% This file was created with JabRef 2.6.
% Encoding: Cp1252

@BOOK{Oksendal2003,
  title = {Stochastic differential equations: an introduction with applications},
  publisher = {Springer Verlag},
  year = {2003},
  author = {B. {\O}ksendal}
}

@article{Aguiar2011,
  title={The role of seasonality and import in a minimalistic multi-strain dengue model capturing differences between primary and secondary infections: complex dynamics and its implications for data analysis},
  author={Aguiar, Ma{\'\i}ra and Ballesteros, Sebastien and Kooi, Bob W and Stollenwerk, Nico},
  journal={Journal of Theoretical Biology},
  volume={289},
  pages={181--196},
  year={2011},
  publisher={Elsevier}
}

@ARTICLE{Ait-Sahalia2002,
  author = {Y. Ait-Sahalia},
  title = {Maximum likelihood estimation of discretely sampled diffusions: a
	closed-form approximation approach},
  journal = {Econometrica},
  year = {2002},
  volume = {70},
  pages = {223--262},
  number = {1},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Ait-Sahalia1996,
  author = {Y. Ait-Sahalia},
  title = {Nonparametric pricing of interest rate derivative securities},
  journal = {Econometrica: Journal of the Econometric Society},
  year = {1996},
  volume = {64},
  pages = {527--560},
  number = {3},
  publisher = {JSTOR}
}

@inproceedings{Akaike1973,
  title={Information theory and an extension of the maximum likelihood principle},
  author={H. Akaike},
  booktitle={International Symposium on Information Theory, 2 nd, Tsahkadsor, Armenian SSR},
  pages={267--281},
  year={1973}
}


@book{Anderson1992,
  title={Infectious diseases of humans: dynamics and control},
  author={R.M. Anderson and R.M. May and B. Anderson},
  volume={28},
  year={1992},
  publisher={Wiley Online Library}
}

@ARTICLE{Anderson1992a,
  author = {R.M. Anderson and R.M.M. Oxford},
  title = {Infectious diseases of humans: dynamics and control},
  journal = {AUSTRALIAN JOURNAL OF PUBLIC HEALTH},
  year = {1992},
  volume = {16},
  pages = {300},
  number = {2}
}

@BOOK{Andersson2000,
  title = {Stochastic epidemic models and their statistical analysis},
  publisher = {Springer Verlag},
  year = {2000},
  author = {H. Andersson and T. Britton}
}



@ARTICLE{Andrieu2010,
  author = {C. Andrieu and A. Doucet and R. Holenstein},
  title = {Particle Markov chain Monte Carlo methods},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2010},
  volume = {72},
  pages = {269--342},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Andrieu2008,
  author = {C. Andrieu and J. Thoms},
  title = {A tutorial on adaptive MCMC},
  journal = {Statistics and Computing},
  year = {2008},
  volume = {18},
  pages = {343--373},
  number = {4},
  publisher = {Springer}
}


@article{Arita2006,
  title={Is polio eradication realistic?},
  author={I. Arita and M. Nakane and F. Fenner},
  journal={Science},
  volume={312},
  number={5775},
  pages={852--854},
  year={2006}
}

@ARTICLE{Arulampalam2002,
  author = {M.S. Arulampalam and S. Maskell and N. Gordon and T. Clapp, T.},
  title = {A tutorial on particle filters for online nonlinear/non-Gaussian
	Bayesian tracking},
  journal = {IEEE Transactions on signal processing},
  year = {2002},
  volume = {50},
  pages = {20},
  number = {2}
}

@ARTICLE{Atkinson2001,
  author = {A. Atkinson and R. Bailey},
  title = {One hundred years of the design of experiments on and off the pages
	of Biometrika},
  journal = {Biometrika},
  year = {2001},
  volume = {88},
  pages = {53},
  number = {1},
  publisher = {Biometrika Trust},
}

@BOOK{Atkinson2001a,
  title = {Optimum design},
  publisher = {Kluwer Academic Pub},
  year = {2001},
  author = {A. Atkinson and B. Bogacka and A. Zhigljavsky},
}

@ARTICLE{Auld2006,
  author = {MC. Auld},
  title = {Estimating behavioral response to the AIDS epidemic},
  journal = {Contributions to Economics Analysis \& Policy},
  year = {2006},
  volume = {5},
  pages = {1235--1235},
  number = {1}
}

@ARTICLE{Baguelin2010,
  author = {M. Baguelin and A.J.V. Hoek and M. Jit and S. Flasche and P.J. White
	and W.J. Edmunds},
  title = {Vaccination against pandemic influenza {A}/{H}1{N}1v in England:
	a real-time economic evaluation},
  journal = {Vaccine},
  year = {2010},
  volume = {28},
  pages = {2370--2384},
  number = {12},
  issn = {0264-410X},
  publisher = {Elsevier}
}

@article{Baguelin2012,
  title={Health and economic impact of the seasonal influenza vaccination programme in England},
  author={M. Baguelin and M. Jit and E. Miller and W.J. Edmunds},
  journal={Vaccine},
  year={2012},
  publisher={Elsevier}
}

@article{Bailey1953,
  title={The total size of a general stochastic epidemic},
  author={N.T.J. Bailey},
  journal={Biometrika},
  pages={177--185},
  year={1953},
  publisher={JSTOR}
}

@BOOK{Bailey1975,
  title = {The mathematical theory of infectious diseases and its applications},
  publisher = {London},
  year = {1975},
  author = {N.T.J. Bailey}
}

@ARTICLE{Banerjee2009,
  author = {Abhijit V. Banerjee and Esther Duflo},
  title = {The experimental approach to development economics},
  journal = {Annual Review of Economics},
  year = {2009},
  volume = {200},
  pages = {151-178},
  publisher = {Annual Reviews},
}

@BOOK{Bartlett1970,
  title = {Stochastic population models in ecology and epidemiology},
  publisher = {Methuen London},
  year = {1970},
  author = {M.S. Bartlett}
}


@ARTICLE{Becker1996,
  author = {N.G. Becker},
  title = {Modeling the AIDS epidemic: planning, policy and prediction},
  journal = {Statistics in Medicine},
  year = {1996},
  volume = {15},
  pages = {563--564},
  number = {5},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Becker1994,
  author = {N.G. Becker and L.R. Egerton},
  title = {A transmission model for HIV with application to the Australian epidemic},
  journal = {Mathematical biosciences},
  year = {1994},
  volume = {119},
  pages = {205--224},
  number = {2},
  publisher = {Elsevier}
}

@BOOK{Berstein2007,
  title = {Nonlinear matroid optimization and experimental design},
  publisher = {Citeseer},
  year = {2007},
  author = {Y. Berstein and J. Lee and H. Maruri-Aguilar and S. Onn and E. Riccomagno
	and R. Weismantel and H. Wynn},
}

@ARTICLE{Beskos2006,
  author = {A. Beskos and O. Papaspiliopoulos and G.O. Roberts and P. Fearnhead},
  title = {Exact and computationally efficient likelihood-based estimation for
	discretely observed diffusion processes (with discussion)},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2006},
  volume = {68},
  pages = {333--382},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@article{Beskos2008,
  title={MCMC methods for diffusion bridges},
  author={A. Beskos and G.  Roberts and A. Stuart and J. Voss},
  journal={Stochastics and Dynamics},
  volume={8},
  number={03},
  pages={319--350},
  year={2008},
  publisher={World Scientific}
}

@article{Beskos2011,
  title={Hybrid monte carlo on hilbert spaces},
  author={A. Beskos and FJ Pinski and JM Sanz-Serna and AM Stuart},
  journal={Stochastic Processes and their Applications},
  volume={121},
  number={10},
  pages={2201--2230},
  year={2011},
  publisher={Elsevier}
}

@article{Beskos2012,
  title={Advanced MCMC Methods for Sampling on Diffusion Pathspace},
  author={Beskos, A. and Kalogeropoulos, K. and Pazos, E.},
  journal={arXiv preprint arXiv:1203.6216},
  year={2012}
}

@ARTICLE{Bettencourt2008,
  author = {L.M.A. Bettencourt and R.M. Ribeiro},
  title = {Real time bayesian estimation of the epidemic potential of emerging
	infectious diseases},
  journal = {PLoS One},
  year = {2008},
  volume = {3},
  pages = {2185},
  number = {5},
  issn = {1932-6203},
  publisher = {PLoS}
}

@article{Beutels2002,
  title={Economic evaluation of vaccination programmes: a consensus statement focusing on viral hepatitis},
  author={P. Beutels and W.J. Edmunds and F.  Antonanzas and G.A. De Wit and D. Evans and R. Feilden and A.M.  Fendrick and G.M.  Ginsberg and H.A.  Glick and E.  Mast and others},
  journal={Pharmacoeconomics},
  volume={20},
  number={1},
  pages={1--7},
  year={2002},
  publisher={Adis International}
}


@ARTICLE{Bilmes1998,
  author = {J.A. Bilmes},
  title = {A gentle tutorial of the EM algorithm and its application to parameter
	estimation for Gaussian mixture and hidden Markov models},
  journal = {International Computer Science Institute},
  year = {1998},
  volume = {4},
  pages = {126},
  publisher = {Citeseer}
}

@article{Bjornstad2001,
  title={Noisy clockwork: time series analysis of population fluctuations in animals},
  author={O.N.  Bjornstad and B.T. Grenfell},
  journal={Science},
  volume={293},
  number={5530},
  pages={638--643},
  year={2001},
  publisher={American Association for the Advancement of Science}
}

@article{Black1973,
  title={The pricing of options and corporate liabilities},
  author={F. Black and M. Scholes},
  journal={The journal of political economy},
  pages={637--654},
  year={1973},
  publisher={JSTOR}
}

@article{Boelle2011,
  title={Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review},
  author={P.Y. Boelle and S. Ansart and A. Cori and A.J. Valleron},
  journal={Influenza and other respiratory viruses},
  volume={5},
  number={5},
  pages={306--316},
  year={2011},
  publisher={Wiley Online Library}
}


@ARTICLE{Boily2008,
  author = {M.C. Boily and L. Abu-Raddad and K. Desai and B. Masse and S. Self
	and R. Anderson},
  title = {Measuring the public-health impact of candidate HIV vaccines as part
	of the licensing process},
  journal = {The Lancet Infectious Diseases},
  year = {2008},
  volume = {8},
  pages = {200--207},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{Boily2007,
  author = {M.C. Boily and CM Lowndes and P. Vickerman and L. Kumaranayake and
	J. Blanchard and S. Moses and BM Ramesh and M Pickles and C Watts
	and R. Washington and others},
  title = {Evaluating large-scale HIV prevention interventions: study design
	for an integrated mathematical modelling approach},
  journal = {Sexually transmitted infections},
  year = {2007},
  volume = {83},
  pages = {582},
  number = {7},
  publisher = {BMJ Publishing Group Ltd}
}

@ARTICLE{Boily2008a,
  author = {M.C. Boily and M. Pickles and P. Vickerman and R. Buzdugan and S.
	Isac and K.N. Deering and J.F. Blanchard and S. Moses and C.M. Lowndes
	and B.M. Ramesh and others},
  title = {Using mathematical modelling to investigate the plausibility of attributing
	observed antenatal clinic declines to a female sex worker intervention
	in Karnataka state, India},
  journal = {AIDS},
  year = {2008},
  volume = {22},
  pages = {S149}
}

@ARTICLE{boily2008using,
  author = {Boily, M.C. and Pickles, M. and Vickerman, P. and Buzdugan, R. and
	Isac, S. and Deering, K.N. and Blanchard, J.F. and Moses, S. and
	Lowndes, C.M. and Ramesh, B.M. and others},
  title = {{Using mathematical modelling to investigate the plausibility of
	attributing observed antenatal clinic declines to a female sex worker
	intervention in Karnataka state, India}},
  journal = {AIDS},
  year = {2008},
  volume = {22},
  pages = {S149}
}

@ARTICLE{Boily2004,
  author = {M-C. Boily and F.I. Bastos and K. Desai and B. M{\^a}sse},
  title = {Changes in the transmission dynamics of the HIV epidemic after the
	wide-scale use of antiretroviral therapy could explain increases
	in sexually transmitted infections: results from mathematical models},
  journal = {Sexually transmitted diseases},
  year = {2004},
  volume = {31},
  pages = {100},
  number = {2}
}

@ARTICLE{Boily2002,
  author = {M-C. Boily and C. Lowndes and M. Alary},
  title = {The impact of HIV epidemic phases on the effectiveness of core group
	interventions: insights from mathematical models},
  journal = {Sexually transmitted infections},
  year = {2002},
  volume = {78},
  pages = {i78},
  number = {suppl 1},
  publisher = {BMJ Publishing Group Ltd}
}


@article{Bolker1993,
  title={Chaos and biological complexity in measles dynamics},
  author={BM Bolker and BT Grenfell},
  journal={Proceedings of the Royal Society of London. Series B: Biological Sciences},
  volume={251},
  number={1330},
  pages={75--81},
  year={1993},
  publisher={The Royal Society}
}

@ARTICLE{Boys2008,
  author = {R.J. Boys and D.J. Wilkinson and T.B.L. Kirkwood},
  title = {Bayesian inference for a discretely observed stochastic kinetic model},
  journal = {Statistics and Computing},
  year = {2008},
  volume = {18},
  pages = {125--135},
  number = {2},
  publisher = {Springer}
}

@article{Boily2012,
  title={HIV treatment as prevention: considerations in the design, conduct, and analysis of cluster randomized controlled trials of combination HIV prevention},
  author={Boily, M.C. and M{\^a}sse, B. and Alsallaq, R. and Padian, N.S. and Eaton, J.W. and Vesga, J.F. and Hallett, T.B.},
  journal={PLoS Medicine},
  volume={9},
  number={7},
  pages={e1001250},
  year={2012},
  publisher={Public Library of Science}
}


