Jonathan Dushoff

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. pmc A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission
    Jean Marc O Depinay
    Fogarty International Center, National Institutes of Health, 16 Center Drive, Bethesda MD 20892, USA
    Malar J 3:29. 2004
  2. pmc Dynamical resonance can account for seasonality of influenza epidemics
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 101:16915-6. 2004
  3. ncbi request reprint Mortality due to influenza in the United States--an annualized regression approach using multiple-cause mortality data
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Am J Epidemiol 163:181-7. 2006
  4. ncbi request reprint Comment on "Metapopulation persistence with age-dependent disturbance or succession"
    Jonathan Dushoff
    Department of Ecology and, Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
    Science 304:684; author reply 684. 2004
  5. pmc Vaccinating to protect a vulnerable subpopulation
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Med 4:e174. 2007
  6. pmc Transmission dynamics and prospects for the elimination of canine rabies
    Katie Hampson
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
    PLoS Biol 7:e53. 2009
  7. pmc Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes
    Sergey Kryazhimskiy
    Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey, USA
    J Virol 82:4938-45. 2008
  8. ncbi request reprint Native bees provide insurance against ongoing honey bee losses
    Rachael Winfree
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Ecol Lett 10:1105-13. 2007
  9. pmc On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A
    Sergey Kryazhimskiy
    Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 3:e159. 2007
  10. pmc On the accessibility of adaptive phenotypes of a bacterial metabolic network
    Wilfred Ndifon
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
    PLoS Comput Biol 5:e1000472. 2009

