, M., Graham, A.L., Grenfell, B.T. 2015. Understanding herd immunity. Trends in Im-
    munology. 36, 753-755.

  12. Griffiths, E., Fairlie-Clarke, K., Allen, J.E., Metcalf, C.J.E., Graham, A.L. 2015. Bottom-up control of malaria
    population dynamics in mice co-infected with lung-migratory nematodes. Ecology Letters. 18, 1387-1396.

  13. Birger, R., Kouyos, R.D., Cohen, T., Griths, E., Huijben, S., Mina, M., Volkova, V., Grenfell, B.T., Metcalf, C.J.E. 2015. The impact of coinfection on anti-microbial chemotherapy and drug resistance. Trends in Microbiology. 23, 537-544.

  14. Wesolowski, A.*, Metcalf, C.J.E.*, Kombich, J., Grenfell, B.T., Bjornstad, O.N., Lessler, J., Eagle, N., Tatem, A.J. & Buckee, C.O. 2015. Quantifying seasonal population fluxes driving rubella transmission dynamics using mobile phone data. PNAS. [*these authors contributed equally] 112, 11114-11119.

  15. Metcalf, C.J.E., Ellner, S.P., Childs, D.Z., McMahon, S.M., Merow, C., Jongejans, E., Salguero-Gomez, R. & Rees, M. 2015. Statistical modelling of annual variation for inference on stochastic population dynamics using Integral Projection Models. Methods in Ecology and Evolution. 6, 1007-1017.

  16. Metcalf, C.J.E., Bughardt, L.T., Koons, D.N. 2015. Avoiding the crowds: the evolution of plastic response to
    seasonal cues in a density dependent world. Journal of Ecology. 103, 819-828.

  17. Mina, M., Metcalf, C.J.E., de Swart, R., Osterhaus, A., Grenfell, B.T. 2015. Long-term measles-induced immune-amnesia explains major reductions in all-cause childhood mortality following measles vaccination. Science. 348, 694-699.

  18. Metcalf, C.J.E., Tatem, A.J., Bjornstad, O.N., Lessler, J., OReilly, K., Takahashi, S., Cutts, F., & Grenfell, B.T.
    2014. Transport networks and inequities in vaccination: remoteness shapes measles vaccine coverage and prospects for elimination across Africa. Epidemiology and Infection. 1-10.

  19. Metcalf, C.J.E., Birger, R., Funk, S., Kouyos, R.D., Lloyd-Smith, J., Janzen, V. 2015. Five challenges in the
    evolution and infectious diseases. Epidemics. 10, 40-44.

  20. Petra Klepac, Sebastian Funk, T Deirdre Hollingsworth, C Jessica E Metcalf, Katie Hampson. 2015. Six challenges in the eradication of infectious diseases. Epidemics. 10, 97-101.

  21. Cunni ffe, N., Koskella, B., Gottwald, T., Parnell, S. Van den Bosch, F. Metcalf, C.J.E., Gilligan, C. A. 2015. Thirteen challenges in modelling plant diseases. Epidemics. 10, 6-10.

  22. Metcalf, C.J.E. , Lessler, J. & Edmunds, W.J. 2015. Six challenges in policy for modeling. Epidemics. 10, 93-96.

  23. Metcalf, C.J.E., Andreasen, V., Bjornstad, O.N., Eames, K.T., Edmunds, W.J., Hollingsworth, T.D., Lessler, J.,
    Viboud, C. & Grenfell, B.T. 2015. Seven challenges in modeling vaccine preventable diseases. Epidemics. 10, 11-15.

  24. Takahashi, S., Metcalf, C.J.E., Ferrari, M., Truelove, S., Grenfell, B.T., & Lessler, J. 2015. Confronting the Growing Risk of a Post-Ebola Epidemic of Childhood Infections Science 347 1240-1242.