@article{Bonds2010,
  title={Poverty trap formed by the ecology of infectious diseases},
  author={M.H.  Bonds and D.C.  Keenan and P. Rohani and J.D. Sachs},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={277},
  number={1685},
  pages={1185--1192},
  year={2010},
  publisher={The Royal Society}
}

@book{Box1987,
  title={Empirical model-building and response surfaces.},
  author={Box, George EP and Draper, Norman R},
  year={1987},
  publisher={John Wiley \& Sons}
}

 @article{Bradley2010,
  title={Assessing reported condom use among female sex workers in southern India through examination of condom availability},
  author={J. Bradley and S. Moses and J.F. Blanchard and S. Rajaram and BM Ramesh and S. Verma and M. Alary},
  journal={Sexually transmitted infections},
  volume={86},
  number={Suppl 1},
  pages={i44--i48},
  year={2010},
  publisher={BMJ Publishing Group Ltd}
}


@ARTICLE{Brauer2006,
  author = {F. Brauer},
  title = {Some simple epidemic models},
  journal = {Mathematical Biosciences and Engineering},
  year = {2006},
  volume = {3},
  pages = {1},
  number = {1},
  publisher = {AMERICAN INSTITUTE OF MATHEMATICAL SCIENCES}
}

@article{Breman1980,
  title={The confirmation and maintenance of smallpox eradication},
  author={J.G. Breman and I. Arita},
  journal={New England Journal of Medicine},
  volume={303},
  number={22},
  pages={1263--1273},
  year={1980},
  publisher={Mass Medical Soc}
}

@ARTICLE{Breto2009,
  author = {C. Breto and D. He and E.L. Ionides and A.A. King and S. Ghosal and
	J. Lember and A. van der Vaart},
  title = {Time series analysis via mechanistic models},
  journal = {Annals},
  year = {2009},
  volume = {3},
  pages = {319--348},
  number = {1},
}

@ARTICLE{Briers2010,
  author = {M. Briers and A. Doucet and S. Maskell},
  title = {Smoothing algorithms for state--space models},
  journal = {Annals of the Institute of Statistical Mathematics},
  year = {2010},
  volume = {62},
  pages = {61--89},
  number = {1},
  publisher = {Springer}
}

@BOOK{Br'emaud1999,
  title = {Markov chains: Gibbs fields, Monte Carlo simulation, and queues},
  publisher = {springer verlag},
  year = {1999},
  author = {P. Br{\'e}maud}
}

@article{Brisson2006,
  title={Impact of model, methodological, and parameter uncertainty in the economic analysis of vaccination programs},
  author={M.  Brisson and WJ Edmunds},
  journal={Medical decision making},
  volume={26},
  number={5},
  pages={434--446},
  year={2006},
  publisher={SAGE Publications}
}

@article{Brooks1998,
  title={Convergence assessment techniques for Markov chain Monte Carlo},
  author={S. Brooks and G. Roberts},
  journal={Statistics and Computing},
  volume={8},
  number={4},
  pages={319--335},
  year={1998},
  publisher={Springer}
}

@ARTICLE{Camacho2011,
  author = {A. Camacho and S. Ballesteros and A. Graham and F. Carrat and O.
	Ratmann and B. Cazelles},
  title = {Explaining rapid reinfections in multiple-wave influenza outbreaks:
	Tristan da Cunha 1971 epidemic as a case study},
  journal = {Proceedings of the Royal Society B},
  year = {2011}
}

@BOOK{Cappe2005,
  title = {Inference in hidden Markov models},
  publisher = {Springer Verlag},
  year = {2005},
  author = {O. Cappe and E. Moulines and T. Ryd{\'e}n}
}

@ARTICLE{Carneiro2009,
  author = {HA Carneiro and E. Mylonakis},
  title = {Google Trends: A Web-Based Tool for Real-Time Surveillance of Disease
	Outbreaks.},
  journal = {Clinical infectious diseases: an official publication of the Infectious
	Diseases Society of America},
  year = {2009}
}

@ARTICLE{Carrat2008,
  author = {F. Carrat and E. Vergu and N.M. Ferguson and M. Lemaitre and S. Cauchemez
	and S. Leach and A.J. Valleron},
  title = {Time lines of infection and disease in human influenza: a review
	of volunteer challenge studies},
  journal = {American journal of epidemiology},
  year = {2008},
  volume = {167},
  pages = {775},
  number = {7},
  publisher = {Oxford Univ Press}
}

@ARTICLE{Cauchemez2011,
  author = {S. Cauchemez and A. Bhattarai and T.L. Marchbanks and R.P. Fagan
	and S. Ostroff and N.M. Ferguson and D. Swerdlow and S.V. Sodha and
	M.E. Moll and F.J. Angulo and others},
  title = {Role of social networks in shaping disease transmission during a
	community outbreak of 2009 H1N1 pandemic influenza},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2011},
  volume = {108},
  pages = {2825},
  number = {7},
  issn = {0027-8424},
  publisher = {National Acad Sciences}
}

@ARTICLE{Cauchemez2006,
  author = {S. Cauchemez and P.Y. Boelle and G. Thomas and A.J. Valleron},
  title = {Estimating in real time the efficacy of measures to control emerging
	communicable diseases},
  journal = {American journal of epidemiology},
  year = {2006},
  volume = {164},
  pages = {591},
  number = {6},
  issn = {0002-9262},
  publisher = {Oxford Univ Press}
}

@ARTICLE{Cauchemez2008a,
  author = {S. Cauchemez and N.M. Ferguson},
  title = {Likelihood-based estimation of continuous-time epidemic models from
	time-series data: application to measles transmission in London},
  journal = {Journal of the Royal Society Interface},
  year = {2008},
  volume = {5},
  pages = {885},
  number = {25},
  publisher = {The Royal Society}
}

@ARTICLE{Cauchemez2008,
  author = {S. Cauchemez and A.J. Valleron. and P.Y. Bo{\"e}lle and A. Flahault
	and N.M. Ferguson},
  title = {Estimating the impact of school closure on influenza transmission
	from Sentinel data},
  journal = {Nature},
  year = {2008},
  volume = {452},
  pages = {750--754},
  number = {7188},
  publisher = {Nature Publishing Group},
}


@ARTICLE{Cazelles1997,
  author = {B. Cazelles and N.P. Chau},
  title = {Using the Kalman filter and dynamic models to assess the changing
	HIV/AIDS epidemic},
  journal = {Mathematical biosciences},
  year = {1997},
  volume = {140},
  pages = {131--154},
  number = {2},
  publisher = {Elsevier},
}

@ARTICLE{Cazelles2005,
  author = {B. Cazelles and M. Chavez and A.J. McMichael and S. Hales and others},
  title = {Nonstationary Influence of EI Nino on the Synchronous Dengue Epidemics
	in Thailand},
  journal = {PLoS Medicine},
  year = {2005},
  volume = {2},
  pages = {313},
  number = {4},
  publisher = {Public Library of Science}
}

@ARTICLE{Celeux2000,
  author = {G. Celeux and M. Hurn and C.P. Robert},
  title = {Computational and Inferential Difficulties with Mixture Posterior
	Distributions.},
  journal = {Journal of the American Statistical Association},
  year = {2000},
  volume = {95},
  number = {451},
  publisher = {American Statistical Association}
}

@article{Champagnat2006,
  title={Unifying evolutionary dynamics: from individual stochastic processes to macroscopic models},
  author={Champagnat, N. and Ferri{\`e}re, R. and M{\'e}l{\'e}ard, S. and others},
  journal={Theoretical Population Biology},
  volume={69},
  number={3},
  pages={297--321},
  year={2006}
}

@article{Chastel2012,
  title={Eventual role of asymptomatic cases of dengue for the introduction and spread of dengue viruses in non-endemic regions},
  author={Chastel, C.},
  journal={Frontiers in Physiology},
  volume={3},
  year={2012},
  publisher={Frontiers Media SA}
}

@ARTICLE{Chen2003,
  author = {Z. Chen},
  title = {Bayesian filtering: From Kalman filters to particle filters, and
	beyond},
  journal = {adaptive Syst. Lab., McMaster Univ., Hamilton, ON, Canada.[Online].
	Available: http://soma. crl. mcmaster. ca/~ zhechen/download/ieee
	bayesian. ps},
  year = {2003},
  volume = {69},
  pages = {1-69},
  publisher = {Citeseer},
  url = {http://soma. crl. mcmaster. ca/~ zhechen/download/ieee bayesian. ps}
}

@ARTICLE{Chib2006,
  author = {S. Chib and M.K. Pitt and N. Shephard},
  title = {Likelihood based inference for diffusion driven state space models},
  journal = {Working Paper},
  year = {2006},
  volume = {4},
  pages = {155},
  number = {12},
  issn = {4155-7496},
  publisher = {Working Paper}
}

@ARTICLE{Chib2004,
  author = {S. Chib and M.K. Pitt and N. Shephard},
  title = {Likelihood based inference for diffusion driven models.},
  year = {2004},
  publisher = {Nuffield College (University of Oxford)}
}



@article{Choi2010,
  title={Transmission dynamic modelling of the impact of human papillomavirus vaccination in the United Kingdom},
  author={Choi, Y.H. and Jit, M. and Gay, N. and Cox, A. and Garnett, G.P. and Edmunds, W.J.},
  journal={Vaccine},
  volume={28},
  number={24},
  pages={4091--4102},
  year={2010},
  publisher={Elsevier}
}

@article{Chopin2012,
  title={${S}{M}{C}^2$: an efficient algorithm for sequential analysis of state space models},
  author={N.  Chopin and P.E. Jacob  and O. Papaspiliopoulos},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year={2012},
  publisher={Wiley Online Library}
}

@ARTICLE{Chowell2007,
  author = {G. Chowell and H. Nishiura and L. Bettencourt},
  title = {Comparative estimation of the reproduction number for pandemic influenza
	from daily case notification data},
  journal = {Journal of the Royal Society Interface},
  year = {2007},
  volume = {4},
  pages = {155},
  number = {12},
  issn = {1742-5689},
  publisher = {The Royal Society}
}

@article{Chronopoulou2012,
  title={Estimation and pricing under long-memory stochastic volatility},
  author={A. Chronopoulou and F.G. Viens},
  journal={Annals of Finance},
  volume={8},
  number={2},
  pages={379--403},
  year={2012},
  publisher={Springer}
}

@ARTICLE{Coffee2007,
  author = {M. Coffee and M.N. Lurie and G.P. Garnett},
  title = {Modelling the impact of migration on the HIV epidemic in South Africa},
  journal = {AIDS},
  year = {2007},
  volume = {21},
  pages = {343},
  number = {3},
  issn = {0269-9370}
}

@ARTICLE{Cohen2010,
  author = {J. Cohen and P. Dupas},
  title = {Free Distribution or Cost-Sharing? Evidence from a Randomized Malaria
	Prevention Experiment},
  journal = {Quarterly Journal of Economics},
  year = {2010},
  volume = {125},
  pages = {1--45},
  number = {1},
  publisher = {MIT Press},
}

@ARTICLE{Conlan2007,
  author = {A.J.K. Conlan and B.T. Grenfell},
  title = {Seasonality and the persistence and invasion of measles},
  journal = {Proceedings of the Royal Society B},
  year = {2007},
  volume = {274},
  pages = {1133},
  number = {1614},
  publisher = {The Royal Society}
}

@article{Comte1998,
  title={Long memory in continuous-time stochastic volatility models},
  author={F. Comte and E. Renault},
  journal={Mathematical Finance},
  volume={8},
  number={4},
  pages={291--323},
  year={1998},
  publisher={Wiley Online Library}
}

@ARTICLE{Cook2008,
  author = {A.R. Cook and G.J. Gibson and T.R. Gottwald and C.A. Gilligan},
  title = {Constructing the effect of alternative intervention strategies on
	historic epidemics},
  journal = {Journal of the Royal Society Interface},
  year = {2008},
  volume = {5},
  pages = {1203},
  number = {27},
  publisher = {The Royal Society}
}

@ARTICLE{Cori2009,
  author = {A. Cori and P.Y. Boelle and G. Thomas and G.M. Leung and A.J.
	Valleron},
  title = {Temporal variability and social heterogeneity in disease transmission:
	The case of SARS in Hong Kong},
  journal = {PLoS computational biology},
  year = {2009},
  volume = {5},
  pages = {e1000471},
  number = {8},
  issn = {1553-7358}
}

@article{Cooley1965,
  title={An algorithm for the machine calculation of complex Fourier series},
  author={J.W.  Cooley and J.W. Tukey},
  journal={Mathematics of computation},
  pages={297--301},
  year={1965},
  publisher={JSTOR}
}



@ARTICLE{Craig2009,
  author = {M.H. Craig},
  title = {The temporal and spatial distribution of malaria in Africa, with
	emphasis on Southern Africa},
  year = {2009}
}

@BOOK{Crassidis2004,
  title = {Optimal estimation of dynamic systems},
  publisher = {Chapman \& Hall},
  year = {2004},
  author = {J.L. Crassidis and J.L. Junkins}
}

@techreport{Dargatz2007,
  title={A diffusion approximation for an epidemic model},
  author={C. Dargatz},
  year={2007},
  institution={Discussion paper//Sonderforschungsbereich 386 der Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen}
}


@article{DeAngelis1998,
  title={Bayesian projection of the acquired immune deficiency syndrome epidemic},
  author={De Angelis, D. and Gilks, WR and Day, NE},
  journal={Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  volume={47},
  number={4},
  pages={449--498},
  year={1998},
  publisher={Wiley Online Library}
}


