M. Shah, G. Ferra, S. Fitzgerald, P. J. Barreira, P. C. Sabeti, and A. Colubri (2022) Containing the spread of mumps on college campuses. Royal Society Open Science 9: 210948. Link
M. Santos-Vega, P. P. Martinez, K. G. Vaishnav, V. Kohli, V. Desai, M. J. Bouma, and M. Pascual (2022) The neglected role of relative humidity in the interannual variability of urban malaria in Indian cities. Nature Communications 13: 533. Link
D. Pak, S. Carran, D. Biddinger, B. Nelson, and O. N. Bjørnstad (2022) Incorporating diapause to predict the interannual dynamics of an important agricultural pest. Population Ecology n/a: Link
A. A. King, Q. Lin, and E. L. Ionides (2022) Markov genealogy processes. Theoretical Population Biology 143: 77–91. Link
S. J. Fox, M. Lachmann, M. Tec, R. Pasco, S. Woody, Z. Du, X. Wang, T. A. Ingle, E. Javan, M. Dahan, K. Gaither, M. E. Escott, S. I. Adler, S. C. Johnston, J. G. Scott, and L. A. Meyers (2022) Real-time pandemic surveillance using hospital admissions and mobility data. Proceedings of the National Academy of Sciences 119: e2111870119. Link
J. E. Domeyer, J. D. Lee, H. Toyoda, B. Mehler, and B. Reimer (2022) Driver-pedestrian perceptual models demonstrate coupling: implications for vehicle automation. IEEE Transactions on Human-Machine Systems 1–10. Link
M. Domenech de Cellès, E. Goult, J.-S. Casalegno, and S. C. Kramer (2022) The pitfalls of inferring virus-virus interactions from co-detection prevalence data: application to influenza and SARS-CoV-2. Proceedings of the Royal Society B: Biological Sciences 289: 20212358. Link
F. Dablander, H. Heesterbeek, D. Borsboom, and J. M. Drake (2022) Overlapping timescales obscure early warning signals of the second COVID-19 wave. Proc. R. Soc. Lond. B 289: 20211809. Link
C. Bravo-Vega, M. Santos-Vega, and J. M. Cordovez (2022) Disentangling snakebite dynamics in Colombia: How does rainfall and temperature drive snakebite temporal patterns?. PLOS Neglected Tropical Diseases 16: e0010270. Link
B. Zhang, S. Liang, G. Wang, C. Zhang, C. Chen, M. Zou, W. Shen, H. Long, D. He, Y. Shu, and X. Du (2021) Synchronized nonpharmaceutical interventions for the control of COVID-19. Nonlinear Dynamics Link
W. Yang, D. Zhang, L. Peng, C. Zhuge, and L. Hong (2021) Rational evaluation of various epidemic models based on the COVID-19 data of China. Epidemics 37: 100501. Link
X. Wang, Z. Du, K. Johnson, R. Pasco, S. Fox, M. Lachmann, J. McLellan, and L. A. Meyers (2021) Effects of COVID-19 Vaccination Timing and Risk Prioritization on Mortality Rates, United States. Emerging Infectious Disease journal 27: 1976. Link
R. Subramanian, Q. He, and M. Pascual (2021) Quantifying asymptomatic infection and transmission of COVID-19 in New York City using observed cases, serology, and testing capacity. Proc Natl Acad Sci 118: e2019716118. Link
X. Rodo, P. P. Martinez, A. Siraj, and M. Pascual (2021) Malaria trends in Ethiopian highlands track the 2000 ’slowdown’ in global warming. Nature Communications 12: 1555. Link
D. Pasetto, J. C. Lemaitre, E. Bertuzzo, M. Gatto, and A. Rinaldo (2021) Range of reproduction number estimates for COVID-19 spread. Biochemical and Biophysical Research Communications 538: 253–258. Link
S. W. Park, M. Pons-Salort, K. Messacar, C. Cook, L. Meyers, J. Farrar, and B. T. Grenfell (2021) Epidemiological dynamics of enterovirus D68 in the United States and implications for acute flaccid myelitis. Science Translational Medicine 13: eabd2400. Link
N. A. Molodecky, H. Jafari, R. M. Safdar, J. A. Ahmed, A. Mahamud, A. S. Bandyopadhyay, H. Shukla, A. Quddus, M. Zaffran, R. W. Sutter, N. C. Grassly, and I. M. Blake (2021) Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in Pakistan and Afghanistan to inform outbreak control strategies in the context of the COVID-19 pandemic. Vaccine Link
M. P. Kain, M. L. Childs, A. D. Becker, and E. A. Mordecai (2021) Chopping the tail: How preventing superspreading can help to maintain COVID-19 control. Epidemics 34: 100430. Link