  25. Heesterbeck, J.A.P., Anderson, R., Dye, C., Eames, K., Edmunds, J., Funk, S., Hollingsworth, D., House, T., Isham,
    V. , Lessler, J., Lloyd-Smith, J., Metcalf, C.J.E., Pellis, L., Pulliam, J., Roberts, M., Isaac Newton Institute IDD group. 2015. Modelling infectious disease dynamics in the complex landscape of global health. Science 347 aaa4339

  26. Morris, S., Pitzer, V.E., Viboud, C., Metcalf, C.J.E., Grenfell, B.T. 2015. Demographic bu ering: titrating the
    e ects of birth rate and imperfect immunity on epidemic dynamics. Journal of the Royal Society Interface 12
    s20141245

  27. Lloyd-Smith, J.O., Mollison, D., Metcalf, C.J.E., Heesterbeck, J.A.P. 2015 Challenges in modeling infectious disease dynamics: preface. Epidemics 10:1-5

  28. Perkins, T.A., Metcalf, C.J.E., Grenfell, B.T., Tatem, A.J. 2015. Chikungunya: forecasting the invasion landscape
    in the Americas PloS Currents

  29. Metcalf, C.J.E. & Jones, J.H. 2015. The evolutionary dynamics of timing of maternal immunity: evaluating the
    role of age-speci c mortality Journal of Evolutionary Biology 28 493-502

  30. Bughardt, L., Metcalf, C.J.E., Wilczek, A. Johanna Schmitt, J. & Donohue, K. 2015 Predicting plant life cycles in
    seasonal environments American Naturalist 185 212-227

  31. Pitzer, V.E., Viboud, C., Alonso, W.J., Wilcox, T., Metcalf, C.J.E., Steiner, C.A., Panozzo, C.A. & Grenfell, B.T.
    2015 Environmental drivers of the spatiotemporal dynamics of respiratory syncytial virus in the United States. PloS
    Pathogens 11 e1004591-e1004591

  32. Caudron, Q., Mahmud, A.S., Metcalf, C.J.E., Gottfreosson, M., Viboud, C., Cli , A.D., Grenfell, B.T. 2015
    Predictability in highly stochastic systems: measles in small populations. Journal of the Royal Society Interface 12: 20141125

  33. Salguero-Gomez, R., Jones, O.R., Archer, C.R., Buckley, Y.M., Che-Castaldo, J., Caswell, H., Scheuerlien, A.,
    Conde, D.A., Baudisch, A., Brinks, E., de Buhr, H., Farack, C., France, G., Hartmann, A., Henning, A., Hoppe,
    G., Romer, G., Runge, J., Ruo , T., Wille, J., Zeh, S., Vierigg, D., Altwegg, R., Colchero, F., Dong, M., Hodgson,
    D., de Kroon, H., Lebreton, J-D., Metcalf, C.J.E., Neel, M., Takada, T., Valverde, T., Velez-Espino, L.A., Wardle,
    G.M., Franco, M. & Vaupel, J. 2015 The COMPADRE Plant Matrix Database: an Open Online Repository for Plant
    Demography. Journal of Ecology 103: 202-218

  34. 2014

  35. Klepac, P., Funk, S., Hollingsworth, T.D., Metcalf, C.J.E., Hampson, K. 2015 Six challenges in the eradication of
    infectious diseases. Epidemics 10:97-101

  36. Merow, C., Dahlgren, J.P., Metcalf, C.J.E., Childs, D.Z., Evans, M.E.K., Jongejans, E., Record, S., Rees, M.,
    Salguero-Gomez, R. & McMahon, S.M. 2014. Advancing population ecology with integral projection models: a
    practical guide Methods in Ecology and Evolution 4 195-200

  37. Kouyos, R.D.*, Metcalf, C.J.E.*, Birger, R.*, Klein, E.Y., Day, T., Huijben, S., Cohen, T., Greenhouse, B., Wale,
    N., Mideo, N., Nimalan, A., Grenfell, B.T., Pollitt, L.,C., Bogich, T.L., Brower, C., zur Wiesch, P.A., Read, A.,
    Smith, D., Bonhoe er, S. 2014 The path of least resistance: aggressive or moderate treatment? Proceedings of the
    Royal Society of London – B 281 20140566 [*contributed equally]

  38. Nimalan Arinaminpathy, Charlotte Jessica E Metcalf, Bryan T Grenfell. Viral Infections of Humans

  39. 2013

  40. Rozhnova, G., Metcalf, C.J.E. & Grenfell, B.T. 2013 Characterizing the dynamics of rubella relative to measles:
    the role of stochasticity. 2013 Journal of the Royal Society Interface 10 20130643

  41. Flegg, J., Metcalf, C.J.E., Gharbi, M., Venkatesan, M., Shewchuk, T., Sibley, C.H., & Guerin, P.J. 2013 Trends in
    antimalarial drug use in Africa American Journal of Tropical Medicine and Hygiene 13 0129