@article{Daum2003,
  title={Curse of Dimensionality and Particle Filters},
  author={Daum, F. and Huang, J.},
  year={2003},
  journal = {Working paper}
}

@article{Davies1987,
  title={Tests for Hurst effect},
  author={Davies, R.B. and Harte, DS},
  journal={Biometrika},
  volume={74},
  number={1},
  pages={95--101},
  year={1987},
  publisher={Biometrika Trust}
}

@ARTICLE{Deering2008,
  author = {K.N. Deering and P. Vickerman and S. Moses and B.M. Ramesh and J.F.
	Blanchard and M.C. Boily},
  title = {The impact of out-migrants and out-migration on the HIV/AIDS epidemic:
	a case study from south-west India},
  journal = {AIDS},
  year = {2008},
  volume = {22},
  pages = {S165},
  issn = {0269-9370}
}

@article{Demiris2005,
  title={Bayesian inference for stochastic multitype epidemics in structured populations via random graphs},
  author={N. Demiris and P.D. O'Neill},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={67},
  number={5},
  pages={731--745},
  year={2005},
  publisher={Wiley Online Library}
}

@article{Demiris2012,
  title={On the epidemic of financial crises},
  author={N. Demiris and T. Kypraios and V. Smith},
  year={2012}
}


@article{Ding1993,
  title={A long memory property of stock market returns and a new model},
  author={Z. Ding and C.W.J. Granger and R.F. Engle},
  journal={Journal of empirical finance},
  volume={1},
  number={1},
  pages={83--106},
  year={1993},
  publisher={Elsevier}
}

@article{DelMoral2006,
  title={Sequential monte carlo samplers},
  author={Del Moral,  Pierre and A. Doucet and A. Jasra},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={68},
  number={3},
  pages={411--436},
  year={2006},
  publisher={Wiley Online Library}
}

@article{DerMerwe2001,
  title={The unscented particle filter},
  author={R. Van Der Merwe and A. Doucet and N. De Freitas and E. Wan},
  journal={Advances in Neural Information Processing Systems},
  pages={584--590},
  year={2001},
  publisher={MIT; 1998}
}

@article{Doob1942,
  title={Topics in the theory of Markoff chains},
  author={J.L. Doob},
  journal={Transactions of the American Mathematical Society},
  pages={37--64},
  year={1942},
  publisher={JSTOR}
}


@article{Doob1945,
  title={Markoff chainsÑdenumerable case},
  author={Doob, J.L.},
  journal={Trans. Amer. Math. Soc},
  volume={58},
  number={3},
  pages={455--473},
  year={1945}
}


@BOOK{Doucet2001,
  title = {Sequential Monte Carlo methods in practice},
  publisher = {Springer Verlag},
  year = {2001},
  author = {A. Doucet and N. De Freitas and N. Gordon}
}

@BOOK{Doucet1998,
  title = {On sequential simulation-based methods for Bayesian filtering},
  publisher = {Citeseer},
  year = {1998},
  author = {A. Doucet and S.J. Godsill and C. Andrieu},
}

@article{Doucet2009,
  title={A tutorial on particle filtering and smoothing: fifteen years later},
  author={Doucet, Arnaud and Johansen, Adam M},
  journal={Handbook of Nonlinear Filtering},
  pages={656--704},
  year={2009},
  publisher={Oxford, UK: Oxford University Press}
}

@article{Drummond1996,
  title={Guidelines for authors and peer reviewers of economic submissions to the BMJ},
  author={MF Drummond and TO Jefferson},
  journal={Bmj},
  volume={313},
  number={7052},
  pages={275--283},
  year={1996},
  publisher={BMJ}
}


@article{Duane1987,
  title={Hybrid monte carlo},
  author={S. Duane and A.D. Kennedy and B.J. Pendleton and D. Roweth},
  journal={Physics letters B},
  volume={195},
  number={2},
  pages={216--222},
  year={1987},
  publisher={Elsevier}
}

@ARTICLE{Dukic2009,
  author = {V.M. Dukic and H.F. Lopes and N. Polson},
  title = {Tracking Flu Epidemics Using Google Flu Trends and Particle Learning},
  journal = {Bla},
  year = {2009},
  volume = {Bla}
}



@article{Dureau2013a,
author = {Dureau, Joseph and Kalogeropoulos, Konstantinos and Baguelin, Marc}, 
title = {Capturing the time-varying drivers of an epidemic using stochastic dynamical systems},
year = {2013}, 
doi = {10.1093/biostatistics/kxs052}, 
eprint = {http://0-biostatistics.oxfordjournals.org.library.hct.ac.ae/content/early/2013/01/04/biostatistics.kxs052.full.pdf+html}, 
journal = {Biostatistics} 
}



@article{dureau2013b,
  title={A Bayesian approach to estimate changes in condom use from limited HIV prevalence data},
  author={Dureau, J. and Kalogeropoulos, K. and Vickerman, P. and Pickles, M. and Boily, M.C.},
  journal={arXiv preprint arXiv:1211.5472},
  year={2013}
}

@PHDTHESIS{Dureau2013c,
  author = {Dureau, J.},
  title = {Bayesian Inference for Indirectly Observed Stochastic Processes, Applications to Epidemic Modelling},
  school = {London School of Economics},
  year = {2013}
}



@ARTICLE{Durham2002,
  author = {G.B. Durham and A.R. Gallant},
  title = {Numerical techniques for maximum likelihood estimation of continuous-time
	diffusion processes},
  journal = {Journal of Business and Economic Statistics},
  year = {2002},
  volume = {20},
  pages = {297--338},
  number = {3},
  publisher = {ASA}
}

@ARTICLE{E.Nevalainen2008,
  author = {E. Nevalainen, E.},
  title = {Survey on Recursive Bayesian State Estimation},
  journal = {none},
  year = {2008},
  volume = {20},
  pages = {20}
}

@ARTICLE{Elerian2001,
  author = {O. Elerian and S. Chib and N. Shephard},
  title = {Likelihood inference for discretely observed non-linear diffusions.},
  journal = {Econometrica},
  year = {2001},
  volume = {69},
  pages = {959--993},
  number = {4}
}

@ARTICLE{Ellner2002,
  author = {S.P. Ellner and Y. Seifu and R.H. Smith},
  title = {Fitting population dynamic models to time-series data by gradient
	matching},
  journal = {Ecology},
  year = {2002},
  volume = {83},
  pages = {2256--2270},
  number = {8},
  publisher = {Eco Soc America}
}

@ARTICLE{Engen1998,
  author = {S. Engen and {\O}. Bakke and A. Islam},
  title = {Demographic and environmental stochasticity-concepts and definitions},
  journal = {Biometrics},
  year = {1998},
  volume = {54},
  pages = {840--846},
  number = {3},
  publisher = {JSTOR}
}

@ARTICLE{Eraker2001,
  author = {B. Eraker},
  title = {MCMC analysis of diffusion models with application to finance},
  journal = {Journal of Business and Economic Statistics},
  year = {2001},
  volume = {19},
  pages = {177--191},
  number = {2},
  publisher = {ASA}
}

@book{Ethier1986,
  title={Markov processes: characterization and convergence},
  author={S.N. Ethier and T.G. Kurtz},
  volume={6},
  year={1986},
  publisher={Wiley}
}

@ARTICLE{Fearnhead2005,
  author = {P. Fearnhead},
  title = {Exact Bayesian curve fitting and signal segmentation},
  journal = {Signal Processing, IEEE Transactions on},
  year = {2005},
  volume = {53},
  pages = {2160--2166},
  number = {6},
  issn = {1053-587X},
  publisher = {IEEE}
}

@article{Fenner1988,
  title={Smallpox and its eradication},
  author={F. Fenner  and D.A. Henderson and I. Arita and Z. Jezek and I.D. Ladnyi and others},
  year={1988},
  publisher={Geneva: World Health Organization},
  journal={technical report}
}

@ARTICLE{Ferguson2007,
  author = {N. Ferguson},
  title = {Capturing human behaviour},
  journal = {Nature},
  year = {2007},
  volume = {446},
  pages = {733},
  number = {7137},
  issn = {0028-0836},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Ferguson1999,
  author = {N. Ferguson and R. Anderson and S. Gupta},
  title = {The effect of antibody-dependent enhancement on the transmission
	dynamics and persistence of multiple-strain pathogens},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {1999},
  volume = {96},
  pages = {790},
  number = {2},
  publisher = {National Acad Sciences}
}

@ARTICLE{Ferguson2006,
  author = {N.M. Ferguson and D.A.T Cummings and C. Fraser and J.C. Cajka and
	P.C. Cooley and D.S. Burke},
  title = {Strategies for mitigating an influenza pandemic},
  journal = {Nature},
  year = {2006},
  volume = {442},
  pages = {448--452},
  number = {7101},
  issn = {0028-0836},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Ferguson2001,
  author = {N.M. Ferguson and C.A. Donnelly and R.M. Anderson},
  title = {Transmission intensity and impact of control policies on the foot
	and mouth epidemic in Great Britain},
  journal = {Nature},
  year = {2001},
  volume = {413},
  pages = {542--548},
  number = {6855},
  issn = {0028-0836},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Ferguson2003,
  author = {N.M. Ferguson and A.P. Galvani and R.M. Bush},
  title = {Ecological and immunological determinants of influenza evolution},
  journal = {Nature},
  year = {2003},
  volume = {422},
  pages = {428--433},
  number = {6930},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Fine1982,
  author = {P.E.M. Fine and J.A. Clarkson},
  title = {Measles in England and Wales--I: An analysis of factors underlying
	seasonal patterns},
  journal = {International Journal of Epidemiology},
  year = {1982},
  volume = {11},
  pages = {5},
  number = {1},
  publisher = {IEA}
}

@ARTICLE{Finkenstadt2000,
  author = {B.F. Finkenst{\\"a}dt and B.T. Grenfell},
  title = {Time series modelling of childhood diseases: a dynamical systems
	approach},
  journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  year = {2000},
  volume = {49},
  pages = {187--205},
  number = {2},
  publisher = {John Wiley \& Sons}
}

@article{Finkenstadt2005,
  title={Modelling antigenic drift in weekly flu incidence},
  author={BF Finkenstadt and  A. Morton and DA Rand},
  journal={Statistics in medicine},
  volume={24},
  number={22},
  pages={3447--3461},
  year={2005},
  publisher={Wiley Online Library}
}

@ARTICLE{Fleming1999,
  author = {DM Fleming and M. Zambon and AIM Bartelds and JC De Jong},
  title = {The duration and magnitude of influenza epidemics: a study of surveillance
	data from sentinel general practices in England, Wales and the Netherlands},
  journal = {European journal of epidemiology},
  year = {1999},
  volume = {15},
  pages = {467--473},
  number = {5},
  issn = {0393-2990},
  publisher = {Springer}
}

@ARTICLE{Florens-Zmirou1993,
  author = {D. Florens-Zmirou},
  title = {On estimating the diffusion coefficient from discrete observations},
  journal = {Journal of applied probability},
  year = {1993},
  volume = {30},
  pages = {790--804},
  number = {4},
  publisher = {JSTOR}
}

@ARTICLE{Fraser2009,
  author = {C. Fraser and C.A. Donnelly and S. Cauchemez and W.P. Hanage and
	M.D. Van Kerkhove and T.D. Hollingsworth and J. Griffin and R.F.
	Baggaley and H.E. Jenkins and E.J. Lyons and others},
  title = {Pandemic potential of a strain of influenza A (H1N1): early findings},
  journal = {Science},
  year = {2009},
  volume = {324},
  pages = {1557},
  number = {5934},
  issn = {0036-8075},
  publisher = {American Association for the Advancement of Science}
}


@book{Fuchs2013,
  title={Inference for Diffusion Processes: With Applications in Life Sciences},
  author={Fuchs, Christiane},
  year={2013},
  publisher={Springer}
}


@article{Funk2010,
  title={Modelling the influence of human behaviour on the spread of infectious diseases: a review},
  author={S.  Funk and M.  Salathe and V.A.A. Jansen},
  journal={Journal of The Royal Society Interface},
  volume={7},
  number={50},
  pages={1247--1256},
  year={2010},
  publisher={The Royal Society}
}

@misc{Galassi2006,
  title={GNU scientific library: reference manual},
  author={Galassi, M. and Gough, B.},
  year={2006},
  publisher={Network Theory Limited Bristol, UK}
}

@article{Garcia1983,
  title={A stochastic differential equation model for the height growth of forest stands},
  author={Garcia, O.},
  number = {4},
  volume = {39},
  journal={Biometrics},
  pages={1059--1072},
  year={1983},
  publisher={JSTOR}
}


@ARTICLE{Garnett2006,
  author = {GP Garnett and S. Gregson and KA Stanecki},
  title = {Criteria for detecting and understanding changes in the risk of HIV
	infection at a national level in generalised epidemics},
  journal = {Sexually transmitted infections},
  year = {2006},
  volume = {82},
  pages = {i48},
  number = {suppl 1},
  publisher = {BMJ Publishing Group Ltd}
}

@article{Garnett2002,
  title={An introduction to mathematical models in sexually transmitted disease epidemiology},
  author={Garnett, G.P.},
  journal={Sexually transmitted infections},
  volume={78},
  number={1},
  pages={7--12},
  year={2002},
  publisher={BMJ Publishing Group Ltd}
}

@ARTICLE{Gazut2008,
  author = {S. Gazut and J.M. Martinez and G. Dreyfus and Y. Oussar},
  title = {Towards the optimal design of numerical experiments},
  journal = {IEEE Transactions on Neural Networks},
  year = {2008},
  volume = {19},
  pages = {874},
  number = {5},
  publisher = {IEEE INSTITUTE OF ELECTRICAL AND ELECTRONICS},
}