E. L. Ionides, K. Asfaw, J. Park, and A. A. King (2021) Bagged filters for partially observed interacting systems. Journal of the American Statistical Association 1–12. Link
M. L. Childs, M. P. Kain, M. J. Harris, D. Kirk, L. Couper, N. Nova, I. Delwel, J. Ritchie, A. D. Becker, and E. A. Mordecai (2021) The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models. Proceedings of the Royal Society B: Biological Sciences 288: 20210811. Link
Y. Cai, S. Zhao, Y. Niu, Z. Peng, K. Wang, D. He, and W. Wang (2021) Modelling the effects of the contaminated environments on tuberculosis in Jiangsu, China. Journal of Theoretical Biology 508: 110453. Link
R. K. Borchering, C. E. Gunning, D. V. Gokhale, K. B. Weedop, A. Saeidpour, T. S. Brett, and P. Rohani (2021) Anomalous influenza seasonality in the United States and the emergence of novel influenza B viruses. Proceedings of the National Academy of Sciences of the United States of America 118: e2012327118. Link
A. D. Becker, K. H. Grantz, S. T. Hegde, S. Bérubé, D. A. T. Cummings, and A. Wesolowski (2021) Development and dissemination of infectious disease dynamic transmission models during the COVID-19 pandemic: what can we learn from other pathogens and how can we move forward?. The Lancet Digital Health 3: e41–e50. Link
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: e01470. Link
L. K. Whittles, P. J. White, and X. Didelot (2020) Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics. Clinical Infectious Diseases Link
P. Szczepocki (2020) Application of iterated filtering to stochastic volatility models based on non-Gaussian Ornstein-Uhlenbeck process. Statistics in Transition New Series 21: 173–187. Link
L. Stone, D. H. He, S. Lehnstaedt, and Y. Artzy-Randrup (2020) Extraordinary curtailment of massive typhus epidemic in the Warsaw Ghetto. Science Advances 6: eabc0927. Link
T. Stocks (2020) Iterated Filtering Methods for Markov Process Epidemic Models. Handbook of Infectious Disease Data Analysis 199–219.
T. Stocks, L. J. Martin, S. Kühlmann-Berenzon, and T. Britton (2020) Dynamic modeling of hepatitis C transmission among people who inject drugs. Epidemics 30: 100378. Link
J. Park and E. L. Ionides (2020) Inference on high-dimensional implicit dynamic models using a guided intermediate resampling filter. Statistics and Computing 30: 1497–1522. Link
S. S. Musa, S. Zhao, D. Gao, Q. Lin, G. Chowell, and D. He (2020) Mechanistic modelling of the large-scale Lassa fever epidemics in Nigeria from 2016 to 2019. Journal of Theoretical Biology 493: 110209. Link
E. C. Lee, D. L. Chao, J. C. Lemaitre, L. Matrajt, D. Pasetto, J. Perez-Saez, F. Finger, A. Rinaldo, J. D. Sugimoto, M. E. Halloran, I. M. Longini, R. Ternier, K. Vissieres, A. S. Azman, J. Lessler, and L. C. Ivers (2020) Achieving coordinated national immunity and cholera elimination in Haiti through vaccination: a modelling study. Lancet Global Health 8: e1081–e1089. Link
D. He, S. Zhao, Q. Lin, S. S. Musa, and L. Stone (2020) New estimates of the Zika virus epidemic attack rate in northeastern Brazil from 2015 to 2016: a modelling analysis based on Guillain-Barré syndrome (gbs) surveillance data. PLOS Neglected Tropical Diseases 14: e0007502. Link
T. Ganyani, C. Faes, and N. Hens (2020) Simulation and analysis methods for stochastic compartmental epidemic models. Annual Review of Statistics and Its Application Link
S. Funk and A. A. King (2020) Choices and trade-offs in inference with infectious disease models. Epidemics 30: 100383. Link
M. Domenech de Cellès, H. Campbell, R. Borrow, M.-K. Taha, and L. Opatowski (2020) Transmissibility and pathogenicity of the emerging meningococcal serogroup W sequence type-11 complex South American strain: a mathematical modeling study. BMC Medicine 18: 1–12. Link
G. G. Cotterill, P. C. Cross, J. A. Merkle, J. D. Rogerson, B. M. Scurlock, and J. T. du Toit (2020) Parsing the effects of demography, climate and management on recurrent brucellosis outbreaks in elk. Journal of Applied Ecology 57: 379–389. Link
