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| A. A. King, Q. Lin, and E. L. Ionides (2024) Exact phylodynamic likelihood via structured Markov genealogy processes. arXiv 2405.17032. |
| Q. Lin, E. E. Goldberg, T. Leitner, C. Molina-París, A. A. King, and E. O. Romero-Severson (2024) The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees. Molecular Biology and Evolution 41(6): msae07. |
| M. A. E. Peters, A. A. King, and N. Wale (2024) Red blood cell dynamics during malaria infection challenge the assumptions of mathematical models of infection dynamics. Frontiers in Malaria 2: |
| J. Li, E. L. Ionides, A. A. King, M. Pascual, and N. Ning (2024) Inference on spatiotemporal dynamics for coupled biological populations. Journal of the Royal Society Interface 21(216): 20240217. |
| E. L. Ionides, K. Asfaw, J. Park, and A. A. King (2023) Bagged filters for partially observed interacting systems. Journal of the American Statistical Association 118(542): 1078–1089. |
| C. Breto, E. L. Ionides, A. A. King, and J. Wheeler (2023) panelPomp: Inference for Panel Partially Observed Markov Processes. CRAN: Contributed Packages |
| D. V. Gokhale, T. S. Brett, B. He, A. A. King, and P. Rohani (2023) Disentangling the causes of mumps reemergence in the United States. Proceedings of the National Academy of Sciences 120(3): e2207595120. |
| A. A. King, Q. Lin, and E. L. Ionides (2022) Markov genealogy processes. Theoretical Population Biology 143: 77–91. |
| V. Romeo-Aznar, L. Picinini Freitas, O. Gonçalves Cruz, A. A. King, and M. Pascual (2022) Fine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics. Nature Communications 13(1): 996. |
| A. Le, A. A. King, F. M. G. Magpantay, A. Mesbahi, and P. Rohani (2021) The impact of infection-derived immunity on disease dynamics. Journal of Mathematical Biology 83(6): 61. |
| M. Auger-Méthé, K. Newman, D. Cole, F. Empacher, R. Gryba, A. A. King, V. Leos-Barajas, J. Mills Flemming, A. Nielsen, G. Petris, and L. Thomas (2021) A guide to state-space modeling of ecological time series. Ecological Monographs 91(4): e01470. |
| K. Asfaw, E. Ionides, and A. A. King (2021) spatPomp: inference for spatiotemporal partially observed Markov processes. CRAN: Contributed Packages |
| A. A. King, Q. Lin, and E. L. Ionides (2020) The sampled Moran genealogy process. arXiv 2002.11184. |
| S. Funk and A. A. King (2020) Choices and trade-offs in inference with infectious disease models. Epidemics 30: 100383. |
| N. Wale, M. J. Jones, D. G. Sim, A. F. Read, and A. A. King (2019) The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections. Proceedings of the National Academy of Sciences 116(44): 201908147. |
| F. M. G. Magpantay, A. A. King, and P. Rohani (2019) Age-structure and transient dynamics in epidemiological systems. Journal of the Royal Society Interface 16(156): 20190151. |
| O. N. Bjørnstad, B. T. Grenfell, C. Viboud, and A. A. King (2019) Comparison of alternative models of human movement and the spread of disease. bioRxiv 2019.12.19.882175. |
| M. Domenech de Cellès, P. Rohani, and A. A. King (2019) Duration of immunity and effectiveness of diphtheria-tetanus-acellular pertussis vaccines in children. JAMA Pediatrics 173(6): 588–594. |
| C. Bretó, E. L. Ionides, and A. A. King (2019) Panel data analysis via mechanistic models. Journal of the American Statistical Association 115(531): 1178–1188. |
| M. Domenech de Cellès, A. A. King, and P. Rohani (2019) Commentary: resolving pertussis resurgence and vaccine immunity using mathematical transmission models. Human Vaccines & Immunotherapeutics 15(3): 683–686. |
| M. Domenech de Cellès, A. A. King, and P. Rohani (2018) Response to Comment on “The impact of past vaccination coverage and immunity on pertussis resurgence”. Science Translational Medicine 10(472): eaau9627. |
| M. Domenech de Cellès, F. M. G. Magpantay, A. A. King, and P. Rohani (2018) The impact of past vaccination coverage and immunity on pertussis resurgence. Science Translational Medicine 10(434): eaaj1748. |
| A. I. Bento, M. A. Riolo, Y. H. Choi, A. A. King, and P. Rohani (2018) Core pertussis transmission groups in England and Wales: A tale of two eras. Vaccine 36(9): 1160–1166. |
| A. A. King, M. D. de Cellès, F. M. G. Magpantay, and P. Rohani (2018) Pertussis immunity and the epidemiological impact of adult transmission: Statistical evidence from Sweden and Massachusetts. In: Pertussis: Epidemiology, Immunology, and Evolution (edited by P. Rohani and S. Scarpino) 225–240. |