@ARTICLE{Gelman1992,
  author = {A. Gelman and D.B. Rubin},
  title = {Inference from iterative simulation using multiple sequences},
  journal = {Statistical science},
  year = {1992},
  volume = {7},
  pages = {457--472},
  number = {4},
  issn = {0883-4237},
  publisher = {JSTOR}
}

@article{Gelman2012,
  title={Philosophy and the practice of Bayesian statistics},
  author={A. Gelman and C.R. Shalizi},
  journal={British Journal of Mathematical and Statistical Psychology},
  year={2012},
  publisher={Wiley Online Library}
}

@ARTICLE{Genon-Catalot1992,
  author = {V. Genon-Catalot and C. Laredo and D. Picard},
  title = {Non-parametric estimation of the diffusion coefficient by wavelets
	methods},
  journal = {Scandinavian Journal of Statistics},
  year = {1992},
  volume = {19},
  pages = {317--335},
  number = {4},
  publisher = {JSTOR}
}

@article {Geyer1992,
  title={Practical {M}arkov {C}hain {M}onte {C}arlo},
  author={Geyer, C.J.},
  journal={Statistical {S}cience},
  volume={7},
  number={4},
  pages={473--483},
  year={1992},
  publisher={Institute of Mathematical Statistics}
}

@ARTICLE{Ghani2009,
  author = {Ghani, A. and Baguelin, M. and Griffin, J. and Flasche, S. and van
	Hoek, A.J. and Cauchemez, S. and Donnelly, C. and Robertson, C. and
	White, M. and Truscott, J. and others},
  title = {The early transmission dynamics of H1N1pdm influenza in the United
	Kingdom},
  journal = {PLoS Currents},
  year = {2009},
  volume = {2},
  publisher = {Public Library of Science}
}

@ARTICLE{Gillespie1977,
  author = {D.T. Gillespie},
  title = {Exact stochastic simulation of coupled chemical reactions},
  journal = {The journal of physical chemistry},
  year = {1977},
  volume = {81},
  pages = {2340--2361},
  number = {25},
  publisher = {ACS Publications}
}



@ARTICLE{Ginsberg2008,
  author = {J. Ginsberg and M.H. Mohebbi and R.S. Patel and L. Brammer and M.S.
	Smolinski and L. Brilliant},
  title = {Detecting influenza epidemics using search engine query data},
  journal = {Nature},
  year = {2008},
  volume = {457},
  pages = {1012--1014},
  number = {7232},
  issn = {0028-0836},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Giordani2010,
  author = {P. Giordani and R. Kohn},
  title = {Adaptive independent Metropolis--Hastings by fast estimation of mixtures
	of normals},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2010},
  volume = {19},
  pages = {243--259},
  number = {2},
  issn = {1061-8600},
  publisher = {ASA}
}



@article{Girolami2011,
  title={Riemann manifold langevin and hamiltonian monte carlo methods},
  author={Girolami, Mark and Calderhead, Ben},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={73},
  number={2},
  pages={123--214},
  year={2011},
  publisher={Wiley Online Library}
}

@ARTICLE{Godsill2004,
  author = {S.J. Godsill and A. Doucet and M. West},
  title = {Monte Carlo smoothing for nonlinear time series},
  journal = {Journal of the American Statistical Association},
  year = {2004},
  volume = {99},
  pages = {156--168},
  number = {465},
  publisher = {ASA}
}

@ARTICLE{Golightly2008,
  author = {A. Golightly and DJ Wilkinson},
  title = {Bayesian inference for nonlinear multivariate diffusion models observed
	with error},
  journal = {Computational Statistics \& Data Analysis},
  year = {2008},
  volume = {52},
  pages = {1674--1693},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{Golightly2006,
  author = {A. Golightly and D.J. Wilkinson.},
  title = {Bayesian sequential inference for nonlinear multivariate diffusions},
  journal = {Statistics and Computing},
  year = {2006},
  volume = {16},
  pages = {323--338},
  number = {4},
  publisher = {Springer}
}

@CONFERENCE{Gordon1993,
  author = {N.J. Gordon and D.J. Salmond and A.F.M. Smith},
  title = {Novel approach to nonlinear/non-Gaussian Bayesian state estimation},
  booktitle = {IEE Proceedings},
  year = {1993},
  volume = {140},
  number = {2},
  pages = {107--113}
}

@article{Goubar2008,
  title={Estimates of human immunodeficiency virus prevalence and proportion diagnosed based on Bayesian multiparameter synthesis of surveillance data},
  author={Goubar, A. and Ades, AE. and De Angelis, D. and McGarrigle, CA and Mercer, CH and Tookey, PA and Fenton, K. and Gill, ON},
  journal={Journal of the Royal Statistical Society: Series A (Statistics in Society)},
  volume={171},
  number={3},
  pages={541--580},
  year={2008},
  publisher={Wiley Online Library}
}


@article{Granich2009,
  title={Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model},
  author={R.M.  Granich and  C.F.  Gilks and C.  Dye and K.M.  De Cock and B.G. Williams},
  journal={The Lancet},
  volume={373},
  number={9657},
  pages={48--57},
  year={2009},
  publisher={Elsevier}
}

@article{Grenfell2001,
  title={Travelling waves and spatial hierarchies in measles epidemics},
  author={B.  Grenfell and O.  Bjornstad and J. Kappey},
  journal={Nature},
  volume={414},
  number={6865},
  pages={716--723},
  year={2001}
}

 @article{Griffin2011,
  title={Joint estimation of the basic reproduction number and generation time parameters for infectious disease outbreaks},
  author={J.T. Griffin  and  T. Garske  and A.C. Ghani  and P.S. Clarke},
  journal={Biostatistics},
  volume={12},
  number={2},
  pages={303},
  year={2011},
  publisher={Biometrika Trust},
}


@ARTICLE{Griffiths2005,
  author = {J.D. Griffiths and Z.F. Lawson and J.E. Williams},
  title = {Modelling treatment effects in the HIV/AIDS epidemic},
  journal = {Journal of the Operational Research Society},
  year = {2005},
  volume = {57},
  pages = {1413--1424},
  number = {12},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Grosskurth1995,
  author = {H. Grosskurth and J. Todd and E. Mwijarubi and P. Mayaud and A. Nicoll
	and others},
  title = {Impact of improved treatment of sexually transmitted diseases on
	HIV infection in rural Tanzania: randomised controlled trial},
  journal = {The Lancet},
  year = {1995},
  volume = {346},
  pages = {530--536},
  number = {8974},
  publisher = {Elsevier}
}

@ARTICLE{Gupta1994,
  author = {S. Gupta and K. Trenholme and R.M. Anderson and K.P. Day},
  title = {Antigenic diversity and the transmission dynamics of Plasmodium falciparum},
  journal = {Science},
  year = {1994},
  volume = {263},
  pages = {961},
  number = {5149},
  publisher = {AAAS}
}

@article{Gupta1998,
  title={Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents},
  author={S.  Gupta and N.  Ferguson and R. Anderson},
  journal={Science},
  volume={280},
  number={5365},
  pages={912--915},
  year={1998},
  publisher={American Association for the Advancement of Science}
}

@article{Guy2013,
  title={Approximation of epidemic models by diffusion processes and their statistical inference},
  author={Guy, Romain and Lar{\'e}do, Catherine and Vergu, Elisabeta},
  journal={arXiv preprint arXiv:1305.3492},
  year={2013}
}


@article{Hanck2008,
  title={Assessment of self-reported sexual behavior and condom use among female sex workers in India using a polling box approach: a preliminary report},
  author={Hanck, S.E. and Blankenship, K.M. and Irwin, K.S. and West, B.S. and Kershaw, T.},
  journal={Sexually transmitted diseases},
  volume={35},
  number={5},
  pages={489},
  year={2008}
}

@ARTICLE{Hastings1970,
  author = {Hastings, W.K.},
  title = {Monte Carlo sampling methods using Markov chains and their applications},
  journal = {Biometrika},
  year = {1970},
  volume = {57},
  pages = {97},
  number = {1},
  publisher = {Biometrika Trust}
}

@article{Hauck2010,
  title={Nanotechnology diagnostics for infectious diseases prevalent in developing countries},
  author={T.S. Hauck and S.  Giri and Y. Gao and W.C.W. Chan},
  journal={Advanced drug delivery reviews},
  volume={62},
  number={4},
  pages={438--448},
  year={2010},
  publisher={Elsevier}
}

@article{Hay2001,
  title={The evolution of human influenza viruses},
  author={A.J. Hay and V. Gregory and A.R. Douglas and Y.P. Lin},
  journal={Philos Trans R Soc Lond B Biol Sci},
  volume={356},
  number={1416},
  pages={1861--70},
  year={2001}
}

@article{He2010,
  title={Plug-and-play inference for disease dynamics: measles in large and small populations as a case study},
  author={D. He and E.L. Ionides and A.A. King},
  journal={Journal of the Royal Society Interface},
  volume={7},
  number={43},
  pages={271--283},
  year={2010},
  publisher={The Royal Society}
}


@ARTICLE{He2011,
  author = {D.H. He and J. Dushoff and T. Day and J. Ma. and D.J.D. Earn},
  title = {Mechanistic modelling of the three waves of the 1918 influenza pandemic},
  journal = {Theoretical Ecology},
  year = {2011},
  volume = {1},
  pages = {1--6},
  publisher = {Springer}
}

@ARTICLE{Heffernan2005,
  author = {JM Heffernan and RJ Smith and LM Wahl},
  title = {Perspectives on the basic reproductive ratio},
  journal = {Journal of the Royal Society Interface},
  year = {2005},
  volume = {2},
  pages = {281},
  number = {4},
  issn = {1742-5689},
  publisher = {The Royal Society}
}

@ARTICLE{Heidelberger1983,
  author = {P. Heidelberger and P.D. Welch},
  title = {Simulation run length control in the presence of an initial transient},
  journal = {Operations Research},
  year = {1983},
  volume = {31},
  pages = {1109--1144},
  number = {6},
  issn = {0030-364X},
  publisher = {JSTOR}
}

@article{Heston1993,
  title={A closed-form solution for options with stochastic volatility with applications to bond and currency options},
  author={S. Heston},
  journal={Review of financial studies},
  volume={6},
  number={2},
  pages={327--343},
  year={1993},
  publisher={Soc Financial Studies}
}

@BOOK{Hethcote1992,
  title = {Modeling HIV transmission and AIDS in the United States},
  publisher = {Springer-Verlag},
  year = {1992},
  author = {H.W. Hethcote and J.W. Van Ark}
}

@ARTICLE{Hethcote1991a,
  author = {J.W. Hethcote and W. Herbert},
  title = {A simulation model of AIDS in San Francisco: II. Simulations, therapy,
	and sensitivity analysis},
  journal = {Mathematical biosciences},
  year = {1991},
  volume = {106},
  pages = {223--247},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{Hethcote1991,
  author = {J.W. Hethcote and W. Herbert and others},
  title = {A simulation model of AIDS in San Francisco: I. Model formulation
	and parameter estimation},
  journal = {Mathematical biosciences},
  year = {1991},
  volume = {106},
  pages = {203--222},
  number = {2},
  publisher = {Elsevier}
}

@article{Hilleman2002,
  title={Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control},
  author={M.R. Hilleman},
  journal={Vaccine},
  volume={20},
  number={25},
  pages={3068--3087},
  year={2002},
  publisher={Elsevier}
}

@ARTICLE{Hoffmann1999,
  author = {M. Hoffmann},
  title = {Adaptive estimation in diffusion processes},
  journal = {Stochastic Processes and their Applications},
  year = {1999},
  volume = {79},
  pages = {135--163},
  number = {1},
  publisher = {Elsevier}
}

@article{Hotez2007,
  title={Control of neglected tropical diseases},
  author={P.J. Hotez and D.H. Molyneux and A. Fenwick and J. Kumaresan and S.E. Sachs and J.D. Sachs and L. Savioli},
  journal={New England Journal of Medicine},
  volume={357},
  number={10},
  pages={1018--1027},
  year={2007},
  publisher={Mass Medical Soc}
}

@ARTICLE{Hsieh2007,
  author = {Y.H. Hsieh and C.C. King and C.W.S Chen and M.S. Ho and S.B. Hsu
	and Y.C. Wu},
  title = {Impact of quarantine on the 2003 SARS outbreak: A retrospective modeling
	study},
  journal = {Journal of theoretical biology},
  year = {2007},
  volume = {244},
  pages = {729--736},
  number = {4},
  publisher = {Elsevier},
}

@article{Ince2012,
  title={The case for open computer programs},
  author={Ince, D.C. and Hatton, L. and Graham-Cumming, J.},
  journal={Nature},
  volume={482},
  number={7386},
  pages={485--488},
  year={2012},
  publisher={Nature Publishing Group}
}

@ARTICLE{Ionides2006,
  author = {E.L. Ionides and C. Breto and A. King},
  title = {Inference for nonlinear dynamical systems},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2006},
  volume = {103},
  pages = {18438},
  number = {49},
  publisher = {National Acad Sciences},
}

@ARTICLE{Ionides2008,
  author = {E.L. Ionides and C. Bret{\^U} and A.A. King},
  title = {Modeling disease dynamics: Cholera as a case study},
  journal = {Statistical advances in the biomedical sciences: clinical trials,
	epidemiology, survival analysis, and bioinformatics},
  year = {2008},
  volume = {10},
  pages = {123},
  publisher = {Wiley-Blackwell}
}

