All Stories

  1. spatPomp: An R package for spatiotemporal partially observed Markov process models

    Article • The Journal of Open Source Software, December 2024, The Open Journal

    Professor Aaron A. King

  2. Red blood cell dynamics during malaria infection challenge the assumptions of mathematical models of infection dynamics

    Article • Frontiers in Malaria, August 2024, Frontiers

    Professor Aaron A. King

  3. Inference on spatiotemporal dynamics for coupled biological populations

    Article • Journal of The Royal Society Interface, July 2024, Royal Society Publishing

    Professor Aaron A. King

  4. The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees

    Article • Molecular Biology and Evolution, April 2024, Oxford University Press (OUP)

    Professor Aaron A. King

  5. Red blood cell dynamics during malaria infection violate the assumptions of mathematical models of infection dynamics

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Professor Aaron A. King

  6. Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Professor Aaron A. King

  7. Disentangling the causes of mumps reemergence in the United States

    Article • Proceedings of the National Academy of Sciences, January 2023, Proceedings of the National Academy of Sciences

    Professor Aaron A. King, Deven Gokhale

  8. Author Correction: Fine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics

    Article • Nature Communications, March 2022, Springer Science + Business Media

    Professor Aaron A. King, Laís Picinini Freitas

  9. Fine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics

    Article • Nature Communications, February 2022, Springer Science + Business Media

    Professor Aaron A. King, Laís Picinini Freitas

  10. Markov genealogy processes

    Article • Theoretical Population Biology, December 2021, Elsevier

    Professor Aaron A. King

  11. Bagged Filters for Partially Observed Interacting Systems

    Article • Journal of the American Statistical Association, October 2021, Taylor & Francis

    Professor Aaron A. King

  12. The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections

    Article • Proceedings of the National Academy of Sciences, October 2019, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  13. Age-structure and transient dynamics in epidemiological systems

    Article • Journal of The Royal Society Interface, July 2019, Royal Society Publishing

    Professor Aaron A. King

  14. Panel Data Analysis via Mechanistic Models

    Article • Journal of the American Statistical Association, June 2019, Taylor & Francis

    Professor Aaron A. King

  15. Duration of Immunity and Effectiveness of Diphtheria-Tetanus–Acellular Pertussis Vaccines in Children

    Article • JAMA Pediatrics, June 2019, American Medical Association (AMA)

    Professor Aaron A. King

  16. Breaking Down Defenses: Quantitative Analysis of Malaria Infection Dynamics Reveals Distinct Immune Defense Strategies

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Professor Aaron A. King

  17. Response to Comment on “The impact of past vaccination coverage and immunity on pertussis resurgence”

    Article • Science Translational Medicine, December 2018, American Association for the Advancement of Science

    Professor Aaron A. King

  18. Commentary: resolving pertussis resurgence and vaccine immunity using mathematical transmission models

    Article • Human Vaccines & Immunotherapeutics, November 2018, Taylor & Francis

    Professor Aaron A. King, Professor Pejman Rohani

  19. Rethinking the efficacy of acellular pertussis vaccines for primary immunization

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Professor Aaron A. King

  20. The impact of past vaccination coverage and immunity on pertussis resurgence

    Article • Science Translational Medicine, March 2018, American Association for the Advancement of Science

    Professor Aaron A. King

  21. Core pertussis transmission groups in England and Wales: A tale of two eras

    Article • Vaccine, February 2018, Elsevier

    Professor Aaron A. King

  22. Evolution-informed forecasting of seasonal influenza A (H3N2)

    Article • Science Translational Medicine, October 2017, American Association for the Advancement of Science

    Professor Aaron A. King

  23. Evolution-informed forecasting of seasonal influenza A (H3N2)

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Aaron A. King

  24. Seasonality in cholera dynamics: A rainfall-driven model explains the wide range of patterns in endemic areas

    Article • Advances in Water Resources, October 2017, Elsevier

    Professor Aaron A. King

  25. Monte Carlo profile confidence intervals for dynamic systems

    Article • Journal of The Royal Society Interface, July 2017, Royal Society Publishing

    Professor Aaron A. King

  26. Maternal pertussis immunisation: clinical gains and epidemiological legacy

    Article • Eurosurveillance, April 2017, European Centre for Disease Control and Prevention (ECDC)

    Professor Aaron A. King

  27. Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo

    Article • Molecular Biology and Evolution, April 2017, Oxford University Press (OUP)