A. Colubri, M. Kemball, K. Sani, C. Boehm, K. Mutch-Jones, B. Fry, T. Brown, and P. C. Sabeti (2020) Preventing outbreaks through interactive, experiential real-life simulations. Cell 182: 1366–1371. Link
A. Colubri, M. Kemball, K. Sani, C. Boehm, K. Mutch-Jones, B. Fry, T. Brown, and P. C. Sabeti (2020) Preventing outbreaks through interactive, experiential real-life simulations. Cell 182: 1366–1371. Link
Q. Clairon and A. Samson (2020) Optimal control for estimation in partially observed elliptic and hypoelliptic linear stochastic differential equations. Statistical Inference for Stochastic Processes 23: 105–127. Link
C. Bretó, E. L. Ionides, and A. A. King (2020) Panel data analysis via mechanistic models. Journal of the American Statistical Association 115: 1178–1188. Link
A. D. Becker, S. H. Zhou, A. Wesolowski, and B. T. Grenfell (2020) Coexisting attractors in the context of cross-scale population dynamics: measles in London as a case study. Proc. R. Soc. Lond. B 287: 20191510. Link
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 of the U S A 201908147. Link
E. B. O'Dea and J. M. Drake (2019) Disentangling reporting and disease transmission. Theoretical Ecology 12: 89–98. Link
N. Noori and P. Rohani (2019) Quantifying the consequences of measles-induced immune modulation for whooping cough epidemiology. Philosophical Transactions of the Royal Society of London, Series B 374: 20180270. Link
J. A. Marino Jr., S. D. Peacor, D. B. Bunnell, H. A. Vanderploeg, S. A. Pothoven, A. K. Elgin, J. R. Bence, J. Jiao, and E. L. Ionides (2019) Evaluating consumptive and nonconsumptive predator effects on prey density using field time-series data. Ecology 100: e02583. Link
F. M. G. Magpantay, A. King A., and P. Rohani (2019) Age-structure and transient dynamics in epidemiological systems. Journal of The Royal Society Interface 16: 20190151. Link
J. Lemaitre, D. Pasetto, J. Perez-Saez, C. Sciarra, J. F. Wamala, and A. Rinaldo (2019) Rainfall as a driver of epidemic cholera: Comparative model assessments of the effect of intra-seasonal precipitation events. Acta Tropica 190: 235–243. Link
M. Domenech de Cellès, H. Arduin, D. Lévy-Bruhl, S. Georges, C. Souty, D. Guillemot, L. Watier, and L. Opatowski (2019) Unraveling the seasonal epidemiology of pneumococcus. Proceedings of the National Academy of Sciences of the U S A 116: 1802. Link
L. E. Coffeng, E. A. Le Rutte, J. Muñoz, E. R. Adams, J. M. Prada, S. J. de Vlas, and G. F. Medley (2019) Impact of changes in detection effort on control of visceral leishmaniasis in the Indian subcontinent. Journal of Infectious Diseases 221: S546–S553. Link
A. D. Becker, A. Wesolowski, O. N. Bjornstad, and B. T. Grenfell (2019) Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination. Plos Computational Biology 15: e1007305. Link
S. Zhao, L. Stone, D. Gao, and D. He (2018) Modelling the large-scale yellow fever outbreak in Luanda, Angola, and the impact of vaccination. PLoS Neglected Tropical Diseases 12: e0006158. Link
T. Stocks, T. Britton, and M. Höhle (2018) Model selection and parameter estimation for dynamic epidemic models via iterated filtering: application to rotavirus in Germany. Biostatistics 400–416. Link
E. O. Romero-Severson, R. M. Ribeiro, and M. Castro (2018) Noise is not error: detecting parametric heterogeneity between epidemiologic time series. Frontiers in Microbiology 9: 1529. Link
M. Pons-Salort and N. C. Grassly (2018) Serotype-specific immunity explains the incidence of diseases caused by human enteroviruses. Science 361: 800. Link
Q. Lin, A. P. Chiu, S. Zhao, and D. He (2018) Modeling the spread of Middle East respiratory syndrome coronavirus in Saudi Arabia. Statistical Methods in Medical Research 27: 1968–1978. Link
D. A. Kennedy, P. A. Dunn, and A. F. Read (2018) Modeling Marek’s disease virus transmission: A framework for evaluating the impact of farming practices and evolution. Epidemics 23: 85–95. Link
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: eaaj1748. Link
C. Bretó (2018) Modeling and inference for infectious disease dynamics: a likelihood-based approach. Statistical Science 33: 57–69. Link