@article{Ionides2011,
  title={Iterated filtering},
  author={E.L. Ionides and A.  Bhadra and Y. Atchade and A. King},
  journal={The Annals of Statistics},
  volume={39},
  number={3},
  pages={1776--1802},
  year={2011},
  publisher={Institute of Mathematical Statistics}
}

@ARTICLE{Jacod2000,
  author = {J. Jacod},
  title = {Non-parametric kernel estimation of the coefficient of a diffusion},
  journal = {Scandinavian journal of statistics},
  year = {2000},
  volume = {27},
  pages = {83--96},
  number = {1},
  publisher = {John Wiley \& Sons}
}

@book{Jazwinski1970,
  title={Stochastic processes and filtering theory},
  author={A.H. Jazwinski},
  volume={63},
  year={1970},
  publisher={Academic press}
}

@TECHREPORT{Jones2007,
  author = {H.J. Jones},
  title = {Notes on r0},
  institution = {Tech. report, Department of Anthropological Sciences, Stanford University},
  year = {2007}
}

@article{Jones2008,
  title={Global trends in emerging infectious diseases},
  author={K.E.  Jones and N.G. Patel and M.A. Levy and A. Storeygard and D. Balk and J.L.  Gittleman and P. Daszak},
  journal={Nature},
  volume={451},
  number={7181},
  pages={990--993},
  year={2008},
  publisher={Nature Publishing Group}
}

@ARTICLE{Kalogeropoulos2007,
  author = {K. Kalogeropoulos},
  title = {Likelihood-based inference for a class of multivariate diffusions
	with unobserved paths},
  journal = {Journal of Statistical Planning and Inference},
  year = {2007},
  volume = {137},
  pages = {3092 - 3102},
  number = {10},
  note = {Special Issue: Bayesian Inference for Stochastic Processes},
  doi = {DOI: 10.1016/j.jspi.2006.05.017},
  issn = {0378-3758},
  keywords = {Data augmentation},
  url = {http://www.sciencedirect.com/science/article/B6V0M-4N8BMX5-7/2/abc45bd59c7672b92b735c5731141ba2}
}

@PHDTHESIS{Kalogeropoulos2006,
  author = {K.P. Kalogeropoulos},
  title = {ATHENS UNIVERSITY OF ECONOMICS AND BUSINESS},
  school = {Athens University of Economics and Business},
  year = {2006},
}

@article{Kalogeropoulos2011,
  title={Likelihood-based inference for correlated diffusions},
  author={K. Kalogeropoulos and P. Dellaportas and G.O. Roberts},
  journal={Canadian journal of statistics},
  volume={39},
  number={1},
  pages={52--72},
  year={2011},
  publisher={Wiley Online Library}
}

@ARTICLE{Kamo2002,
  author = {M. Kamo and A. Sasaki},
  title = {The effect of cross-immunity and seasonal forcing in a multi-strain
	epidemic model},
  journal = {Physica D: Nonlinear Phenomena},
  year = {2002},
  volume = {165},
  pages = {228--241},
  number = {3-4},
  publisher = {Elsevier}
}

@BOOK{Kantz2004,
  title = {Nonlinear time series analysis},
  publisher = {Cambridge Univ Pr},
  year = {2004},
  author = {H. Kantz and T. Schreiber}
}

@ARTICLE{Kass1995,
  author = {R.E. Kass and A.E. Raftery},
  title = {Bayes factors},
  journal = {Journal of the American Statistical Association},
  year = {1995},
  volume = {90},
  pages = {773--795},
  number = {430},
  issn = {0162-1459},
  publisher = {JSTOR}
}

@ARTICLE{Katriel2010,
  author = {G. Katriel and L. Stone},
  title = {Pandemic Dynamics and the Breakdown of Herd Immunity},
  journal = {PloS one},
  year = {2010},
  volume = {5},
  pages = {e9565},
  number = {3},
  publisher = {Public Library of Science}
}

@article{Keeling2001,
  title={Seasonally forced disease dynamics explored as switching between attractors},
  author={ M.J. Keeling and P.  Rohani and B.T. Grenfell},
  journal={Physica D: Nonlinear Phenomena},
  volume={148},
  number={3},
  pages={317--335},
  year={2001},
  publisher={Elsevier}
}


@ARTICLE{Kendall2005,
  author = {B.E. Kendall and S.P. Ellner and E. McCauley and S.N. Wood and C.J.
	Briggs and W.W. Murdoch and P. Turchin},
  title = {Population cycles in the pine looper moth: Dynamical tests of mechanistic
	hypotheses},
  journal = {Ecological Monographs},
  year = {2005},
  volume = {75},
  pages = {259--276},
  number = {2},
  publisher = {Eco Soc America}
}

@ARTICLE{Kent1978,
  author = {J. Kent},
  title = {Time-reversible diffusions},
  journal = {Advances in Applied Probability},
  year = {1978},
  pages = {819--835},
  publisher = {JSTOR}
}

@ARTICLE{Kerkhove2010,
  author = {M.D. Van Kerkhove and T. Asikainen and N.G. Becker and S. Bjorge
	and J.C. Desenclos and T. Dos Santos and C. Fraser and G.M. Leung
	and M. Lipsitch and Jr I.M. Longini and others},
  title = {Studies needed to address public health challenges of the 2009 H1N1
	influenza pandemic: insights from modeling},
  journal = {PLoS Medicine},
  year = {2010},
  volume = {7},
  number = {6},
  publisher = {Public Library of Science}
}

@article{Kew2012,
  title={Reaching the last one per cent: progress and challenges in global polio eradication},
  author={O. Kew},
  journal={Current Opinion in Virology},
  year={2012},
  publisher={Elsevier}
}

@ARTICLE{Kiefer1959,
  author = {J. Kiefer},
  title = {Optimum experimental designs},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1959},
  volume = {21},
  pages = {272--319},
  number = {2},
  publisher = {Royal Statistical Society},
}

@ARTICLE{Kim1998,
  author = {S. Kim and N. Shepherd and S. Chib},
  title = {Stochastic volatility: likelihood inference and comparison with ARCH
	models},
  journal = {Review of Economic studies},
  year = {1998},
  volume = {65},
  pages = {361--393},
  number = {3},
  issn = {1467-937X},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{King2008,
  author = {A.A. King and E.L. Ionides and M. Pascual and M.J. Bouma},
  title = {Inapparent infections and cholera dynamics},
  journal = {Nature},
  year = {2008},
  volume = {454},
  pages = {877--880},
  number = {7206},
  publisher = {Nature Publishing Group},
}

@ARTICLE{Kitagawa1996,
  author = {G. Kitagawa},
  title = {Monte Carlo filter and smoother for non-Gaussian nonlinear state
	space models},
  journal = {Journal of computational and graphical statistics},
  year = {1996},
  volume = {5},
  pages = {1--25},
  number = {1},
  publisher = {JSTOR}
}

@CONFERENCE{Klaas2006,
  author = {M. Klaas and M. Briers and N. De Freitas and A. Doucet and S. Maskell
	and D. Lang},
  title = {Fast particle smoothing: if I had a million particles},
  booktitle = {Proceedings of the 23rd international conference on Machine learning},
  year = {2006},
  pages = {488},
  organization = {ACM}
}

@BOOK{Kloeden1999,
  title = {Numerical Solution to Stochastic Differential Equations.},
  publisher = {Springer},
  year = {1999},
  author = {P.E. Kloeden and E. Platen}
}

@ARTICLE{Knorr-Held1999,
  author = {L. Knorr-Held},
  title = {Conditional prior proposals in dynamic models},
  journal = {Scandinavian Journal of Statistics},
  year = {1999},
  volume = {26},
  pages = {129--144},
  number = {1},
  issn = {1467-9469},
  publisher = {Wiley Online Library}
}

@ARTICLE{Koelle2006,
  author = {K. Koelle and s. Cobey and B. Grenfell and M. Pascual},
  title = {Epochal evolution shapes the phylodynamics of interpandemic influenza
	A (H3N2) in humans},
  journal = {Science},
  year = {2006},
  volume = {314},
  pages = {1898},
  number = {5807},
  publisher = {AAAS}
}

@ARTICLE{Koelle2004,
  author = {K. Koelle and M. Pascual},
  title = {Disentangling extrinsic from intrinsic factors in disease dynamics:
	a nonlinear time series approach with an application to cholera},
  journal = {Am Nat},
  year = {2004},
  volume = {163},
  pages = {901--913},
  publisher = {UChicago Press}
}

@ARTICLE{Koelle2006a,
  author = {K. Koelle and M. Pascual and M. Yunus},
  title = {Serotype cycles in cholera dynamics},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2006},
  volume = {273},
  pages = {2879},
  number = {1603},
  publisher = {The Royal Society}
}

@ARTICLE{Koelle2005,
  author = {K. Koelle and X. Rod{\'o} and M. Pascual and M. Yunus and G. Mostafa},
  title = {Refractory periods and climate forcing in cholera dynamics},
  journal = {Nature},
  year = {2005},
  volume = {436},
  pages = {696--700},
  number = {7051},
  publisher = {Nature Publishing Group}
}

@ARTICLE{Koopman2002,
  author = {J.S. Koopman},
  title = {Modeling infection transmission-the pursuit of complexities that
	matter},
  journal = {Epidemiology},
  year = {2002},
  volume = {13},
  pages = {622},
  number = {6}
}

@BOOK{Kurtz1981,
  title = {Approximation of population processes},
  publisher = {Society for Industrial Mathematics},
  year = {1981},
  author = {T.G. Kurtz},
  volume = {1},
  number = {36-40},
  isbn = {089871169X}
}

@CONFERENCE{Kuck2006,
  author = {H. K{\"u}ck and N. de Freitas and A. Doucet},
  title = {SMC samplers for Bayesian optimal nonlinear design},
  booktitle = {Nonlinear Statistical Signal Processing Workshop (NSSPW)},
  year = {2006},
  organization = {Citeseer},
}

@article{Kumar2011,
  title={Impact of targeted interventions on heterosexual transmission of HIV in India},
  author={Kumar, R. and Mehendale, S.M. and Panda, S. and Venkatesh, S. and Lakshmi, PVM and Kaur, M. and Prinja, S. and Singh, T. and Virdi, N.K. and Bahuguna, P. and others},
  journal={BMC public health},
  volume={11},
  number={1},
  pages={549},
  year={2011},
  publisher={BioMed Central Ltd}
}


@ARTICLE{Laneri2010,
  author = {K. Laneri and A. Bhadra and E.L. Ionides M. and Bouma R.C. and Dhiman
	R.S. and Yadav M. and Pascual},
  title = {Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest
	India},
  journal = {PLoS Comput Biol},
  year = {2010},
  volume = {6},
  pages = {e1000898},
  number = {9},
  publisher = {Public Library of Science}
}

@ARTICLE{Lavine1999,
  author = {M. Lavine and M.J. Schervish},
  title = {Bayes factors: What they are and what they are not},
  journal = {The American Statistician},
  year = {1999},
  volume = {53},
  pages = {23},
  number = {2},
  publisher = {American Statistical Association}
}

@article{Lei2004,
  title={Features and partial derivatives of Bertalanffy-Richards growth model in forestry},
  author={Lei, YC and Zhang, SY},
  journal={Nonlinear Analysis: Modelling and Control},
  volume={9},
  number={1},
  pages={65--73},
  year={2004}
}

@article{Lessne1988,
  title={Growth curve analysis in marketing: Method and application},
  author={Lessne, G.J. and Hanumara, R.C.},
  number = {4},
  volume = {25},
  journal={Journal of Marketing Research},
  pages={391--396},
  year={1988},
  publisher={JSTOR}
}

@inproceedings{Ionides2012,
  title={Efficient Iterated Filtering},
  author={Ionides, Edward and Frydendall, Jan and Madsen, Henrik and others},
  booktitle={System Identification},
  volume={16},
  number={1},
  pages={1785--1790},
  year={2012}
}

@article{Lindstrom2013,
  title={Tuned Iterated Filtering},
  author={Lindstr{\"o}m, Erik},
  journal={Statistics \& Probability Letters},
  year={2013},
  publisher={Elsevier}
}


@article{Lipsitch2009,
  title={Influenza seasonality: lifting the fog},
  author={M. Lipsitch and C. Viboud},
  journal={Proceedings of the National Academy of Sciences},
  volume={106},
  number={10},
  pages={3645--3646},
  year={2009},
  publisher={National Acad Sciences}
}

@article{Lobato1998,
  title={Real and spurious long-memory properties of stock-market data},
  author={I.N. Lobato and N.E. Savin},
  journal={Journal of Business \& Economic Statistics},
  volume={16},
  number={3},
  pages={261--268},
  year={1998},
  publisher={Taylor \& Francis}
}

@ARTICLE{Lofgren2007,
  author = {E. Lofgren and NH. Fefferman and YN. Naumov and J. Gorski and EN.
	Naumova},
  title = {Influenza seasonality: underlying causes and modeling theories},
  journal = {Journal of virology},
  year = {2007},
  volume = {81},
  pages = {5429},
  number = {11},
  issn = {0022-538X},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{Longini2004,
  author = {Jr I.M. Longini and M.E. Halloran and A. Nizam and Y. Yang},
  title = {Containing pandemic influenza with antiviral agents},
  journal = {American Journal of Epidemiology},
  year = {2004},
  volume = {159},
  pages = {623},
  number = {7},
  publisher = {Oxford Univ Press}
}

@ARTICLE{Louis1982,
  author = {T.A. Louis},
  title = {Finding the observed information matrix when using the EM algorithm},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1982},
  volume = {44},
  pages = {226--233},
  number = {2},
  issn = {0035-9246},
  publisher = {JSTOR}
}