| X. Du, A. A. King, R. J. Woods, and M. Pascual (2017) Evolution-informed forecasting of seasonal influenza A (H3N2). Science Translational Medicine 9(413): eaan5325. |
| R. A. Smith, E. L. Ionides, and A. A. King (2017) Infectious disease dynamics inferred from genetic data via sequential Monte Carlo. Molecular Biology and Evolution 34(8): 2065–2084. |
| E. L. Ionides, C. Breto, J. Park, R. A. Smith, and A. A. King (2017) Monte Carlo profile confidence intervals for dynamic systems. Journal of the Royal Society, Interface 14: 20170126. |
| T. Baracchini, A. A. King, M. J. Bouma, X. Rodó, E. Bertuzzo, and M. Pascual (2017) Seasonality in cholera dynamics: a rainfall-driven model explains the wide range of patterns in endemic areas. Advances in Water Resources 108C: 357–366. |
| P. P. Martinez, R. C. Reiner Jr., B. A. Cash, X. Rodó, M. Shahjahan Mondal, M. Roy, M. Yunus, A. S. G. Faruque, S. Huq, A. A. King, and M. Pascual (2017) Cholera forecast for Dhaka, Bangladesh, with the 2015–2016 El Niño: lessons learned. PLOS ONE 12(3): e0172355. |
| A. I. Bento, A. A. King, and P. Rohani (2017) Maternal pertussis immunisation: clinical gains and epidemiological legacy. Eurosurveillance 22(15): 3. |
| J. Perez-Saez, A. A. King, A. Rinaldo, M. Yunus, A. S. G. Faruque, and M. Pascual (2017) Climate-driven endemic cholera is modulated by human mobility in a megacity. Advances in Water Resources 108C: 367–376. |
| A. A. King, D. Nguyen, and E. L. Ionides (2016) Statistical inference for partially observed Markov processes via the R package pomp. Journal of Statistical Software 69(12): 1–43. |
| M. Domenech de Cellès, F. M. G. Magpantay, A. A. King, and P. Rohani (2016) The pertussis enigma: reconciling epidemiology, immunology and evolution. Proceedings of the Royal Society of London, Series B 283(1822): 20152309. |
| F. M. G. Magpantay, M. Domenech de Cellès, P. Rohani, and A. A. King (2016) Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity. Parasitology 143(7): 835–849. |
| P. P. Martinez, A. A. King, M. Yunus, A. S. G. Faruque, and M. Pascual (2016) Differential and enhanced response to climate forcing in diarrheal disease due to rotavirus across a megacity of the developing world. Proceedings of the National Academy of Sciences 113(15): 4092–4097. |
| A. A. King, M. Domenech de Cellès, F. M. G. Magpantay, and P. Rohani (2015) Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola. Proceedings of the Royal Society of London, Series B 282(1806): 20150347. |
| C. E. Cressler, M. A. Butler, and A. A. King (2015) Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model. Systematic Biology 64(6): 953–968. |
| E. L. Ionides, D. Nguyen, Y. Atchadé, S. Stoev, and A. A. King (2015) Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. Proceedings of the National Academy of Sciences 112(3): 719–724. |
| M. Martinez-Bakker, A. A. King, and P. Rohani (2015) Unraveling the transmission ecology of polio. PLOS Biology 13(6): e1002172. |
| S. Shrestha, O. N. Bjørnstad, and A. A. King (2014) Evolution of acuteness in pathogen metapopulations: conflicts between “classical” and invasion-persistence trade-offs. Theoretical Ecology 7(3): 299–311. |
| M. Domenech de Cellès, M. A. Riolo, F. M. G. Magpantay, P. Rohani, and A. A. King (2014) Epidemiological evidence for herd immunity induced by acellular pertussis vaccines. Proceedings of the National Academy of Sciences 111(7): E716–E717. |
| F. Magpantay, M. Riolo, M. de Cellès, A. A. King, and P. Rohani (2014) Epidemiological consequences of imperfect vaccines for immunizing infections. SIAM Journal on Applied Mathematics 74: 1810–1830. |
| M. Martinez-Bakker, K. M. Bakker, A. A. King, and P. Rohani (2014) Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics. Proceedings of the Royal Society of London. Series B 281(1783): 20132438. |
| R. C. Reiner, Jr, S. T. Stoddard, B. M. Forshey, A. A. King, A. M. Ellis, A. L. Lloyd, K. C. Long, C. Rocha, S. Vilcarromero, H. Astete, I. Bazan, A. Lenhart, G. M. Vazquez-Prokopec, V. A. Paz-Soldan, P. J. McCall, U. Kitron, J. P. Elder, E. S. Halsey, A. C. Morrison, T. J. Kochel, and T. W. Scott (2014) Time-varying, serotype-specific force of infection of dengue virus. Proceedings of the National Academy of Sciences 111(26): E2694–E2702. |
| J. S. Lavine, A. A. King, V. Andreasen, and O. N. Bjørnstad (2013) Immune boosting explains regime-shifts in prevaccine-era pertussis dynamics. PLOS ONE 8(8): e72086. |