  42. Metcalf, C.J.E., Hampson, K., Tatem, A., Grenfell, B.T., & Bjornstad, O.N. 2013 Persistence in epidemic metapopulations: quantifying the rescue e ects for measles, mumps, rubella and whooping cough. PLoS ONE 10 e1371

  43. Klepac, P., Metcalf, C.J.E., McLean, A., Hampson, K. 2013 Towards the endgame and beyond: complexities and
    challenges for the elimination of infectious diseases. Philosophical Transactions of the Royal Society 368 20120137

  44. Cutts, F.T., Lessler, J. & Metcalf, C.J.E. 2013 Measles elimination: progress, challenges and implications for rubella control Expert Reviews Vaccines 12 917-932

  45. Lessler, J. & Metcalf, C.J.E. 2013 Balancing evidence and uncertainty when considering rubella vaccine introduction. PLoS ONE 8, e67639

  46. Vaupel, J.W., Missov, T. & Metcalf, C.J.E. 2013 Optimal Semelparity. Plos One 8, e57133

  47. Metcalf, C.J.E., McMahon, S.M., Salguero-Gomez, R. & Jongejans, E. 2012. IPMpack: an R package for Integral
    Projection Models Methods in Ecology and Evolution 4, 195-200

  48. Mideo, N., Reece, S.E., Smith, A.L., & Metcalf, C.J.E. 2012. The Cinderella Syndrome: Why do malaria-infected
    red blood cells burst at midnight? Trends in Parasitology 29, 10-16

  49. Gharbi, M., Flegg, J., Hubert, V., Kendjo, E., Metcalf, C.J.E., Bertaux, L., Guerin, P.J., Le Bras, J. & Members
    of the French National Reference Centre for Imported Malaria Study. 2013 Longitudinal study assessing the return
    of chloroquine susceptibility of Plasmodium falciparum in isolates from travellers returning from West and Central
    Africa between 2000-2011. Malaria Journal 12, 35

  50. Metcalf, C.J.E., Cohen, C., Lessler, J., McAnerney, J.M., Ntsohe, G.M., Puren, A., Klepac, P., Tatem, A., Grenfell,
    B.T., & Bjrnstad, O.N. 2013 Implications of spatially heterogeneous vaccination coverage for the risk of Congenital
    Rubella Syndrome in South Africa J. Roy. Soc. Interface 10, 20120756

  51. Gharbi, M., Flegg, J., Hubert, V., Kendjo, E., Metcalf, C.J.E., Bertaux, L., Guerin, P.J., Le Bras, J. & Members
    of the French National Reference Centre for Imported Malaria Study. 2013 Longitudinal study assessing the return
    of chloroquine susceptibility of Plasmodium falciparum in isolates from travellers returning from West and Central
    Africa between 2000-2011. Malaria Journal 12, 35

  52. 2012

  53. Metcalf, C.J.E., Lessler, J., Klepac, P., Morice, A., Grenfell, B.T., Bjrnstad, O.N. 2012 Structured models of
    infectious disease: inference with discrete data Theoretical Population Biology 82, 275-282

  54. CJE Metcalf, J Lessler, P Klepac, F Cutts, BT Grenfell. Epidemiology and infection.

  55. Klepac, P., Bjrnstad, O.N., Metcalf, C.J.E. & Grenfell, B.T. 2012. Optimizing reactive responses to outbreaks of
    immunizing infections: balancing case management and vaccination PLoS One 7, e41428

  56. Cutts, F.T.,Metcalf, C.J.E., Lessler, J. & Grenfell, B.T. 2012. Rubella vaccination: must not be business as usual
    The Lancet Correspondence 380, 217-218

  57. Lessler, J., Metcalf, C.J.E., & Grenfell, B.T. 2012. Measurement of vaccine derived immunity: how do we use all the data? Expert Reviews Vaccines 11, 747-749

  58. Metcalf, C.J.E., Long, G.H., Mideo, N. Forrester, J.D., Bjrnstad, O.N., Graham, A.L. 2012. Revealing mechanisms
    underlying variation in malaria parasite virulence: e ective propagation and host control of uninfected red blood cell supply. J. R. Soc. Interface 9, 2804-2813