@ARTICLE{Lowndes2010,
  author = {CM Lowndes and M. Alary and S. Verma and E. Demers and J. Bradley
	and AA. Jayachandran and BM. Ramesh and S. Moses and R. Adhikary
	and MK. Mainkar},
  title = {Assessment of intervention outcome in the absence of baseline data:
	"reconstruction" of condom use time trends using retrospective analysis
	of survey data},
  journal = {Sexually transmitted infections},
  year = {2010},
  volume = {86},
  pages = {i49},
  number = {Suppl 1},
  publisher = {BMJ Publishing Group Ltd}
}


@misc{Lunn2004,
    author={Lunn, D.},
    citeulike-article-id = {3042849},
    citeulike-linkout-0 = {http://www.winbugs-development.org.uk/wbdiff.html},
    institution = {Dept. Epidemiology and Public Health, Imperial College London},
    key = {WBDiff},
    keywords = {software, wbdiff, winbugs},
    posted-at = {2008-07-25 15:58:21},
    priority = {2},
    title = {{WinBUGS Differential Interface - Worked Examples}},
    url = {http://www.winbugs-development.org.uk/wbdiff.html},
    year = {2004}
}

@article{Lunn2000,
  title={WinBUGS-a Bayesian modelling framework: concepts, structure, and extensibility},
  author={Lunn, D. J and Thomas, A. and Best, N. and Spiegelhalter, D.},
  journal={Statistics and computing},
  volume={10},
  number={4},
  pages={325--337},
  year={2000},
  publisher={Springer}
}

@BOOK{Massart2007,
  title = {Concentration inequalities and model selection: Ecole d'Et{\'e} de
	Probabilit{\'e}s de Saint-Flour XXXIII-2003},
  publisher = {Springer},
  year = {2007},
  author = {P. Massart and J. Picard},
}

@ARTICLE{Mathews2007,
  author = {J.D. Mathews and C.T. McCaw and J. McVernon and E.S. McBryde and
	J.M. McCaw},
  title = {A biological model for influenza transmission: pandemic planning
	implications of asymptomatic infection and immunity},
  journal = {PLoS One},
  year = {2007},
  volume = {2},
  pages = {1220},
  number = {11},
  issn = {1932-6203},
  publisher = {PLoS}
}

@ARTICLE{McCaw2009,
  author = {JM McCaw and J McVernon and ES McBryde and JD Mathews},
  title = {Influenza: accounting for prior immunity},
  journal = {Science},
  year = {2009},
  volume = {325},
  pages = {1071},
  number = {5944},
  publisher = {AAAS}
}

@article{McMichael2006,
  title={Climate change and human health: present and future risks},
  author={A.J. McMichael and R.E.  Woodruff and S. Hales},
  journal={The Lancet},
  volume={367},
  number={9513},
  pages={859--869},
  year={2006},
  publisher={Elsevier}
}

@article{Meehl1987,
  title={The annual cycle and interannual variability in the tropical Pacific and Indian Ocean regions},
  author={G.A. Meehl},
  journal={Monthly Weather Review},
  volume={115},
  number={1},
  pages={27--50},
  year={1987}
}

@article{Melegaro2011,
  title={What types of contacts are important for the spread of infections? Using contact survey data to explore European mixing patterns},
  author={ A.  Melegaro and M.  Jit and N. Gay and E. Zagheni and W.J. Edmunds},
  journal={Epidemics},
  volume={3},
  number={3},
  pages={143--151},
  year={2011},
  publisher={Elsevier}
}

@ARTICLE{Meng1998,
  author = {X.L. Meng and D. van Dyk},
  title = {Fast EM-type implementations for mixed effects models},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {1998},
  volume = {60},
  pages = {559--578},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Meng1997,
  author = {X.L. Meng and D. van Dyk},
  title = {The EM algorithm: an old folk-song sung to a fast new tune},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {1997},
  volume = {59},
  pages = {511--567},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@article{Metropolis1953,
  title={Equation of state calculations by fast computing machines},
  author={N. Metropolis and A.W. Rosenbluth and M.N. Rosenbluth and, A.H. Telle and E. Teller},
  journal={The journal of chemical physics},
  volume={21},
  pages={1087},
  year={1953}
}

@ARTICLE{Meyer2000,
  author = {R. Meyer and J. Yu},
  title = {BUGS for a Bayesian analysis of stochastic volatility models},
  journal = {Econometrics Journal},
  year = {2000},
  volume = {3},
  pages = {198--215},
  number = {2},
  issn = {1368-423X},
  publisher = {Wiley Online Library}
}

@ARTICLE{Miller2010,
  author = {E. Miller and K. Hoschler and P. Hardelid and E. Stanford and N.
	Andrews and M. Zambon},
  title = {Incidence of 2009 pandemic influenza A H1N1 infection in England:
	a cross-sectional serological study},
  journal = {The Lancet},
  year = {2010},
  volume = {375},
  pages = {1100--1108},
  number = {9720},
  publisher = {Elsevier}
}

@book{Moral2004,
  title={Feynman-Kac formulae: genealogical and interacting particle systems with applications},
  author={Del Moral, P.},
  year={2004},
  publisher={Springer}
}

@ARTICLE{Moral2006,
  author = {P. Del Moral and A. Doucet and A. Jasra},
  title = {Sequential monte carlo samplers},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2006},
  volume = {68},
  pages = {411--436},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Moral2000,
  author = {P. Del Moral and L. Miclo},
  title = {Branching and interacting particle systems approximations of Feynman-Kac
	formulae with applications to non-linear filtering},
  journal = {Seminaire de Probabilites XXXIV},
  year = {2000},
  volume = {100},
  pages = {1--145},
  publisher = {Springer}
}

@ARTICLE{Morel2005,
  author = {C.M. Morel and J.A. Lauer and D.B. Evans},
  title = {Cost effectiveness analysis of strategies to combat malaria in developing
	countries},
  journal = {British Medical Journal},
  year = {2005},
  volume = {331},
  pages = {1299},
  number = {7528},
  publisher = {Br Med Assoc},
}

@ARTICLE{Morel2008,
  author = {C.M. Morel and N.D. Thang and N.X. Xa and L.X. Hung and L.K. Thuan
	and P. Van Ky and A. Erhart and A.J. Mills and U. D'Alessandro},
  title = {The economic burden of malaria on the household in south-central
	Vietnam},
  journal = {Malaria Journal},
  year = {2008},
  volume = {7},
  pages = {166},
  number = {1},
  publisher = {BioMed Central Ltd},
}

@article{Morris1993,
  title={Epidemiology and social networks: Modeling structured diffusion},
  author={M. Morris},
  journal={Sociological Methods \& Research},
  volume={22},
  number={1},
  pages={99--126},
  year={1993},
  publisher={Sage Publications}
}

@ARTICLE{Morton2005,
  author = {A. Morton and B.F. Finkenst{\\"a}dt},
  title = {Discrete time modelling of disease incidence time series by using
	Markov chain Monte Carlo methods},
  journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  year = {2005},
  volume = {54},
  pages = {575--594},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@article{Nagashima1968,
  title={Comparative pharmacokinetics of coumarin anticoagulants IV. Application of a three-compartmental model to the analysis of the dose-dependent kinetics of bishydroxycoumarin elimination},
  author={R. Nagashima and G. Levy and RA O'Reilly},
  journal={Journal of pharmaceutical sciences},
  volume={57},
  number={11},
  pages={1888--1895},
  year={1968},
  publisher={Wiley Online Library}
}

@article{Neal2010,
  title={MCMC using Hamiltonian dynamics},
  author={R.M. Neal},
  journal={Handbook of Markov Chain Monte Carlo},
  volume={54},
  pages={113--162},
  year={2010}
}

@ARTICLE{Newman2009,
  author = {K.B. Newman and C. Fernandez and L. Thomas and S.T. Buckland},
  title = {Monte Carlo Inference for State--Space Models of Wild Animal Populations},
  journal = {Biometrics},
  year = {2009},
  volume = {65},
  pages = {572--583},
  number = {2},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Nishiura2007,
  author = {H. Nishiura},
  title = {Time variations in the transmissibility of pandemic influenza in
	Prussia, Germany, from 1918 -- 19},
  journal = {Theoretical Biology and Medical Modelling},
  year = {2007},
  volume = {4},
  pages = {20},
  number = {1},
  issn = {1742-4682},
  publisher = {BioMed Central Ltd}
}

@ARTICLE{O'neill2009,
  author = {P.D. O'neill},
  title = {Bayesian inference for stochastic multitype epidemics in structured
	populations using sample data},
  journal = {Biostatistics},
  year = {2009},
  volume = {20},
  pages = {20},
  issn = {1465-4644},
  publisher = {Biometrika Trust}
}

@ARTICLE{O'Neill2003,
  author = {P.D. O'Neill},
  title = {Perfect simulation for Reed-Frost epidemic models},
  journal = {Statistics and Computing},
  year = {2003},
  volume = {13},
  pages = {37--44},
  number = {1},
  issn = {0960-3174},
  publisher = {Springer}
}

@ARTICLE{O'Neill2002,
  author = {P.D. O'Neill},
  title = {A tutorial introduction to Bayesian inference for stochastic epidemic
	models using Markov chain Monte Carlo methods},
  journal = {Mathematical Biosciences},
  year = {2002},
  volume = {180},
  pages = {103--114},
  number = {1-2},
  issn = {0025-5564},
  publisher = {Elsevier}
}

@ARTICLE{O'Neill2000,
  author = {P.D. O'Neill and D.J. Balding and N.G. Becker and M. Eerola and D.
	Mollison},
  title = {Analyses of infectious disease data from household outbreaks by Markov
	chain Monte Carlo methods},
  journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  year = {2000},
  volume = {49},
  pages = {517--542},
  number = {4},
  issn = {1467-9876},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{O'Neill2001,
  author = {P.D. O'Neill and N.G. Becker},
  title = {Inference for an epidemic when susceptibility varies},
  journal = {Biostatistics},
  year = {2001},
  volume = {2},
  pages = {99},
  number = {1},
  issn = {1465-4644},
  publisher = {Biometrika Trust}
}

@ARTICLE{O'Neill2005,
  author = {P.D. O'Neill and P.J. Marks},
  title = {Bayesian model choice and infection route modelling in an outbreak
	of Norovirus},
  journal = {Statistics in medicine},
  year = {2005},
  volume = {24},
  pages = {2011--2024},
  number = {13},
  issn = {1097-0258},
  publisher = {John Wiley \& Sons}
}


 @article{Omran1971,
  title={The epidemiologic transition: a theory of the epidemiology of population change},
  author={Omran, A.R.},
  journal={The Milbank Memorial Fund Quarterly},
  volume={49},
  number={4},
  pages={509--538},
  year={1971},
  publisher={JSTOR}
}

@article{Ovidio2010,
  title={Fluid dynamical niches of phytoplankton types},
  author={dÕOvidio, F. and De Monte, S. and Alvain, S. and Dandonneau, Y. and L{\'e}vy, M.},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={43},
  pages={18366--18370},
  year={2010},
  publisher={National Acad Sciences}
}



@ARTICLE{Papaspiliopoulos2007,
  author = {O. Papaspiliopoulos and G.O. Roberts and M. Skold},
  title = {A general framework for the parametrization of hierarchical models},
  journal = {Statistical Science},
  year = {2007},
  volume = {22},
  pages = {59--73},
  number = {1},
  issn = {0883-4237},
  publisher = {[Hayward, Calif.]: The Institute,[c1986-}
}

@ARTICLE{Pellis2010,
  author = {L. Pellis and N.M. Ferguson and C. Fraser},
  title = {Epidemic growth rate and household reproduction number in communities
	of households, schools and workplaces},
  journal = {Journal of Mathematical Biology},
  year = {2010},
  pages = {1--44},
  issn = {0303-6812},
  publisher = {Springer}
}

@ARTICLE{Pickles2010,
  author = {M. Pickles and A.M. Foss and P. Vickerman and K. Deering and S. Verma
	and E. Demers and R. Washington and B.M. Ramesh andS. Moses and J.
	Blanchard and others},
  title = {Interim modelling analysis to validate reported increases in condom
	use and assess HIV infections averted among female sex workers and
	clients in southern India following a targeted HIV prevention programme},
  journal = {British Medical Journal},
  year = {2010},
  volume = {86},
  pages = {i33},
  number = {Suppl 1},
  issn = {1472-3263},
  publisher = {BMJ Publishing Group Ltd}
}

@article{Plummer2006,
  title={CODA: Convergence diagnosis and output analysis for MCMC},
  author={Plummer, Martyn and Best, Nicky and Cowles, Kate and Vines, Karen},
  journal={R news},
  volume={6},
  number={1},
  pages={7--11},
  year={2006}
}

@article{Pokern2009,
 author               = {Y. Pokern and A.M. Stuart and P. Wiberg},
 journal              = {Journal of the Royal Statistical Society: Series B},
 number               = {1},
 pages                = {49},
 title                = {Parameter estimation for partially observed hypoelliptic diffusions},
 volume               = {71},
 year                 = {2009},
 }

@ARTICLE{Pollicott2009,
  author = {M. Pollicott and H. Wang and H. Weiss},
  title = {Recovering the time-dependent transmission rate from infection data},
  journal = {Arxiv preprint arXiv:0907.3529},
  year = {2009}
}

@ARTICLE{Polson2008,
  author = {N.G. Polson and J.R. Stroud and P. M{\\"u}ller},
  title = {Practical filtering with sequential parameter learning},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2008},
  volume = {70},
  pages = {413--428},
  number = {2},
  publisher = {John Wiley \& Sons}
}