    Professor Aaron A. King

  28. Cholera forecast for Dhaka, Bangladesh, with the 2015-2016 El Niño: Lessons learned

    Article • PLOS One, March 2017, PLOS

    Professor Aaron A. King

  29. Climate-driven endemic cholera is modulated by human mobility in a megacity

    Article • Advances in Water Resources, November 2016, Elsevier

    Professor Aaron A. King

  30. Differential and enhanced response to climate forcing in diarrheal disease due to rotavirus across a megacity of the developing world

    Article • Proceedings of the National Academy of Sciences, March 2016, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  31. The pertussis enigma: reconciling epidemiology, immunology and evolution

    Article • Proceedings of the Royal Society B Biological Sciences, January 2016, Royal Society Publishing

    Professor Pejman Rohani, Professor Aaron A. King

  32. Statistical Inference for Partially Observed Markov Processes via theRPackagepomp

    Article • Journal of Statistical Software, January 2016, Foundation for Open Access Statistic

    Professor Aaron A. King

  33. Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity

    Article • Parasitology, September 2015, Cambridge University Press

    Professor Aaron A. King

  34. Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein–Uhlenbeck Model

    Article • Systematic Biology, June 2015, Oxford University Press (OUP)

    Professor Aaron A. King

  35. Unraveling the Transmission Ecology of Polio

    Article • PLoS Biology, June 2015, PLOS

    Professor Aaron A. King

  36. Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola

    Article • Proceedings of the Royal Society B Biological Sciences, April 2015, Royal Society Publishing

    Professor Aaron A. King

  37. Inference for dynamic and latent variable models via iterated, perturbed Bayes maps

    Article • Proceedings of the National Academy of Sciences, January 2015, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  38. Time-varying, serotype-specific force of infection of dengue virus

    Article • Proceedings of the National Academy of Sciences, May 2014, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  39. Evolution of acuteness in pathogen metapopulations: conflicts between “classical” and invasion-persistence trade-offs

    Article • Theoretical Ecology, April 2014, Springer Science + Business Media

    Professor Aaron A. King

  40. Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics

    Article • Proceedings of the Royal Society B Biological Sciences, April 2014, Royal Society Publishing

    Professor Aaron A. King

  41. Epidemiological evidence for herd immunity induced by acellular pertussis vaccines

    Article • Proceedings of the National Academy of Sciences, February 2014, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  42. Correction: Immune Boosting Explains Regime-Shifts in Prevaccine-Era Pertussis Dynamics

    Article • PLOS One, January 2014, PLOS

    Professor Aaron A. King

  43. Epidemiological Consequences of Imperfect Vaccines for Immunizing Infections

    Article • SIAM Journal on Applied Mathematics, January 2014, Society for Industrial & Applied Mathematics (SIAM)

    Professor Aaron A. King

  44. Can vaccine legacy explain the British pertussis resurgence?

    Article • Vaccine, December 2013, Elsevier

    Professor Aaron A. King

  45. Immune Boosting Explains Regime-Shifts in Prevaccine-Era Pertussis Dynamics

    Article • PLOS One, August 2013, PLOS

    Professor Aaron A. King

  46. Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity

    Article • Journal of The Royal Society Interface, July 2013, Royal Society Publishing

    Professor Aaron A. King

  47. Highly localized sensitivity to climate forcing drives endemic cholera in a megacity

    Article • Proceedings of the National Academy of Sciences, January 2012, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  48. Statistical Inference for Multi-Pathogen Systems

    Article • PLoS Computational Biology, August 2011, PLOS

    Professor Aaron A. King

  49. Iterated filtering

    Article • The Annals of Statistics, June 2011, Institute of Mathematical Statistics

    Professor Aaron A. King

  50. Natural immune boosting in pertussis dynamics and the potential for long-term vaccine failure

    Article • Proceedings of the National Academy of Sciences, March 2011, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  51. Contact Network Structure Explains the Changing Epidemiology of Pertussis

    Article • Science, November 2010, American Association for the Advancement of Science

    Professor Aaron A. King

  52. Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy

    Article • Trends in Ecology & Evolution, October 2010, Elsevier

    Professor Aaron A. King

  53. How Infections Propagate After Point-Source Outbreaks

    Article • Epidemiology, September 2010, Wolters Kluwer Health

    Professor Aaron A. King

  54. Interactions between Behavioral and Life‐History Trade‐Offs in the Evolution of Integrated Predator‐Defense Plasticity

    Article • The American Naturalist, September 2010, University of Chicago Press

    Professor Aaron A. King

  55. Consequential classes of resources: Subtle global bifurcation with dramatic ecological consequences in a simple population model

    Article • Journal of Theoretical Biology, March 2010, Elsevier

    Professor Aaron A. King

  56. Time Lags and the Balance of Positive and Negative Interactions in Driving Grassland Community Dynamics

    Article • The American Naturalist, February 2010, University of Chicago Press

    Professor Aaron A. King

  57. Faculty Opinions recommendation of Successional state dynamics: a novel approach to modeling nonequilibrium foodweb dynamics.