L. K. Whittles, P. J. White, and X. Didelot (2017) Estimating the fitness cost and benefit of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy: A modelling study. PLOS Medicine 14: e1002416. Link
T. Stocks (2017) Iterated filtering methods for Markov process epidemic models. Link
S. L. Ranjeva, E. B. Baskerville, V. Dukic, L. L. Villa, E. Lazcano-Ponce, A. R. Giuliano, G. Dwyer, and S. Cobey (2017) Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity. Proceedings of the National Academy of Sciences of the U.S.A. 114: 13573–13578. Link
P. P. Martinez, R. C. Reiner Jr, M. Roy, B. A. Cash, 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: e0172355. Link
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. Link
X. Du, A. A. King, R. J. Woods, and M. Pascual (2017) Evolution-informed forecasting of seasonal influenza A (H3N2). Science Translational Medicine 9: eaan5325. Link
M. G. Buhnerkempe, K. C. Prager, C. C. Strelioff, D. J. Greig, J. L. Laake, S. R. Melin, R. L. DeLong, F. M. D. Gulland, and J. O. Lloyd-Smith (2017) Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions. Journal of Animal Ecology 86: 460–472. Link
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. Link
S. Tavakoli and V. M. Panaretos (2016) Detecting and localizing differences in functional time series dynamics: a case study in molecular biophysics. Journal of the American Statistical Association 111: 1020–1035. Link
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 of the U.S.A. 113: 4092–4097. Link
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. Link
Q. Lin, Z. Lin, A. P. Y. Chiu, and D. He (2016) Seasonality of Influenza A(H7N9) Virus in China-Fitting Simple Epidemic Models to Human Cases. PLoS ONE 11: e0151333. Link
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: 1–43. Link
M. Fasiolo, N. Pya, and S. N. Wood (2016) A comparison of inferential methods for highly nonlinear state space models in ecology and epidemiology. Statistical Science 31: 96–118. Link
A. Bhadra and E. L. Ionides (2016) Adaptive particle allocation in iterated sequential Monte Carlo via approximating meta-models. Statistics and Computing 26: 393–407. Link
A. D. Becker, R. B. Birger, A. Teillant, P. A. Gastanaduy, G. S. Wallace, and B. T. Grenfell (2016) Estimating enhanced prevaccination measles transmission hotspots in the context of cross-scale dynamics. Proceedings of the National Academy of Sciences of the U.S.A. 113: 14595–14600. Link
D. Barrows (2016) A comparative study of techniques for estimation and inference of nonlinear stochastic time series. Thesis: McMaster University. Link
K. M. Bakker, M. E. Martinez-Bakker, B. Helm, and T. J. Stevenson (2016) Digital epidemiology reveals global childhood disease seasonality and the effects of immunization. Proceedings of the National Academy of Sciences of the U.S.A. 113: 6689–6694. Link
S. Shrestha, B. Foxman, J. Berus, W. G. van Panhuis, C. Steiner, C. Viboud, and P. Rohani (2015) The role of influenza in the epidemiology of pneumonia. Scientific Reports 5: 15314–. Link
E. O. Romero-Severson, E. Volz, J. S. Koopman, T. Leitner, and E. L. Ionides (2015) Dynamic variation in sexual contact rates in a cohort of HIV-negative gay men. American Journal of Epidemiology 182: 255–262. Link
M. Martinez-Bakker, A. A. King, and P. Rohani (2015) Unraveling the transmission ecology of polio. PLoS Biology 13: e1002172. Link
K. Laneri, R. E. Paul, A. Tall, J. Faye, F. Diene-Sarr, C. Sokhna, J.-F. Trape, and X. Rodó (2015) Dynamical malaria models reveal how immunity buffers effect of climate variability. Proceedings of the National Academy of Sciences of the U.S.A. 112: 8786–8791. Link
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: 20150347. Link
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 of the U.S.A. 112: 719–724. Link
D. T. S. Hayman (2015) Biannual birth pulses allow filoviruses to persist in bat populations. Proceedings of the Royal Society of London, Series B 282: 20142591. Link