| M. A. Riolo, A. A. King, and P. Rohani (2013) Can vaccine legacy explain the British pertussis resurgence?. Vaccine 31(49): 5903–5908. |
| N. G. Reich, S. Shrestha, A. A. King, P. Rohani, J. Lessler, S. Kalayanarooj, I.-K. Yoon, R. V. Gibbons, D. S. Burke, and D. A. T. Cummings (2013) Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity. Journal of the Royal Society, Interface 10(86): 20130414. |
| R. C. Reiner, A. A. King, M. Emch, M. Yunus, A. S. G. Faruque, and M. Pascual (2012) Highly localized sensitivity to climate forcing drives endemic cholera in a megacity. Proceedings of the National Academy of Sciences 109(6): 2033–2036. |
| S. Shrestha, A. A. King, and P. Rohani (2011) Statistical inference for multi-pathogen systems. PLOS Computational Biology 7(8): e1002135. |
| E. L. Ionides, A. Bhadra, Y. Atchadé, and A. A. King (2011) Iterated filtering. Annals of Statistics 39(3): 1776–1802. |
| J. S. Lavine, A. A. King, and O. N. Bjørnstad (2011) Natural immune boosting in pertussis dynamics and the potential for long-term vaccine failure. Proceedings of the National Academy of Sciences 108(17): 7259–7264. |
| D. He, E. L. Ionides, and A. A. King (2010) Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. Journal of the Royal Society, Interface 7: 271–283. |
| P. Rohani, X. Zhong, and A. A. King (2010) Contact network structure explains the changing epidemiology of pertussis. Science 330(6006): 982–985. |
| P. Rohani and A. A. King (2010) Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy. Trends in Ecology and Evolution 25(10): 611–618. |
| E. C. Farrer, D. E. Goldberg, and A. A. King (2010) Time lags and the balance of positive and negative interactions in driving grassland community dynamics. American Naturalist 175(2): 160–173. |
| J. L. Zelner, A. A. King, C. L. Moe, and J. N. S. Eisenberg (2010) How infections propagate after point-source outbreaks: an analysis of secondary norovirus transmission. Epidemiology 21(5): 711–718. |
| A. A. King, S. Shrestha, E. T. Harvill, and O. N. Bjørnstad (2009) Evolution of acute infections and the invasion-persistence trade-off. American Naturalist 173(4): 446–455. |
| C. Bretó, D. He, E. L. Ionides, and A. A. King (2009) Time series analysis via mechanistic models. Annals of Applied Statistics 3(1): 319–348. |
| J. A. Scales, A. A. King, and M. A. Butler (2009) Running for your life or running for your dinner: what drives fiber-type evolution in lizard locomotor muscles?. American Naturalist 173(5): 543–553. |
| A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008) Inapparent infections and cholera dynamics. Nature 454(7206): 877–880. |
| A. A. King, E. L. Ionides, and C. Bretó (2007) pomp: Statistical Inference for Partially Observed Markov Processes. CRAN: Contributed Packages |
| E. L. Ionides, C. Bretó, and A. A. King (2006) Inference for nonlinear dynamical systems. Proceedings of the National Academy of Sciences 103(49): 18438–18443. |
| R. A. Desharnais, R. F. Costantino, J. M. Cushing, S. M. Henson, B. Dennis, and A. A. King (2006) Experimental support of the scaling rule for demographic stochasticity. Ecology Letters 9: 537–547. |
| A. A. King, R. F. Costantino, J. M. Cushing, S. M. Henson, R. A. Desharnais, and B. Dennis (2004) Anatomy of a chaotic attractor: subtle model-predicted patterns revealed in population data. Proceedings of the National Academy of Sciences 101(1): 408–413. |
| M. A. Butler and A. A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164: 683–695. |
| A. A. King and A. Hastings (2003) Spatial mechanisms for coexistence of species sharing a common natural enemy. Theoretical Population Biology 64(4): 431–438. |
| S. M. Henson, A. A. King, R. F. Costantino, J. M. Cushing, B. Dennis, and R. A. Desharnais (2003) Explaining and predicting patterns in stochastic population systems. Proceedings of the Royal Society of London, Series B 270: 1549–1553. |
| A. A. King and W. M. Schaffer (2001) The geometry of a population cycle: a mechanistic model of snowshoe hare demography. Ecology 82(3): 814–830. |
| S. M. Henson, R. F. Costantino, J. M. Cushing, R. A. Desharnais, B. Dennis, and A. A. King (2001) Lattice effects observed in chaotic dynamics of experimental populations. Science 294: 602–605. |
| A. A. King and W. M. Schaffer (1999) The rainbow bridge: Hamiltonian limits and resonance in predator-prey dynamics. Journal of Mathematical Biology 39(5): 439–469. |
