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Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens [article]

Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall
2018 biorxiv/medrxiv   pre-print
To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance.  ...  This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological  ...  Simulations were performed using the Pearcey cluster within the CSIRO supercomputer platform.  ... 
doi:10.1101/260836 fatcat:hcntj6xl7natnb3wr3alhdsazq

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall, Samuel Alizon
2018 PLoS Computational Biology  
To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance.  ...  This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological  ...  Acknowledgments The authors thank Loïc Houde for computing assistance and Jeremy Burdon for stimulating discussions and for reviewing this manuscript.  ... 
doi:10.1371/journal.pcbi.1006067 pmid:29649208 pmcid:PMC5918245 fatcat:igybalkxeffunpyhtmozbhwhli

Surrogate Assisted Strategies (The Parameterisation of an Infectious Disease Agent-Based Model) [article]

Rylan Perumal, Terence L van Zyl
2021 arXiv   pre-print
We propose a more comprehensive and adaptive ABMS Framework that can effectively swap out parameterisation strategies and surrogate models to parameterise an infectious disease ABM.  ...  An agent-based model's (ABM) complexity grows as the number of parameters required to be calibrated increases. This parameter expansion leads to the ABMS equivalent of the curse of dimensionality.  ...  . 2 Background and Related Work Agent-Based Modelling and Simulation for Infectious Disease Epidemiology Agent-based modelling and simulation (ABMS) is an effective natural fit for modelling infectious  ... 
arXiv:2108.08809v1 fatcat:wuxahruvgza7zf2aoodimf73zm

Eight challenges in phylodynamic inference

Simon D.W. Frost, Oliver G. Pybus, Julia R. Gog, Cecile Viboud, Sebastian Bonhoeffer, Trevor Bedford
2015 Epidemics  
Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place.  ...  The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade.  ...  Kühnert et al. (2014) fitted a stochastic epidemiological model by simulating epidemiological trajectories, which were used to parameterise a stochastic birth-death process with piecewise constant rates  ... 
doi:10.1016/j.epidem.2014.09.001 pmid:25843391 pmcid:PMC4383806 fatcat:gtrobnfsgrh6pak5r2lrv2qhla

Towards a comprehensive simulation model of malaria epidemiology and control

2008 Parasitology  
Planning of the control of Plasmodium falciparum malaria leads to a need for models of malaria epidemiology that provide realistic quantitative prediction of likely epidemiological outcomes of a wide range  ...  We use individual-based stochastic simulations of malaria epidemiology to predict the impacts of interventions on infection, morbidity, mortality, health services use and costs.  ...  is included in the simultaneous multi-objective fitting of the model, or whether the data are used to separately parameterise model components. $ Some scenarios are used to predict several outcomes, so  ... 
doi:10.1017/s0031182008000371 pmid:18694530 fatcat:d6rgps3ce5h2dosq66ihtdi5ay

Advances in the Application of Machine Learning Techniques in Drug Discovery, Design and Development [chapter]

S. J. Barrett, W. B. Langdon
2006 Advances in Intelligent and Soft Computing  
In silico screening), bioinformatic (i.e. bio-marker studies, using DNA chip data) and other types of drug research studies.  ...  They are inherently suitable for use with 'noisy', high dimensional (many variables) data, as is commonly used in cheminformatic (i.e.  ...  The authors wish to thank GSK colleagues, past and present, for their efforts in expressing the nature of their research.  ... 
doi:10.1007/978-3-540-36266-1_10 fatcat:gdq5kxmbfjfbbaccdcjpsopg4e

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond, Katia Koelle
2014 PLoS Computational Biology  
We apply this method to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental  ...  We use a family of birth-death models where individuals may remain in the tree process after the sampling, in particular we extend the birth-death skyline model [Stadler et al, 2013] to sampled ancestor  ...  We also acknowledge the New Zealand eScience Infrastructure (NeSI) for use of their high-performance computing facilities. Author Contributions Conceived and designed the experiments: AJD AG DW TS.  ... 
doi:10.1371/journal.pcbi.1003919 pmid:25474353 pmcid:PMC4263412 fatcat:re2tyrzcv5hqjpvvwnnujuvniq

Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates

Simon M. Firestone, Yoko Hayama, Max S. Y. Lau, Takehisa Yamamoto, Tatsuya Nishi, Richard A. Bradhurst, Haydar Demirhan, Mark A. Stevenson, Toshiyuki Tsutsui, Fernanda C. Dórea
2020 PLoS ONE  
To improve accessibility the modified model has been implemented as the R package 'BORIS' for use in future outbreaks.  ...  The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in  ...  Acknowledgments Components of this research were undertaken on The University of Melbourne's High Performance Computing system SPARTAN [55] .  ... 
doi:10.1371/journal.pone.0235660 pmid:32667952 fatcat:tbn5yo7dvza77jcwsioqjbkeuy