A. Doucet, M. K. Pitt, G. Deligiannidis, and R. Kohn (2015) Efficient implementation of Markov chain Monte Carlo when using an unbiased likelihood estimator. Biometrika 102: 295–313. Link
C. Bretó (2014) On idiosyncratic stochasticity of financial leverage effects. Statistics and Probability Letters 91: 20–26. Link
I. M. Blake, R. Martin, A. Goel, N. Khetsuriani, J. Everts, C. Wolff, S. Wassilak, R. B. Aylward, and N. C. Grassly (2014) The role of older children and adults in wild poliovirus transmission. Proceedings of the National Academy of Sciences of the U.S.A. 111: 10604–10609. Link
S. Shrestha, B. Foxman, D. M. Weinberger, C. Steiner, C. Viboud, and P. Rohani (2013) Identifying the interaction between influenza and pneumococcal pneumonia using incidence data. Science Translational Medicine 5: 191ra84. Link
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: e72086. Link
D. He, J. Dushoff, T. Day, J. Ma, and D. J. D. Earn (2013) Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales. Proceedings of the Royal Society of London, Series B 280: 20131345. Link
D. He, J. Dushoff, R. Eftimie, and D. J. D. Earn (2013) Patterns of spread of influenza A in Canada. Proceedings of the Royal Society of London, Series B 280: 20131174. Link
J. C. Blackwood, D. G. Streicker, S. Altizer, and P. Rohani (2013) Resolving the roles of immunity, pathogenesis, and immigration for rabies persistence in vampire bats. Proceedings of the National Academy of Sciences of the U.S.A. 110: 20837–20842. Link
J. C. Blackwood, D. A. T. Cummings, H. Broutin, S. Iamsirithaworn, and P. Rohani (2013) Deciphering the impacts of vaccination and immunity on pertussis epidemiology in Thailand. Proceedings of the National Academy of Sciences of the U.S.A. 110: 9595–9600. Link
M. Roy, M. J. Bouma, E. L. Ionides, R. C. Dhiman, and M. Pascual (2012) The Potential Elimination of Plasmodium Vivax Malaria by Relapse Treatment: Insights from a Transmission Model and Surveillance Data from NW India. PLoS Neglected Tropical Diseases 7: e1979. Link
J.-M. Marin, P. Pudlo, C. P. Robert, and R. J. Ryder (2012) Approximate Bayesian computational methods. Statistics and Computing 22: 1167–1180. Link
Y. Xia and H. Tong (2011) Feature matching in time series modeling. Statistical Science 26: 21–46. Link
S. Shrestha, A. A. King, and P. Rohani (2011) Statistical inference for multi-pathogen systems. PLoS Computational Biology 7: e1002135. Link
J. Knape and P. de Valpine (2011) Fitting complex population models by combining particle filters with Markov chain Monte Carlo. Ecology 93: 256–263. Link
E. L. Ionides (2011) Discussion of “Feature Matching in Time Series Modeling” by Y. Xia and H. Tong. Statistical Science 26: 49–52. Link
E. L. Ionides, A. Bhadra, Y. Atchadé, and A. A. King (2011) Iterated filtering. Annals of Statistics 39: 1776–1802. Link
D. He, J. Dushoff, T. Day, J. Ma, and D. Earn (2011) Mechanistic modelling of the three waves of the 1918 influenza pandemic. Theoretical Ecology 4: 1–6. Link
A. Camacho, S. Ballesteros, A. L. Graham, F. Carrat, O. Ratmann, and B. Cazelles (2011) Explaining rapid reinfections in multiple-wave influenza outbreaks: Tristan da Cunha 1971 epidemic as a case study. Proceedings of the Royal Society of London, Series B 278: 3635–3643. Link
C. Bretó and E. L. Ionides (2011) Compound Markov counting processes and their applications to modeling infinitesimally over-dispersed systems. Stochastic Processes and their Applications 121: 2571–2591. Link
A. Bhadra, E. L. Ionides, K. Laneri, M. Pascual, M. Bouma, and R. C. Dhiman (2011) Malaria in northwest India: data analysis via partially observed stochastic differential equation models driven by Lévy noise. Journal of the American Statistical Association 106: 440–451. Link
S. N. Wood (2010) Statistical inference for noisy nonlinear ecological dynamic systems. Nature 466: 1102–1104. Link
T. Toni and M. P. H. Stumpf (2010) Simulation-based model selection for dynamical systems in systems and population biology. Bioinformatics 26: 104–110. Link
