Aaron A. King, Ph.D.

Nelson G. Hairston Collegiate Professor of Ecology, Evolutionary Biology,
Complex Systems, and Mathematics, University of Michigan
External Professor, Santa Fe Institute
Fellow of the American Association for the Advancement of Science

Selected Publications.

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E. L. Ionides, K. Asfaw, J. Park, and A. A. King (2023) Bagged filters for partially observed interacting systems. J Am Stat Assoc 118(542): 1078–1089.

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. Proc Natl Acad Sci 120(3): e2207595120.

A. A. King, Q. Lin, and E. L. Ionides (2022) Markov genealogy processes. Theor Popul Biol 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. Nat Commun 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. J Math Biol 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. Ecol Monogr 91(4): e01470.

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.

S. Funk and A. A. King (2020) Choices and trade-offs in inference with infectious disease models. Epidemics 30: 100383.

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.

F. M. G. Magpantay, A. A. King, and P. Rohani (2019) Age-structure and transient dynamics in epidemiological systems. J Roy Soc 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.

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”. 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.

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: The Integrative Biology of Pertussis (edited by P. Rohani and S. Scarpino)

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.

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.

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.

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. I. Bento, A. A. King, and P. Rohani (2017) Maternal pertussis immunisation: clinical gains and epidemiological legacy. Eurosurveillance 22(15): 3.

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.

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. Proc Natl Acad Sci 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. 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.

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. Proc Natl Acad Sci 112(3): 719–724.

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.

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. J R Soc 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. Proc Natl Acad Sci 109(6): 2033–2036.

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.

P. Rohani, X. Zhong, and A. A. King (2010) Contact network structure explains the changing epidemiology of pertussis. Science 330(6006): 982–985.

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. Am Nat 175(2): 160–173.

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.

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. Am Nat 173(4): 446–455.

C. Bretó, D. He, E. L. Ionides, and A. A. King (2009) Time series analysis via mechanistic models. Ann Appl Stat 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?. Am Nat 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.

E. L. Ionides, C. Bretó, and A. A. King (2006) Inference for nonlinear dynamical systems. Proc Natl Acad Sci 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. Ecol Lett 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. Proc Natl Acad Sci 101(1): 408–413.

M. A. Butler and A. A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am Nat 164: 683–695.

A. A. King and A. Hastings (2003) Spatial mechanisms for coexistence of species with a shared natural enemy. Theor Popul Biol 64: 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. Proc R Soc London, Ser 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. J Math Biol 39: 439–469.

My ORCID is 0000-0001-6159-3207 and my ResearcherID is B-8092-2012. I have a Google Scholar profile and an NCBI Bibliography.