@book{Popper2002,
  title={The logic of scientific discovery},
  author={Popper, K.},
  number={117},
  year={2002},
  series={A},
  publisher={Routledge}
}

@ARTICLE{Poyiadjis2009,
  author = {G. Poyiadjis and A. Doucet and SS. Singh},
  title = {Sequential Monte Carlo computation of the score and observed information
	matrix in state-space models with application to parameter estimation},
  journal = {Biometrika},
  year = {2009},
  volume = {20},
  pages = {20},
  publisher = {Cambridge University Engineering Department}
}

@article{Presanis2011,
  title={Bayesian evidence synthesis for a transmission dynamic model for HIV among men who have sex with men},
  author={Presanis, AM and De Angelis, D. and Goubar, A. and Gill, ON and Ades, AE},
  journal={Biostatistics},
  volume={12},
  number={4},
  pages={666--681},
  year={2011},
  publisher={Biometrika Trust}
}

@article{Pulliam1988,
  title={Sources, sinks, and population regulation},
  author={R. Pulliam},
  journal={American Naturalist},
  pages={652--661},
  year={1988},
  publisher={JSTOR}
}

@article{Race1995,
  title={Some further consideration of the plague in Eyam, 1665/6},
  author={Race, Philip},
  journal={Local Population Studies},
  volume={54},
  pages={56--57},
  year={1995}
}

@article{Raghavendra2011,
  title={Malaria vector control: from past to future},
  author={K.  Raghavendra and T.K. Barik and B.P.N. Reddy and P. Sharma and A.P. Dash},
  journal={Parasitology research},
  volume={108},
  number={4},
  pages={757--779},
  year={2011},
  publisher={Springer}
}

@article{Ranjit2011,
  title={Dengue hemorrhagic fever and shock syndromes*},
  author={S. Ranjit and N. Kissoon},
  journal={Pediatric Critical Care Medicine},
  volume={12},
  number={1},
  pages={90--100},
  year={2011},
  publisher={LWW}
}

@article{Rao1967,
  title={Distribution, density and seasonal prevalence of aedes aegypti in the Indian subcontinent and South-East Asia.},
  author={Rao, T Ramachandra},
  journal={Bulletin of the World Health Organization},
  volume={36},
  number={4},
  pages={547},
  year={1967},
  publisher={World Health Organization}
}


@article{Rasmussen2011,
  title={Inference for nonlinear epidemiological models using genealogies and time series},
  author={Rasmussen, D.A. and Ratmann, O. and Koelle, K.},
  journal={PLoS computational biology},
  volume={7},
  number={8},
  pages={e1002136},
  year={2011},
  publisher={Public Library of Science}
}

@article{Raue2009,
  title={Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood},
  author={A. Raue and C. Kreutz and T. Maiwald and J. Bachmann and M. Schilling and U. Klingm{\"u}ller and J. Timmer},
  journal={Bioinformatics},
  volume={25},
  number={15},
  pages={1923--1929},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{Read2006,
  title={Disease evolution across a range of spatio-temporal scales},
  author={J.M. Read and M.J. Keeling},
  journal={Theoretical population biology},
  volume={70},
  number={2},
  pages={201--213},
  year={2006},
  publisher={Elsevier}
}

@ARTICLE{Reza-Paul2008,
  author = {S. Reza-Paul and T. Beattie and H.U.R. Syed and K.T. Venukumar and
	M.S. Venugopal and M.P. Fathima and H.R. Raghavendra and P. Akram
	and R. Manjula and M. Lakshmi and others},
  title = {Declines in risk behaviour and sexually transmitted infection prevalence
	following a community-led HIV preventive intervention among female
	sex workers in Mysore, India},
  journal = {AIDS},
  year = {2008},
  volume = {22},
  pages = {S91}
}

@article{Richards1959,
  title={A flexible growth function for empirical use},
  author={Richards, FJ},
  journal={Journal of experimental Botany},
  volume={10},
  number={2},
  pages={290--301},
  year={1959},
  publisher={Soc Experiment Biol}
}


@BOOK{Ristic2004,
  title = {Beyond the Kalman filter: Particle filters for tracking applications},
  publisher = {Artech House Publishers},
  year = {2004},
  author = {B. Ristic and S. Arulampalam and N. Gordon}
}

@ARTICLE{Roberts1997,
  author = {G.O. Roberts and A. Gelman and W.R. Gilks},
  title = {Weak convergence and optimal scaling of random walk Metropolis algorithms},
  journal = {The Annals of Applied Probability},
  year = {1997},
  volume = {7},
  pages = {110--120},
  number = {1},
  issn = {1050-5164},
  publisher = {JSTOR}
}

@ARTICLE{Roberts2009,
  author = {G.O. Roberts and J.S. Rosenthal},
  title = {Examples of adaptive MCMC},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2009},
  volume = {18},
  pages = {349--367},
  number = {2},
  issn = {1061-8600},
  publisher = {ASA}
}

@ARTICLE{Roberts1998,
  author = {G.O. Roberts and J.S. Rosenthal},
  title = {Optimal scaling of discrete approximations to Langevin diffusions},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {1998},
  volume = {60},
  pages = {255--268},
  number = {1},
  publisher = {Wiley Online Library}
}

@ARTICLE{Roberts2002,
  author = {GO Roberts and O. Stramer},
  title = {Langevin diffusions and Metropolis-Hastings algorithms},
  journal = {Methodology and computing in applied probability},
  year = {2002},
  volume = {4},
  pages = {337--357},
  number = {4},
  publisher = {Springer}
}

@ARTICLE{Roberts2001,
  author = {G.O. Roberts and O. Stramer},
  title = {On inference for partially observed nonlinear diffusion models using
	the Metropolis-Hastings algorithm},
  journal = {Biometrika},
  year = {2001},
  volume = {88},
  pages = {603},
  number = {3},
  publisher = {Biometrika Trust}
}

@ARTICLE{Rod'o2002,
  author = {X. Rodo and M. Pascual and G. Fuchs and ASG. Faruque},
  title = {ENSO and cholera: A nonstationary link related to climate change?},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2002},
  volume = {99},
  pages = {12901},
  number = {20},
  publisher = {National Acad Sciences}
}

@article{Rohani1999,
  title={Opposite patterns of synchrony in sympatric disease metapopulations},
  author={P.  Rohani and D.J.D.  Earn and B.T. Grenfell},
  journal={Science},
  volume={286},
  number={5441},
  pages={968--971},
  year={1999},
  publisher={American Association for the Advancement of Science}
}

@article{Rohani2002,
  title={The interplay between determinism and stochasticity in childhood diseases},
  author={P.  Rohani and M.J. Keeling and B.T. Grenfell},
  journal={The American Naturalist},
  volume={159},
  number={5},
  pages={469--481},
  year={2002},
  publisher={JSTOR}
}


@ARTICLE{Ross2009,
  author = {J.V. Ross and D.E. Pagendam and P.K. Pollett},
  title = {On parameter estimation in population models II: multi-dimensional
	processes and transient dynamics},
  journal = {Theoretical population biology},
  year = {2009},
  volume = {75},
  pages = {123--132},
  number = {2-3},
  publisher = {Elsevier}
}

@ARTICLE{Ross2006,
  author = {JV. Ross and T. Taimre and PK. Pollett},
  title = {On parameter estimation in population models},
  journal = {Theoretical population biology},
  year = {2006},
  volume = {70},
  pages = {498--510},
  number = {4},
  publisher = {Elsevier}
}

@article{Rota2003,
  title={Update on the global distribution of genotypes of wild type measles viruses},
  author={P.A.  Rota and W.J. Bellini},
  journal={Journal of Infectious Diseases},
  volume={187},
  number={Supplement 1},
  pages={S270--S276},
  year={2003},
  publisher={Oxford University Press}
}

@BOOK{Rubinstein2004,
  title = {The cross-entropy method: a unified approach to combinatorial optimization,
	Monte-Carlo simulation, and machine learning},
  publisher = {Springer-Verlag New York Inc},
  year = {2004},
  author = {R.Y. Rubinstein and D.P. Kroese}
}

@BOOK{Russell2009,
  title = {Artificial intelligence: a modern approach},
  publisher = {Prentice hall},
  year = {2009},
  author = {S.J. Russell and P. Norvig}
}

@ARTICLE{Scalia-Tomba1991,
  author = {G. Scalia-Tomba},
  title = {The effect of structural behavior change on the spread of HIV in
	a one-sex population},
  journal = {Mathematical Biosciences},
  year = {1991},
  volume = {107},
  pages = {547--555},
  number = {2},
  publisher = {Elsevier}
}

@article{Schultz1993,
  title={Seasonal abundance of dengue vectors in Manila, Republic of the Philippines},
  author={GW. Schultz},
  journal={Southeast Asian Journal of Tropical Medicine and Public Health},
  volume={24},
  number={2},
  pages={369--375},
  year={1993},
  publisher={SEAMO, Regional Tropical Medicine and Public Health Network}
}

@ARTICLE{Shaman2009,
  author = {J. Shaman and M. Kohn},
  title = {Absolute humidity modulates influenza survival, transmission, and
	seasonality},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2009},
  volume = {106},
  pages = {3243},
  number = {9},
  publisher = {National Acad Sciences}
}

@ARTICLE{Shephard1997,
  author = {N. Shephard and M.K. Pitt},
  title = {Likelihood analysis of non-Gaussian measurement time series},
  journal = {Biometrika},
  year = {1997},
  volume = {84},
  pages = {653--667},
  number = {3},
  publisher = {JSTOR}
}

@BOOK{Spall2003,
  title = {Introduction to stochastic search and optimization: estimation, simulation,
	and control},
  publisher = {John Wiley and Sons},
  year = {2003},
  author = {J.C. Spall}
}

@article{Spiegelhalter2002,
  title={Bayesian measures of model complexity and fit},
  author={D.J. Spiegelhalter and N.G. Best and B.P. Carlin and A. Van Der Linde},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={64},
  number={4},
  pages={583--639},
  year={2002},
  publisher={Wiley Online Library}
}

@PHDTHESIS{Stoltz2005,
  author = {G. Stoltz},
  title = {Incomplete information and internal regret in prediction of individual
	sequences},
  school = {PhD thesis, Dept. of Mathematics, University Paris XI, ORSAY, 2005},
  year = {2005},
}

@ARTICLE{Streftaris2004,
  author = {G. Streftaris and G. Gibson},
  title = {Bayesian analysis of experimental epidemics of foot-and-mouth disease},
  journal = {Proceedings: Biological Sciences},
  year = {2004},
  volume = {271},
  pages = {1111--1117},
  number = {1544},
  issn = {0962-8452},
  publisher = {JSTOR}
}

@CONFERENCE{Streftaris2002,
  author = {G. Streftaris and G.J. Gibson},
  title = {Statistical inference for stochastic epidemic models},
  booktitle = {Proc. of the 17th Int’l Workshop on Statistical Modelling. Chania},
  year = {2002},
  volume = {609616}
}



@ARTICLE{Sarkka2010a,
  author = {S. S{\"a}rkk{\"a}},
  title = {Continuous-time and continuous-discrete-time unscented Rauch-Tung-Striebel
	smoothers},
  journal = {Signal Processing},
  year = {2010},
  volume = {90},
  pages = {225--235},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{Sarkka2008a,
  author = {S. S{\"a}rkk{\"a}},
  title = {Unscented rauch-tung-striebel smoother},
  journal = {IEEE Transactions on Automatic Control},
  year = {2008},
  volume = {53},
  pages = {845--849},
  number = {3},
  publisher = {Citeseer}
}

@ARTICLE{Sarkka2007,
  author = {S. S{\"a}rkk{\"a}},
  title = {On unscented Kalman filtering for state estimation of continuous-time
	nonlinear systems},
  journal = {IEEE Transactions on Automatic Control},
  year = {2007},
  volume = {52},
  pages = {1631--1641},
  number = {9}
}

@ARTICLE{Sarkka2007a,
  author = {S. S{\"a}rkk{\"a}},
  title = {On unscented Kalman filtering for state estimation of continuous-time
	nonlinear systems},
  journal = {IEEE Transactions on Automatic Control},
  year = {2007},
  volume = {52},
  pages = {1631--1641},
  number = {9}
}

@ARTICLE{Sarkka2006,
  author = {S. S{\"a}rkk{\"a}},
  title = {Recursive Bayesian inference on stochastic differential equations},
  journal = {PhD dissertation},
  year = {2006},
  volume = {150},
  pages = {1-150}
}

@ARTICLE{Sarkka2010b,
  author = {S. S{\"a}rkk{\"a} and J. Hartikainen},
  title = {On Gaussian Optimal Smoothing of Non-Linear State Space Models},
  journal = {submitted for publication},
  year = {2010},
  volume = {100},
  pages = {100}
}

@ARTICLE{Sarkka2008b,
  author = {S. S{\"a}rkk{\"a} and T. Sottinen},
  title = {Application of Girsanov Theorem to Particle Filtering of Discretely
	Observed Continuous-Time Non-Linear Systems},
  journal = {Bayesian Analysis},
  year = {2008},
  volume = {3},
  pages = {555--584},
  number = {3}
}

@article{Schwarz1978,
  title={Estimating the dimension of a model},
  author={G. Schwarz},
  journal={The annals of statistics},
  volume={6},
  number={2},
  pages={461--464},
  year={1978},
  publisher={Institute of Mathematical Statistics}
}

@article{Shah2007,
  title={Worldwide emergence of extensively drug-resistant tuberculosis},
  author={N.S. Shah and A.  Wright and G.H.  Bai and L.  Barrera and  F. Boulahbal and N.  Martin-Casabona and F.  Drobniewski and C. Gilpin and M. Havelkova and R. Lepe and others},
  journal={Emerging infectious diseases},
  volume={13},
  number={3},
  pages={380},
  year={2007},
  publisher={Centers for Disease Control}
}