    Article • January 2010, F1000Research

    Professor Aaron A. King

  58. An Introduction to the Biocomplexity of Sanak Island, Western Gulf of Alaska 1

    Article • Pacific Science, October 2009, Pacific Science

    Professor Aaron A. King

  59. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study

    Article • Journal of The Royal Society Interface, June 2009, Royal Society Publishing

    Professor Aaron A. King, Daihai He

  60. Running for Your Life or Running for Your Dinner: What Drives Fiber‐Type Evolution in Lizard Locomotor Muscles?

    Article • The American Naturalist, May 2009, University of Chicago Press

    Professor Aaron A. King

  61. Evolution of Acute Infections and the Invasion‐Persistence Trade‐Off

    Article • The American Naturalist, April 2009, University of Chicago Press

    Professor Aaron A. King

  62. Time series analysis via mechanistic models

    Article • The Annals of Applied Statistics, March 2009, Institute of Mathematical Statistics

    Professor Aaron A. King, Daihai He

  63. Modeling evolution and persistence of neurological viral diseases in wild populations

    Article • Mathematical Biosciences and Engineering, October 2008, American Institute of Mathematical Sciences (AIMS)

    Professor Aaron A. King

  64. Inapparent infections and cholera dynamics

    Article • Nature, August 2008, Springer Science + Business Media

    Professor Aaron A. King

  65. Inference for nonlinear dynamical systems

    Article • Proceedings of the National Academy of Sciences, December 2006, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  66. Experimental support of the scaling rule for demographic stochasticity

    Article • Ecology Letters, May 2006, Wiley

    Professor Aaron A. King

  67. Nonlinear Stochastic Population Dynamics: The Flour Beetle Tribolium as an Effective Tool of Discovery

    Article • January 2005, Elsevier

    Professor Aaron A. King

  68. Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

    Article • The American Naturalist, December 2004, University of Chicago Press

    Professor Aaron A. King

  69. Anatomy of a chaotic attractor: Subtle model-predicted patterns revealed in population data

    Article • Proceedings of the National Academy of Sciences, December 2003, Proceedings of the National Academy of Sciences

    Professor Aaron A. King

  70. Spatial mechanisms for coexistence of species sharing a common natural enemy

    Article • Theoretical Population Biology, December 2003, Elsevier

    Professor Aaron A. King

  71. Explaining and predicting patterns in stochastic population systems

    Article • Proceedings of the Royal Society B Biological Sciences, August 2003, Royal Society Publishing

    Professor Aaron A. King

  72. Random Perturbations and Lattice Effects in Chaotic Population Dynamics

    Article • Science, September 2002, American Association for the Advancement of Science

    Professor Aaron A. King

  73. Lattice Effects Observed in Chaotic Dynamics of Experimental Populations

    Article • Science, October 2001, American Association for the Advancement of Science

    Professor Aaron A. King

  74. The Geometry of a Population Cycle: A Mechanistic Model of Snowshoe Hare Demography

    Article • Ecology, March 2001, Wiley

    Professor Aaron A. King

  75. THE GEOMETRY OF A POPULATION CYCLE: A MECHANISTIC MODEL OF SNOWSHOE HARE DEMOGRAPHY

    Article • Ecology, March 2001, Wiley

    Professor Aaron A. King

  76. A chaotic attractor in ecology: theory and experimental data

    Article • Chaos Solitons & Fractals, January 2001, Elsevier

    Professor Aaron A. King

  77. Sub-harmonic resonance and multi-annual oscillations in northern mammals: a non-linear dynamical systems perspective

    Article • Chaos Solitons & Fractals, January 2001, Elsevier

    Professor Aaron A. King

  78. The rainbow bridge: Hamiltonian limits and resonance in predator-prey dynamics

    Article • Journal of Mathematical Biology, November 1999, Springer Science + Business Media

    Professor Aaron A. King

  79. Modeling Disease Dynamics: Cholera as a Case Study

    Article • Wiley

    Professor Aaron A. King