K. Laneri, A. Bhadra, E. L. Ionides, M. Bouma, R. C. Dhiman, R. S. Yadav, and M. Pascual (2010) Forcing versus feedback: epidemic malaria and monsoon rains in northwest India. PLoS Computational Biology 6: e1000898. Link
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. Link
A. Bhadra (2010) Discussion of ‘Particle Markov chain Monte Carlo methods’ by C. Andrieu, A. Doucet and R. Holenstein. Journal of the Royal Statistical Society, Series B 72: 314–315. Link
C. Andrieu, A. Doucet, and R. Holenstein (2010) Particle Markov chain Monte Carlo methods. Journal of the Royal Statistical Society, Series B 72: 269–342. Link
T. Toni, D. Welch, N. Strelkowa, A. Ipsen, and M. P. H. Stumpf (2009) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society, Interface 6: 187–202. Link
G. Evensen (2009) Data Assimilation: The Ensemble Kalman Filter. Link
C. Bretó, D. He, E. L. Ionides, and A. A. King (2009) Time series analysis via mechanistic models. Annals of Applied Statistics 3: 319–348. Link
A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008) Inapparent infections and cholera dynamics. Nature 454: 877–880. Link
X. Cai and Z. Xu (2007) K-leap method for accelerating stochastic simulation of coupled chemical reactions. Journal of Chemical Physics 126: 074102. Link
D. C. Reuman, R. A. Desharnais, R. F. Costantino, O. S. Ahmad, and J. E. Cohen (2006) Power spectra reveal the influence of stochasticity on nonlinear population dynamics. Proceedings of the National Academy of Sciences of the U.S.A. 103: 18860–18865. Link
E. L. Ionides, C. Bretó, and A. A. King (2006) Inference for nonlinear dynamical systems. Proceedings of the National Academy of Sciences of the U.S.A. 103: 18438–18443. Link
S. Kucherenko and Y. Sytsko (2005) Application of deterministic low-discrepancy sequences in global optimization. Computational Optimization and Applications 30: 297–318. Link
B. E. Kendall, S. P. Ellner, E. McCauley, S. N. Wood, C. J. Briggs, W. M. Murdoch, and P. Turchin (2005) Population cycles in the pine looper moth: Dynamical tests of mechanistic hypotheses. Ecological Monographs 75: 259–276. Link
M. S. Arulampalam, S. Maskell, N. Gordon, and T. Clapp (2002) A tutorial on particle filters for online nonlinear, non-Gaussian Bayesian tracking. IEEE Transactions on Signal Processing 50: 174–188. Link
J. Liu and M. West (2001) Combining parameter and state estimation in simulation-based filtering. In: Sequential Monte Carlo Methods in Practice (edited by A. Doucet, N. de Freitas, and N. J. Gordon) 197–224.
J. L. Anderson (2001) An ensemble adjustment Kalman filter for data assimilation. Monthly Weather Review 129: 2884–2903. Link
B. E. Kendall, C. J. Briggs, W. W. Murdoch, P. Turchin, S. P. Ellner, E. McCauley, R. M. Nisbet, and S. N. Wood (1999) Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches. Ecology 80: 1789–1805. Link
S. P. Ellner, B. A. Bailey, G. V. Bobashev, A. R. Gallant, B. T. Grenfell, and D. W. Nychka (1998) Noise and nonlinearity in measles epidemics: Combining mechanistic and statistical approaches to population modeling. American Naturalist 151: 425–440. Link
C. Gouriéroux and A. Monfort (1997) Simulation-based Econometric Methods. Link
G. Evensen (1994) Sequential data assimilation with a nonlinear quasi-geostrophic model using Monte Carlo methods to forecast error statistics. Journal of Geophysical Research: Oceans 99: 10143–10162. Link
D. T. Gillespie (1977) Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81: 2340–2361. Link


This software has been made possible by support from the U.S. National Science Foundation (Grants #EF-0545276, #EF-0430120), by the “Inference for Mechanistic Models” Working Group supported by the National Center for Ecological Analysis and Synthesis (a Center funded by N.S.F. (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California), and by the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security and the Fogarty International Center, U.S. National Institutes of Health.