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| A. A. King, Q. Lin, and E. L. Ionides (2022) Markov genealogy processes. Theor Popul Biol 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. |
| C. Bretó, E. L. Ionides, and A. A. King (2020) Panel data analysis via mechanistic models. J Am Stat Assoc 115(531): 1178–1188. |
| 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. Proc Natl Acad Sci 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. |
| 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”. Sci Transl Med 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. Sci Transl Med 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. |
| X. Du, A. A. King, R. J. Woods, and M. Pascual (2017) Evolution-informed forecasting of seasonal influenza A (H3N2). Sci Transl Med 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. Mol Biol Evol 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. Adv Water Res 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. J R Soc 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. Adv Water Res 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. J Stat Softw 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. Proc R Soc London, Ser 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: 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. Proc R Soc London, Ser 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. Syst Biol 64(6): 953–968. |
| M. Martinez-Bakker, A. A. King, and P. Rohani (2015) Unraveling the transmission ecology of polio. PLoS Biol 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. Theor Ecol 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. Proc Natl Acad Sci 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 J Appl Math 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. Proc R Soc London, Ser 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. Proc Natl Acad Sci 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. Proc Natl Acad Sci 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 Comput Biol 7(8): e1002135. |
| E. L. Ionides, A. Bhadra, Y. Atchadé, and A. A. King (2011) Iterated filtering. Ann Stat 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. Proc Natl Acad Sci 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. J R Soc 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. Am Nat 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 Ecol Evol 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. Am Nat 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. |
| A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008) Inapparent infections and cholera dynamics. Nature 454(7206): 877–880. |
| E. L. Ionides, C. Bretó, and A. A. King (2007) 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) |
| E. L. Ionides, C. Bretó, and A. A. King (2006) Inference for nonlinear dynamical systems. Proc Natl Acad Sci 103(49): 18438–18443. |
