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View article: Diagnostics of dated phylogenies in microbial population genetics
Diagnostics of dated phylogenies in microbial population genetics Open
Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Many tools have recently been developed to date the nodes of a standard phylogeny, but all make …
View article: Impacts of disease surveillance frequency on understanding and controlling Rift Valley fever virus
Impacts of disease surveillance frequency on understanding and controlling Rift Valley fever virus Open
Effective livestock disease surveillance faces numerous socio-economic and disease-specific challenges, particularly within resource-limited settings. Rift Valley fever (RVF), a zoonotic vector-borne disease which is of growing threat to h…
View article: Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks
Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks Open
Pathogen genomic data are increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this…
View article: Incorporating epidemiological data into the genomic analysis of partially sampled infectious disease outbreaks
Incorporating epidemiological data into the genomic analysis of partially sampled infectious disease outbreaks Open
Pathogen genomic data is increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this …
View article: Polymorph Identification for Flexible Molecules: Linear Regression Analysis of Experimental and Calculated Solution- and Solid-State NMR Data
Polymorph Identification for Flexible Molecules: Linear Regression Analysis of Experimental and Calculated Solution- and Solid-State NMR Data Open
The Δδ regression approach of Blade et al. [ J. Phys. Chem. A 2020, 124(43), 8959-8977] for accurately discriminating between solid forms using a combination of experimental solution- and solid-state NMR data with density functional…
View article: Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host
Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host Open
In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However,…
View article: Inference of infectious disease transmission using multiple genomes per host
Inference of infectious disease transmission using multiple genomes per host Open
In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However,…
View article: The bounded coalescent model: Conditioning a genealogy on a minimum root date
The bounded coalescent model: Conditioning a genealogy on a minimum root date Open
The coalescent model represents how individuals sampled from a population may have originated from a last common ancestor. The bounded coalescent model is obtained by conditioning the coalescent model such that the last common ancestor mus…
View article: The bounded coalescent model: conditioning a genealogy on a minimum root date
The bounded coalescent model: conditioning a genealogy on a minimum root date Open
The coalescent model represents how individuals sampled from a population may have originated from a last common ancestor. The bounded coalescent model is obtained by conditioning the coalescent model such that the last common ancestor mus…
View article: Efficient Bayesian model selection for coupled hidden Markov models with application to infectious diseases
Efficient Bayesian model selection for coupled hidden Markov models with application to infectious diseases Open
Performing model selection for coupled hidden Markov models (CHMMs) is highly challenging, owing to the large dimension of the hidden state process. Whilst in principle the hidden state process can be marginalized out via forward filtering…
View article: Quantifying age and model uncertainties in palaeoclimate data and dynamical climate models with a joint inferential analysis
Quantifying age and model uncertainties in palaeoclimate data and dynamical climate models with a joint inferential analysis Open
The study of palaeoclimates relies on information sampled in natural archives such as deep sea cores. Scientific investigations often use such information in multi-stage analyses, typically with an age model being fitted to a core to conve…
View article: Bayesian modelling and quantification of Raman spectroscopy
Bayesian modelling and quantification of Raman spectroscopy Open
Raman spectroscopy can be used to identify molecules such as DNA by the characteristic scattering of light from a laser. It is sensitive at very low concentrations and can accurately quantify the amount of a given molecule in a sample. The…
View article: <i>In vivo</i> multiplex molecular imaging of vascular inflammation using surface-enhanced Raman spectroscopy
<i>In vivo</i> multiplex molecular imaging of vascular inflammation using surface-enhanced Raman spectroscopy Open
Vascular immune-inflammatory responses play a crucial role in the progression and outcome of atherosclerosis. The ability to assess localized inflammation through detection of specific vascular inflammatory biomarkers would significantly i…
View article: Bayesian Model Selection for the Glacial–Interglacial Cycle
Bayesian Model Selection for the Glacial–Interglacial Cycle Open
Summary A prevailing viewpoint in paleoclimate science is that a single paleoclimate record contains insufficient information to discriminate between typical competing explanatory models. Here we show that, by using the algorithm SMC2 (‘se…
View article: Bayesian modelling and quantification of Raman spectroscopy
Bayesian modelling and quantification of Raman spectroscopy Open
Raman spectroscopy can be used to identify molecules such as DNA by the characteristic scattering of light from a laser. It is sensitive at very low concentrations and can accurately quantify the amount of a given molecule in a sample. The…
View article: Unbiased local solutions of partial differential equations via the Feynman-Kac Identities
Unbiased local solutions of partial differential equations via the Feynman-Kac Identities Open
The Feynman-Kac formulae (FKF) express local solutions of partial differential equations (PDEs) as expectations with respect to some complementary stochastic differential equation (SDE). Repeatedly sampling paths from the complementary SDE…
View article: Uncertainty quantification in palaeoclimate reconstruction
Uncertainty quantification in palaeoclimate reconstruction Open
Studying the dynamics of the palaeoclimate is a challenging problem. Part of the challenge lies in the fact that our understanding must be based on only a single realisation of the climate system. With only one climate history, it is essen…