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages

Antonello Di Nardo, Luca Ferretti, Jemma Wadsworth, Valerie Mioulet, Boris Gelman, Sharon Karniely, Alexey Scherbakov, Ghulam Ziay, Fuat Özyörük, Ünal Parlak, Pelin Tuncer- Göktuna, Reza Hassanzadeh (+8 others)
2021 Molecular biology and evolution  
Here, we map the eco-evolutionary landscape of co-circulating FMDV lineages within an important endemic virus pool encompassing Western, Central and parts of Southern Asia, reconstructing the evolutionary  ...  Livestock farming across the world is constantly threatened by evolutionary turnover of foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics of which remain to be elucidated  ...  Acknowledgements We thank Prof Daniel Haydon for his insightful revision and constructive comments during the preparation of the manuscript.  ... 
doi:10.1093/molbev/msab172 pmid:34115138 pmcid:PMC8476141 fatcat:an7zj27j3zgizdvh5z3fx3n7z4

Epidemiological Inference From Pathogen Genomes: A Review of Phylodynamic Models and Applications

Leo A Featherstone, Joshua M Zhang, Timothy G Vaughan, Sebastian Duchene
2022 Virus Evolution  
We discuss the assumptions linking evolutionary models of pathogen population size to epidemiological models of the infected population size.  ...  Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and sta- tistical inference.  ...  Birth-death models can also include time dependent rates (i.e. not constant/piecewise-constant), though they tend to be applied more in macroevolutionary work than genomic epidemiology.  ... 
doi:10.1093/ve/veac045 pmid:35775026 pmcid:PMC9241095 fatcat:7g7x7xopvvcqpn42lckibmk37i

Prioritising COVID-19 vaccination in changing social and epidemiological landscapes [article]

Peter Jentsch, Madhur Anand, Chris T Bauch
2020 medRxiv   pre-print
We used evolutionary game theory and mobility data to model individual adherence to NPIs.  ...  We developed a coupled social-epidemiological model of SARS-CoV-2 transmission. Schools and workplaces are closed and re-opened based on reported cases.  ...  TC Reluga, Game theory of social distancing in response to an epidemic. PLoS Comput.  ... 
doi:10.1101/2020.09.25.20201889 fatcat:jlhjgt7snneohebuw5pakdeyqu

A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A Eller, Merlin L Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A Lythgoe, Gertrude Nakigozi (+4 others)
2016 eLife  
We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations.  ...  Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce.  ...  Here we integrated extensive data from a single 59 cohort in Uganda into an epidemiological-evolutionary model describing the transmission cycle 60 of HIV.  ... 
doi:10.7554/elife.20492 pmid:27815945 pmcid:PMC5115872 fatcat:f7yjevk4zraghj2vog5ayt4vw4

The space of ultrametric phylogenetic trees

Alex Gavryushkin, Alexei J. Drummond
2016 Journal of Theoretical Biology  
In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events.  ...  More generally, statistical consistency is ensured by the tree space used to analyse the sample.  ...  Acknowledgements We are grateful to Mike Steel, David Bryant, and Steffen Klaere for useful comments and advice on possible approaches to the problems considered in this paper.  ... 
doi:10.1016/j.jtbi.2016.05.001 pmid:27188249 fatcat:i77yrdkxnzba5levvh6eqqi5qu

Understanding and Modelling the Impact of Climate Change on Infectious Diseases – Progress and Future Challenges [chapter]

Paul E., Celine Christiansen-Jucht, Diane Pople, Edwin Michael
2011 Climate Change - Socioeconomic Effects  
Other considerations may include computational resources (e.g. IBMs and climate models are very computationally intensive) and known uncertainties (or variability) in disease and climate inputs.  ...  The use of multi-model ensembles in climate modelling has already become an established technique (e.g.  ...  They are part of an introduction to the researches being done around the globe in connection with this topic.  ... 
doi:10.5772/23139 fatcat:7fc4kric2vf6nl66dyw5l7zhv4

Agile Development of an Attitude-Behaviour Driven Simulation of Alcohol Consumption Dynamics

Daniel Moyo, Abdallah K. Ally, Alan Brennan, Paul Norman, Robin C. Purshouse, Mark Strong
2015 Journal of Artificial Societies and Social Simulation  
This paper sets out the methods of Scrum agile software development, and discusses the experience of using Scrum to organise workflow and guide the development of an agent-based model of alcohol consumption  ...  Whilst there have been several advocates for the application of software engineering (SE) methodologies in the development of agent-based models and simulations in the social sciences, the uptake of these  ...  (CAMH) at the University of Toronto for helpful discussions, as well as the JASSS reviewers for their useful comments.  ... 
doi:10.18564/jasss.2841 fatcat:262z5uq5dfca7ettjx5zxe4gpy
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