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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. |
| 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. |
| 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: |
| C. Breto, E. L. Ionides, A. A. King, and J. Wheeler (2023) panelPomp: Inference for Panel Partially Observed Markov Processes. CRAN: Contributed Packages |
| A. A. King, Q. Lin, and E. L. Ionides (2022) Markov genealogy processes. Theoretical Population Biology 143: 77–91. |
| K. Asfaw, J. Park, A. Ho, A. A. King, and E. L. Ionides (2021) Statistical inference for spatiotemporal partially observed Markov processes via the R package spatPomp. arXiv 2101.01157. |
| A. A. King, Q. Lin, and E. L. Ionides (2020) The sampled Moran genealogy process. arXiv 2002.11184. |
| 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. |
| 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 (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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| S. D. Peacor and C. E. Cressler (2013) The implications of adaptive prey behaviour for ecological communities: a review of current theory. In: Trait-Mediated Indirect Interactions: Linking Evolution, Community, and Ecosystem (edited by T. Ohgushi, O. Schmitz, and R. D. Holt) 131–160. |
| 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. |
| C. E. Cressler (2011) Multi-Trait Selection and the Evolution of the Integrated Phenotype. Ph.D. thesis, University of Michigan. |
| 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. |
| C. E. Cressler, A. A. King, and E. E. Werner (2010) Interactions between behavioral and life-history trade-offs in the evolution of integrated predator-defense plasticity. American Naturalist 176(3): 276–288. |
| 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. |
| 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. |
| S. Shrestha (2009) Different Levels of Host-Pathogen Interactions and Consequences for the Pathogen Life History Evolution. Ph.D. thesis, University of Michigan. |
| E. L. Ionides, C. Bretó, and A. A. King (2008) Modeling disease dynamics: cholera as a case study. In: Statistical Advances in the Biomedical Sciences (edited by A. Biswas, S. Datta, J. Fine, and M. Segal) |
| 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. |