Detail Information

Publications32

  1. pmc A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission
    Jean Marc O Depinay
    Fogarty International Center, National Institutes of Health, 16 Center Drive, Bethesda MD 20892, USA
    Malar J 3:29. 2004
    ..However, malaria remains uncontrolled and is increasing in many areas, as are vector and parasite resistance to insecticides and drugs...
  2. pmc Dynamical resonance can account for seasonality of influenza epidemics
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 101:16915-6. 2004
    ..Here we show that the large oscillations in incidence may be caused by undetectably small seasonal changes in the influenza transmission rate that are amplified by dynamical resonance...
  3. ncbi request reprint Mortality due to influenza in the United States--an annualized regression approach using multiple-cause mortality data
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Am J Epidemiol 163:181-7. 2006
    ..The study also uses regional death data to investigate the effects of cold weather on annualized excess deaths...
  4. ncbi request reprint Comment on "Metapopulation persistence with age-dependent disturbance or succession"
    Jonathan Dushoff
    Department of Ecology and, Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
    Science 304:684; author reply 684. 2004
  5. pmc Vaccinating to protect a vulnerable subpopulation
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Med 4:e174. 2007
    ..Here we investigate the question of how to protect a population against a disease when one group is particularly effective at spreading disease and another group is more vulnerable to the effects of the disease...
  6. pmc Transmission dynamics and prospects for the elimination of canine rabies
    Katie Hampson
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
    PLoS Biol 7:e53. 2009
    ..Nonetheless our analyses suggest that with sustained, international commitment, global elimination of rabies from domestic dog populations, the most dangerous vector to humans, is a realistic goal...
  7. pmc Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes
    Sergey Kryazhimskiy
    Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey, USA
    J Virol 82:4938-45. 2008
    ....
  8. ncbi request reprint Native bees provide insurance against ongoing honey bee losses
    Rachael Winfree
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Ecol Lett 10:1105-13. 2007
    ..The honey bee is currently undergoing extensive die-offs because of Colony Collapse Disorder. We predict that in our region native bees will buffer potential declines in agricultural production because of honey bee losses...
  9. pmc On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A
    Sergey Kryazhimskiy
    Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 3:e159. 2007
    ..It permits computational, and even analytical, investigation and thus serves as a useful tool for understanding the evolution and ecology of multi-strain pathogens...
  10. pmc On the accessibility of adaptive phenotypes of a bacterial metabolic network
    Wilfred Ndifon
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
    PLoS Comput Biol 5:e1000472. 2009
    ....
  11. doi request reprint On the use of hemagglutination-inhibition for influenza surveillance: surveillance data are predictive of influenza vaccine effectiveness
    Wilfred Ndifon
    Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, United States
    Vaccine 27:2447-52. 2009
    ..We suggest directions for further studies aimed at improving vaccine-strain selection and present a large collection of HI titers that will be useful to such studies...
  12. ncbi request reprint Evolution and persistence of influenza A and other diseases
    Simon A Levin
    Department of Ecology and Evolutionary Biology, Princeton University, 203 Eno Hall, Princeton, NJ 08544 1003, USA
    Math Biosci 188:17-28. 2004
    ..We suggest that this effect might be involved in the explanations of some persistent empirical anomalies...
  13. doi request reprint Intraspecific variation and species coexistence
    Jeremy W Lichstein
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
    Am Nat 170:807-18. 2007
    ..Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities...
  14. pmc Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis
    Juliet R C Pulliam
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    J R Soc Interface 9:89-101. 2012
    ..Thus, we provide empirical evidence for a causative mechanism previously proposed as a precursor to widespread infection with H5N1 avian influenza and other emerging pathogens...
  15. ncbi request reprint Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors
    Jeremy W Lichstein
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
    Ecol Appl 20:684-99. 2010
    ..Our approach could be extended to estimate parameters relating sapling mortality to L from inventory data, as well as to deal with uncertainty in other resources (e.g., water or nutrients) or environmental factors (e.g., temperature)...
  16. pmc Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites
    Georgii A Bazykin
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 103:19396-401. 2006
    ..We identified many conservative sites of HIV-1 proteins that occasionally experience positive selection...
  17. pmc Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus
    Joshua B Plotkin
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 99:6263-8. 2002
    ..We also investigate the relationship between cluster structure and the primary antibody-combining regions of the HA protein...
  18. pmc Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus
    Joshua B Plotkin
    Institute for Advanced Study, Olden Lane, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 100:7152-7. 2003
    ..We also introduce information-theoretic methods that use sequence data to detect regions of recent positive selection and potential protein conformational changes...
  19. ncbi request reprint Testing simple indices of habitat proximity
    Rachael Winfree
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
    Am Nat 165:707-17. 2005
    ..However, none of the indices performed well in predicting population response variables. The results suggest that the pattern of habitat cover alone may be insufficient to predict the process of animal movement...
  20. pmc Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts
    Katie Hampson
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 104:7717-22. 2007
    ....
  21. ncbi request reprint Network metrics reveal differences in social organization between two fission-fusion species, Grevy's zebra and onager
    Siva R Sundaresan
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Oecologia 151:140-9. 2007
    ..From our analysis, we can make testable predictions about behavioral mechanisms underlying social structure and its effects on transmission processes...
  22. ncbi request reprint Metapopulations, community assembly, and scale invariance in aspect space
    Jonathan Dushoff
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Theor Popul Biol 62:329-38. 2002
    ..We show that this geometric model is scale invariant in the rescaled aspect space and use this fact to investigate the limits to diversity and explore how communities assemble under this model...
  23. doi request reprint Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses
    Juliet R C Pulliam
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
    J Infect Dis 199:565-8. 2009
    ..This finding highlights nuclear entry as a barrier to transmission and suggests that the ability to complete replication in the cytoplasm may prove to be a useful indicator of the threat of cross-species transmission...
  24. ncbi request reprint The combined effects of pathogens and predators on insect outbreaks
    Greg Dwyer
    Department of Ecology and Evolution, 1101 E 57th Street, University of Chicago, Chicago, Illinois 60637 1573, USA
    Nature 430:341-5. 2004
    ..Outbreaks in this model occur at long but irregular intervals, matching the data. Our results suggest that explanations of insect outbreaks must go beyond classical models to consider interactions among multiple species...
  25. pmc Directionality in the evolution of influenza A haemagglutinin
    Sergey Kryazhimskiy
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Biol Sci 275:2455-64. 2008
    ..Our results suggest that the evolution of the influenza A HA, including evolution by positive selection, is strongly affected by the long-term site-specific preferences for individual amino acids...
  26. pmc The risk of a mosquito-borne infection in a heterogeneous environment
    David L Smith
    Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Biol 2:e368. 2004
    ..Finally, we show that estimates for the average risk of infection that are based on the average entomological inoculation rate are strongly biased in heterogeneous environments...
  27. ncbi request reprint Estimating selection pressures from limited comparative data
    Joshua B Plotkin
    Mol Biol Evol 23:1457-9. 2006
    ..The regression technique does not depend on an underlying population-genetic mechanism. This new approach to estimating selection across a genome should be more powerful and more widely applicable than volatility itself...
  28. pmc Agricultural antibiotics and human health
    David L Smith
    Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Med 2:e232. 2005
  29. ncbi request reprint Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum
    Joshua B Plotkin
    Harvard Society of Fellows and Bauer Center for Genomics Research, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 428:942-5. 2004
    ..Our method of estimating selective pressures requires far fewer data than comparative sequence analysis, and it measures selection across an entire genome; the method can readily be applied to a large range of sequenced organisms...
  30. ncbi request reprint The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance
    Lone Simonsen
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:1811-20. 2007
    ..More generally, these findings illustrate that drug selection pressure is not the sole factor determining the evolution and maintenance of drug resistance in human pathogens...
  31. ncbi request reprint Codon usage and selection on proteins
    Joshua B Plotkin
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Mol Evol 63:635-53. 2006
    ..We also discuss several confounding factors, neglected by the Fisher-Wright model, that may limit the applicability of volatility in practice...