  59. Metcalf, C.J.E., Lessler, J., Klepac, P., Cutts, F., Grenfell, B.T. 2012.Impact of birth rate, seasonality and transmission rate on minimum levels of coverage needed for rubella vaccination Epidemiology and Infection 140, 2290-2301

  60. 2011

  61. Lessler, J., Metcalf, C.J.E., Grais, R.F., Luquero, F.J., Cummings, D.A.T., Grenfell, B.T. 2011. Measuring the
    performance of vaccination programs using cross-sectional surveys PloS Medicine 8, e1001110

  62. Metcalf, C.J.E., Graham, A.L., Huijben, S.L., Barclay, V.C., Long, G., Grenfell, B.T., Read, A.F., Bjrnstad, O.N.
    2011. Partitioning regulatory mechanisms of within host malaria dynamics using the e ective propagation number
    Science 333, 984-988

  63. Metcalf, C.J.E., Bjrnstad, O.N., Klepac, P., Ferrari, M., Bharti, N., Lopez-Gatell, H. & Grenfell, B.T. 2011. The
    epidemiology of rubella in Mexico: transients, seasonality, and spatial dynamics. Epidemiology and Infection 139,
    1029-1038

  64. CJE Metcalf, P Klepac, M Ferrari, RF Grais, A Djibo, BT Grenfell. Epidemiology and infection.

  65. McMahon, S.M., Metcalf, C.J.E., & Woodall, C. 2011. High-dimensional coexistence of temperate tree species:
    functional traits, demographic rates, life-history stages, and their physical context PloS One 6, e16253

  66. Metcalf, C.J.E., Muayco-Escate, C., Chowell, G., Grenfell, B.T. & Bjrnstad, O.N. 2011. Rubella meta-population
    dynamics and importance of spatial coupling to the risk of Congenital Rubella Syndrome in Peru J. R. Soc. Interface
    8, 369-376

  67. 2010

  68. Clark, J.S., Bell, D.M., Chu, C., Courbaud, B., Dietze, M.C., Hersh, M., HilleRisLambers, J., Ibanez, I., LaDeau,
    S., McMahon, S., Metcalf, C.J.E., Mohan, J.E., Moran, E., Pangle, L., Pearson, S.F., Salk, C.F., Shen, Z., Valle,
    D.R., Wycko , P. 2010 High dimensional coexistence based on individual variation: a synthesis of evidence Ecol.
    Monogr. 80, 569

  69. Childs, D.Z., Metcalf, C.J.E., & Rees, M. 2010 Evolutionary bet-hedging in the real world: empirical evidence and
    challenges revealed by plants Proc. R. Soc. B 277, 3055-3064

  70. Rees, M., Metcalf, C.J.E. & Childs, D.Z. 2010. Commentary on Olofsson et al. 2010. Bet-hedging as an evolutionary game: the trade-o between egg size and number Proc. Roy. Soc. B. 277, 1149-1151

  71. James S Clark, Dave Bell, Michael Dietze, Michelle Hersh, Ines Ibanez, S LaDeau, Sean McMahon, Jessica Metcalf, Emily Moran, Luke Pangle, Mike Wolosin. The Oxford handbook of applied Bayesian analysis. Oxford University Press, New York, New York, USA 2010/3/18

  72. 2009

  73. Metcalf, C.J.E., Bjrnstad, O.N., Grenfell, B.T., & Andreasen, V. 2009 Seasonality and comparative dynamics of
    six childhood infections in pre-vaccination Copenhagen. Proc. Roy. Soc. B. 276, 4111-4118

  74. Metcalf, C.J.E., Rees, M., Buckley, Y.M., & Sheppard, A.W. 2009. Seed predators determine the evolutionarily
    stable flowering strategy in the invasive plant Carduus nutans. Evol. Ecol. 23, 893-906

  75. Metcalf, C.J.E., Horvitz, C.C., Tuljapurkar, S. & Clark, D.A. 2009 A time to grow and a time to die: a new way
    to analyze the dynamics of size, light, age and death of tropical trees. Ecology 90, 2766-2778

  76. Metcalf, C.J.E., Clark, J.S., & McMahon, S.M. 2009 Modeling tree mortality as a non-parametric function of
    diameter and growth, with prior weights on mortality of large trees. Canad. J. Forest. Res. 39, 1677-1687

  77. Koons, D.N., Pavard, S, Baudisch, A, & Metcalf, C.J.E. 2009 Is Life-History Bu ering or Lability Adaptive in
    Stochastic Environments? Oikos 118, 972-980

  78. Metcalf, C.J.E. & Mitchell-Olds, T. 2009 Life-history in a model system: opening the black box with Arabidopsis
    thaliana Ecology Letters 12, 593-600

  79. Metcalf, C.J.E., Stephens, D., Rees, M., Louda, S.M. & Keeler, K.H. 2009 Understanding allocation of resources
    between vegetative and sexual reproduction: Using Bayesian inference to capture interdependent demography with
    incomplete observations. J. Appl. Stat. 58, 143-170.