@ARTICLE{Sorensen2004,
  author = {H. S{\o}rensen},
  title = {Parametric inference for diffusion processes observed at discrete
	points in time: a survey},
  journal = {International Statistical Review},
  year = {2004},
  volume = {72},
  pages = {337--354},
  number = {3},
  publisher = {John Wiley \& Sons}
}

@article{Stollenwerk2012,
  title={Dynamic noise, chaos and parameter estimation in population biology},
  author={N. Stollenwerk and M. Aguiar and S. Ballesteros and J. Boto and B. Kooi  and L. Mateus},
  journal={Interface Focus},
  volume={2},
  number={2},
  pages={156--169},
  year={2012},
  publisher={The Royal Society}
}

@article{Suhrcke2011,
  title={The impact of economic crises on communicable disease transmission and control: a systematic review of the evidence},
  author={M.  Suhrcke and D. Stuckler and J.E. Suk and M. Desai and M. Senek and M. McKee and S. Tsolova and S. Basu and I. Abubakar and P. Hunter and others},
  journal={PloS one},
  volume={6},
  number={6},
  pages={e20724},
  year={2011},
  publisher={Public Library of Science}
}

@article{Stark2012,
  title={Local Variations in Spatial Synchrony of Influenza Epidemics},
  author={J. Stark and D. Cummings and B. Ermentrout and S. Ostroff and R. Sharma and S. Stebbins and D. Burke and S. Wisniewski},
  journal={PloS one},
  volume={7},
  number={8},
  pages={e43528},
  year={2012},
  publisher={Public Library of Science}
}

@ARTICLE{Tierney1994,
  author = {L. Tierney},
  title = {Markov chains for exploring posterior distributions},
  journal = {the Annals of Statistics},
  year = {1994},
  volume = {22},
  pages = {1701--1728},
  number = {4},
  issn = {0090-5364},
  publisher = {JSTOR}
}

@ARTICLE{Tjelmeland2004,
  author = {H. Tjelmeland and J. Eidsvik},
  title = {On the use of local optimizations within Metropolis--Hastings updates},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2004},
  volume = {66},
  pages = {411--427},
  number = {2},
  issn = {1467-9868},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{Toni2009,
  author = {T. Toni and D. Welch and N. Strelkowa and A. Ipsen and M.P.H. Stumpf},
  title = {Approximate Bayesian computation scheme for parameter inference and
	model selection in dynamical systems},
  journal = {Journal of The Royal Society Interface},
  year = {2009},
  volume = {6},
  pages = {187},
  number = {31},
  publisher = {The Royal Society}
}

@BOOK{Turchin2003,
  title = {Complex population dynamics: a theoretical/empirical synthesis},
  publisher = {Princeton University Press Princeton, USA:},
  year = {2003},
  author = {P. Turchin}
}

 @article{Turner1997,
  title={Zenilman's anomaly reconsidered: Fallible reports, ceteris paribus, and other hypotheses},
  author={Turner, C.F. and Miller, H.G.},
  journal={Sexually transmitted diseases},
  volume={24},
  number={9},
  pages={522},
  year={1997}
}

@book{Unaids2009,
  title={AIDS epidemic update},
  author={UNAIDS},
  year={2009},
  publisher={WHO Regional Office Europe}
}

@article{UNAIDS2000,
  title = {Costing Guidelines for HIV Prevention Strategies},
  year = {2000},
  author = {UNAIDS},
  journal={official communication}  
  }
  
  @article{Unkel2012,
  title={Statistical methods for the prospective detection of infectious disease outbreaks: a review},
  author={S. Unkel and C. Farrington and P.H. Garthwaite and C. Robertson and N. Andrews},
  journal={Journal of the Royal Statistical Society: Series A},
  year={2012},
   volume               = {175},
    number               = {1},
     pages                = {49-82},
  publisher={Wiley Online Library}
}

@inproceedings{Van2001,
  title={The square-root unscented Kalman filter for state and parameter-estimation},
  author={Van Der Merwe, Rudolph and Wan, Eric A},
  booktitle={Acoustics, Speech, and Signal Processing, 2001. Proceedings.(ICASSP'01). 2001 IEEE International Conference on},
  volume={6},
  pages={3461--3464},
  year={2001},
  organization={IEEE}
}

@article{Van2004,
  title={Emergent trade-offs and selection for outbreak frequency in spatial epidemics},
  author={W.M.  Van Ballegooijen and M.C. Boerlijst},
  journal={Proceedings of the National Academy of Sciences},
  volume={101},
  number={52},
  pages={18246--18250},
  year={2004},
  publisher={National Acad Sciences}
}

@ARTICLE{Velasco-Hernandez1994,
  author = {J.X. Velasco-Hernandez and Y.H. Hsieh},
  title = {Modelling the effect of treatment and behavioral change in HIV transmission
	dynamics},
  journal = {Journal of mathematical biology},
  year = {1994},
  volume = {32},
  pages = {233--249},
  number = {3},
  publisher = {Springer}
}

@ARTICLE{Viboud2004,
  author = {C. Viboud and K. Pakdaman and P. Boelle and M.L. Wilson and
	M.F. Myers and A.J. Valleron and A. Flahault},
  title = {Association of influenza epidemics with global climate variability},
  journal = {European Journal of Epidemiology},
  year = {2004},
  volume = {19},
  pages = {1055--1059},
  number = {11},
  issn = {0393-2990},
  publisher = {Springer}
}


@article{Viboud2013,
  title={Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission},
  author={C. Viboud and M. Nelson and Y. Tan and E. Holmes},
  journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
  volume={368},
  number={1614},
  year={2013},
  publisher={The Royal Society}
}



@ARTICLE{Vickerman2010,
  author = {P. Vickerman and A.M. Foss and M. Pickles and K. Deering and S. Verma
	and E. Demers and C.M. Lowndes and S. Moses and M. Alary and M.C.
	Boily},
  title = {To what extent is the HIV epidemic in southern India driven by commercial
	sex? A modelling analysis},
  journal = {AIDS},
  year = {2010},
  volume = {24},
  pages = {2563},
  number = {16}
}

@article{Volz2012,
  title={Complex population dynamics and the coalescent under neutrality},
  author={Volz, E.M.},
  journal={Genetics},
  volume={190},
  number={1},
  pages={187--201},
  year={2012},
  publisher={Genetics Soc America}
}

@article{Vynnycky2008,
  title={Analyses of the 1957 (Asian) influenza pandemic in the United Kingdom and the impact of school closures},
  author={Vynnycky, E. and Edmunds, WJ and others},
  journal={Epidemiology and infection},
  volume={136},
  number={2},
  pages={166--179},
  year={2008},
  publisher={Cambridge Univ Press}
}

@BOOK{Wahba1990,
  title = {Spline models for observational data},
  publisher = {Society for Industrial Mathematics},
  year = {1990},
  author = {G. Wahba},
  isbn = {0898712440},
  issn = {0163-9439}
}

@article{Wallinga2006,
  title={Using data on social contacts to estimate age-specific transmission parameters for respiratory-spread infectious agents},
  author={J. Wallinga and P. Teunis and M. Kretzschmar},
  journal={American journal of epidemiology},
  volume={164},
  number={10},
  pages={936--944},
  year={2006},
  publisher={Oxford Univ Press}
}

@ARTICLE{Wallinga2004,
  author = {J. Wallinga and P. Teunis},
  title = {Different epidemic curves for severe acute respiratory syndrome reveal
	similar impacts of control measures},
  journal = {American Journal of Epidemiology},
  year = {2004},
  volume = {160},
  pages = {509},
  number = {6},
  issn = {0002-9262},
  publisher = {Oxford Univ Press}
}

@ARTICLE{Wan2001,
  author = {E.A. Wan and R. Van Der Merwe},
  title = {The unscented Kalman filter},
  journal = {Kalman filtering and neural networks},
  year = {2001},
  volume = {100},
  pages = {221--280},
  publisher = {Wiley Publishing}
}

@ARTICLE{Wawer1999,
  author = {M.J. Wawer and N.K. Sewankambo and D. Serwadda and T.C. Quinn and
	L.A. Paxton and N. Kiwanuka and F. Wabwire-Mangen and C. Li and T.
	Lutalo and F. Nalugoda and others},
  title = {Control of sexually transmitted diseases for AIDS prevention in Uganda:
	a randomised community trial},
  journal = {The Lancet},
  year = {1999},
  volume = {353},
  pages = {525--535},
  number = {9152},
  publisher = {Elsevier}
}

@ARTICLE{Weiss1998,
  author = {G. Weiss and A. Von Haeseler},
  title = {Inference of population history using a likelihood approach},
  journal = {Genetics},
  year = {1998},
  volume = {149},
  pages = {1539},
  number = {3},
  publisher = {Genetics Soc America}
}

@article{Welford2009,
  title={Validation of inverse seasonal peak mortality in medieval plagues, including the Black Death, in comparison to modern Yersinia pestis-variant diseases},
  author={M. Welford and B. Bossak},
  journal={PloS one},
  volume={4},
  number={12},
  pages={e8401},
  year={2009},
  publisher={Public Library of Science}
}

@ARTICLE{West1993,
  author = {M. West},
  title = {Approximating posterior distributions by mixture},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1993},
  volume = {55},
  pages = {409--422},
  number = {2},
  issn = {0035-9246},
  publisher = {JSTOR}
}

@article{Whitaker2004,
  title={Infections with varying contact rates: application to varicella},
  author={HJ. Whitaker and CP. Farrington},
  journal={Biometrics},
  volume={60},
  number={3},
  pages={615--623},
  year={2004},
  publisher={Wiley Online Library}
}


@ARTICLE{White2008,
  author = {L.F. White and M. Pagano},
  title = {A likelihood-based method for real-time estimation of the serial
	interval and reproductive number of an epidemic},
  journal = {Stat Med},
  year = {2008},
  volume = {27},
  pages = {2999--3016},
  number = {16}
}

@ARTICLE{Wolf1985,
  author = {A. Wolf and J.B. Swift and H.L. Swinney and J.A. Vastano},
  title = {Determining Lyapunov exponents from a time series},
  journal = {Physica D: Nonlinear Phenomena},
  year = {1985},
  volume = {16},
  pages = {285--317},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{WHO2012x,
 author = {World Health Organisation},
  title = {World Health Statisics},
  institution = {World Health Organisation},
  year = {2012},
  journal={official communication}
}

 @report{WHOpolio,
      institution = {World Health Organisation},
      author = {WHO},
      title = {Polio Case Count},
      type = {official communication},
      year = {2012}
 }

@report{WHO2012,
      institution = {World Health Organisation},  
      author = {WHO},
      title = {World Health Statisics},
      type = {official communication},
      year = {2012}
 }
 


@ARTICLE{WHOpolioxx,
  author = {World Health Organisation},
  title = {Polio Case Count},
  institution = {World Health Organisation},
  year = {2012},
 url = {http://apps.who.int/immunization_monitoring/en/diseases/poliomyelitis/case_count.cfm},
  journal={official communication}
}

@article {Wood1994,
    AUTHOR = {A. Wood and G. Chan},
     TITLE = {Simulation of Stationary {G}aussian processes in $[0,1]^d$},
   JOURNAL = {J. Comput. Graph. Statist.},
  FJOURNAL = {Journal of Computational and Graphical Statistics},
    VOLUME = {3},
      YEAR = {1994},
    NUMBER = {4},
     PAGES = {409--432},
}


@ARTICLE{Yin2008,
  author = {Y. Yin},
  title = {Bayesian analysis of infectious disease time series data and optimal
	constrained Bayesian updating},
  journal = {THE JOHNS HOPKINS UNIVERSITY},
  year = {2008},
  volume = {90},
  pages = {90},
  publisher = {D., THE JOHNS HOPKINS UNIVERSITY}
}

@article{Yuancai1997,
  title={Comparison of Schnute's and Bertalanffy-Richards' growth functions},
  author={Yuancai, L. and Marques, C.P. and Macedo, F.W.},
  journal={Forest Ecology and management},
  volume={96},
  number={3},
  pages={283--288},
  year={1997},
  publisher={Elsevier}
}



@ARTICLE{Zaba2000,
  author = {B. Zaba and T. Boerma and R. White},
  title = {Monitoring the AIDS epidemic using HIV prevalence data among young
	women attending antenatal clinics: prospects and problems},
  journal = {Aids},
  year = {2000},
  volume = {14},
  pages = {1633},
  number = {11}
}

@article{Zanzonico2000,
  title={Age-dependent thyroid absorbed doses for radiobiologically significant radioisotopes of iodine},
  author={P. Zanzonico},
  journal={Health physics},
  volume={78},
  number={1},
  pages={60--67},
  year={2000},
  publisher={LWW}
}

 @article{Zenilman1995,
  title={Condom use to prevent incident STDs: the validity of self-reported condom use.},
  author={Zenilman, J.M. and Weisman, C.S. and Rompalo, A.M. and Ellish, N. and Upchurch, D.M. and Hook 3rd, EW and Celentano, D. and others},
  journal={Sexually transmitted diseases},
  volume={22},
  number={1},
  pages={15},
  year={1995}
}


@article{Zwietering1990,
  title={Modeling of the bacterial growth curve},
  author={Zwietering, MH and Jongenburger, I. and Rombouts, FM and Van't Riet, K.},
  journal={Applied and Environmental Microbiology},
  volume={56},
  number={6},
  pages={1875--1881},
  year={1990},
  publisher={Am Soc Microbiol}
}