  80. Rees, M., Metcalf, C.J.E. & Childs, D.Z. 2010. When Worlds collide: reconciling models, data, and analysis Israel
    Journal of Ecology and Evolution 55, 227-231

  81. Metcalf, C.J.E., Clark. J.S. & Clark, D.A. 2009. Tree growth inference and prediction when the point of measurement changes: modeling around buttresses in tropical forests. J. Trop. Ecol. 25,1-12.

  82. 2008

  83. Koons, D.N., Metcalf, C.J.E., & Tuljapurkar, S. 2008. Evolution of delayed reproduction in uncertain environments: a life history perspective. Am. Nat. 172, 797-805

  84. McMahon, S.M., & Metcalf, C.J.E. 2008. Transient sensitivities of non-indigenous shrub species indicate complicated invasion dynamics Biol. Inv. 10, 833-846.

  85. Metcalf, C.J.E., Rees, M., Rose, K.E., Sheppard, A., & Grubb, P.J. 2008. Evolution of
    flowering decisions in a stochastic, density-dependent environment. PNAS 105, 10466-10470.

  86. Pavard, S., Metcalf, C.J.E., & Heyer, E. 2008. Senescence of Reproduction may explain Adaptive Menopause in Humans: a Test of the “Mother” Hypothesis Am. J. Phys. Anth. 136, 194-203.

  87. 2007

  88. Metcalf, C.J.E., Hampson, K., Gray, A., & Andrianirina, R. 2007. Herpetofaunal assemblages on seven o ffshore islands of Northwestern Madagascar. Trop. Zool. 20, 151-161.

  89. Metcalf, C.J.E., & Pavard, S. 2007. All paths to tness lead through demography Trends Ecol. Evol. 22, 563-564.

  90. Pavard, S., & Metcalf, C.J.E. 2007. Negative selection on BRCA1 susceptibility alleles sheds light on the population genetics of late-onset diseases and aging theory PloS-One 11, e1206.

  91. Metcalf, C.J.E., Hampson, K., & Koons, D.N. 2007. What happens when density increases? Sudden and gradual
    infux into refuges and implications for conservation. Animal Cons. 10, 478-486.

  92. Metcalf, C.J.E., & Koons, D.N. 2007. Environmental Autocorrelation and the Evolution of Survival Proc. Roy.
    Soc. B. 1622, 2153-2160.

  93. Metcalf, C.J.E., & Pavard, S. 2007. Why evolutionary biologists should be demographers Trends Ecol. Evol. 22,
    205-212.

  94. Metcalf, C.J.E., Hampson, K., Andriamizava, A., Andrianirina, R., Cairnes, T., Gray, A. Ramiarisoa, C., & Sondotra,
    H. 2007. The beaches of Northwest Madagascar: an important nesting habitat for green (Chelonia mydas) and
    hawksbill (Eretmochelys imbricata) turtles. Oryx 41, 232-238.

  95. 2006

  96. Rees, M., Childs, D.Z., Metcalf, C.J.E., Rose, K.E., Sheppard, A., Grubb, P.J., & Ellner, S.P. 2006. Evolution of seed dormancy and delayed owering in monocarpic plants: selective interactions in a stochastic environment Am. Nat. 168, E53-E71.

  97. Metcalf, C.J.E., Rees, M., Alexander, J.M., & Rose, K.E. 2006. Growth-survival trade-os and allometries in rosette-forming perennials. Funct. Ecol. 20, 217-225.

  98. Y Buckley, J Metcalf
    Conceptual ecology and invasion biology: reciprocal approaches to nature …
  99. 2005 And Earlier

  100. Metcalf, C.J.E., Bayly, N., Bisoa, M., Rabearivony, J., & Stewart-Jones, A. 2005. Edge eect from paths on two chameleon species in Madagascar African J. Herp. 54, 99-102.