List of works - Daniel T. Haydon

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

scientific article published on 11 March 2014

A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data

scientific article

A centuries-long epidemic of scrapie in British sheep?

scientific article published on February 2001

An analysis of foot-and-mouth-disease epidemics in the UK

article

An ecological and comparative perspective on the control of bovine tuberculosis in Great Britain and the Republic of Ireland

scientific article

An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

scientific article published on 16 November 2011

Analysing noisy time-series: describing regional variation in the cyclic dynamics of red grouse

article

Analysis of Foot-and-mouth disease virus nucleotide sequence variation within naturally infected epithelium

scientific article

Assembling evidence for identifying reservoirs of infection

scientific article published on 11 April 2014

Assessing the impact of marine wind farms on birds through movement modelling

scientific article

Barriers to movement: Modelling energetic costs of avoiding marine wind farms amongst breeding seabirds

scientific article published on 25 February 2010

Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing

scientific article

Building the bridge between animal movement and population dynamics

scientific article

Can parasites drive population cycles in mountain hares?

scientific article published on 20 January 2009

Characterisation of a SAT-1 outbreak of foot-and-mouth disease in captive African buffalo (Syncerus caffer): clinical symptoms, genetic characterisation and phylogenetic comparison of outbreak isolates.

scientific article published on 27 December 2006

Characterizing sequence variation in the VP1 capsid proteins of foot and mouth disease virus (serotype 0) with respect to virion structure

scientific article published in April 1998

Competitive suppression in mixed-clone parasite cultures

scientific article published on March 2005

Conservation and economic benefits of a road around the Serengeti

scientific article published on 24 February 2015

Critical interplay between parasite differentiation, host immunity, and antigenic variation in trypanosome infections.

scientific article

Cross-disciplinary demands of multihost pathogens

scientific article

Culling wildlife hosts to control disease: mountain hares, red grouse and louping ill virus

article by Annabel Harrison et al published 9 June 2010 in Journal of Applied Ecology

Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study

scientific article (publication date: 2013)

Disrupted seasonal biology impacts health, food security and ecosystems

scientific article

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

scientific article

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

scientific article

Distinguishing technology from biology: a critical review of the use of GPS telemetry data in ecology

scientific article (publication date: 27 July 2010)

Does IBV change slowly despite the capacity of the spike protein to vary greatly?

scientific article published on 01 January 1998

Driving improvements in emerging disease surveillance through locally relevant capacity strengthening

scientific article

Dynamics of a morbillivirus at the domestic-wildlife interface: Canine distemper virus in domestic dogs and lions

scientific article

Dynamics of the 2001 UK Foot and Mouth Epidemic: Stochastic Dispersal in a Heterogeneous Landscape

scientific article published in Science

Emerging pathogens: the epidemiology and evolution of species jumps

article

Epidemiology. Foot-and-mouth disease under control in the UK.

scientific article published on May 2001

Estimates of the duration of the early and late stage of gambiense sleeping sickness

scientific article (publication date: 8 February 2008)

Estimating the Probability of a Major Outbreak from the Timing of Early Cases: An Indeterminate Problem? ⬇️

scientific article published on March 6, 2013

Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution

scientific article published on 13 December 2019

Evaluating the potential for the environmentally sustainable control of foot and mouth disease in Sub-Saharan Africa

scientific article published on September 2013

Evolution of foot-and-mouth disease virus intra-sample sequence diversity during serial transmission in bovine hosts

scientific article published on March 2013

Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem

scientific article published in August 2008

Fewer pests and more ecosystem service‐providing arthropods in shady African cocoa farms: Insights from a data integration study

scientific article published in 2023

Foot-and-mouth disease vaccine potency testing: determination and statistical validation of a model using a serological approach

scientific article published in July 2003

From phenotype to genotype: a Bayesian solution.

scientific article published on 27 October 2010

Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains

scientific article

Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases

scientific article

Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa ⬇️

scientific article published on August 1, 2001

Habitat loss and raptor predation: disentangling long- and short-term causes of red grouse declines

scientific article published on 01 April 2000

Heterogeneity in the spread and control of infectious disease: consequences for the elimination of canine rabies

scientific article published on 15 December 2015

High levels of somatic DNA diversity at the myotonic dystrophy type 1 locus are driven by ultra-frequent expansion and contraction mutations

scientific article published on 24 February 2012

Identifying reservoirs of infection: a conceptual and practical challenge

scientific article

Ikoma lyssavirus, highly divergent novel lyssavirus in an African civet

scientific article published in April 2012

Immune avoidance strategies in RNA viruses: fitness continuums arising from trade-offs between immunogenicity and antigenic variability

scientific article published in August 1998

Inferring the disruption of rabies circulation in vampire bat populations using a betaherpesvirus-vectored transmissible vaccine

scientific article published on 6 March 2023

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus.

scientific article published in April 2008

Integrating serological and genetic data to quantify cross-species transmission: brucellosis as a case study

scientific article

Introduction. Cross-scale influences on epidemiological dynamics: from genes to ecosystems.

scientific article published on 21 August 2007

Linking the antigen archive structure to pathogen fitness in African trypanosomes

scientific article published on 2 January 2013

Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments.

scientific article published in May 2004

Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border

scientific article published on 28 February 2019

Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data

scientific article

Metapopulation dynamics of rabies and the efficacy of vaccination

scientific article published on 15 December 2010

Methods for the detection of non-random base substitution in virus genes: models of synonymous nucleotide substitution in picornavirus genes

scientific article published in January 1998

Mobile Phones As Surveillance Tools: Implementing and Evaluating a Large-Scale Intersectoral Surveillance System for Rabies in Tanzania

scientific article (publication date: April 2016)

Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain

scientific article published in January 1997

Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti

scientific article published on 01 September 2007

Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001

scientific article

Multiple movement modes by large herbivores at multiple spatiotemporal scales

scholarly article

Neighbourhood control policies and the spread of infectious diseases.

scientific article published in August 2003

New directions in biogeography?

scientific article published on 01 October 1994

Observing micro-evolutionary processes of viral populations at multiple scales

scientific article

On the generality of stability-complexity relationships in Lotka-Volterra ecosystems

scientific article published on 20 August 2010

One Health Research in Northern Tanzania – Challenges and Progress

article

Parasites and climate synchronize red grouse populations.

scientific article published in February 2005

Phylodynamic reconstruction of O CATHAY topotype foot-and-mouth disease virus epidemics in the Philippines

scientific article

Phylogenetic analysis of GBV-C/hepatitis G virus.

scientific article published in March 2000

Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects

scientific article

Pollinator-mediated assortative mating in mixed ploidy populations of Chamerion angustifolium (Onagraceae).

scientific article published on 22 September 2006

Predicting the public health benefit of vaccinating cattle against Escherichia coli O157

scientific article

Prediction and characterization of novel epitopes of serotype A foot-and-mouth disease viruses circulating in East Africa using site-directed mutagenesis

scientific article published on 22 January 2015

Prevalence and under-detection of gambiense human African trypanosomiasis during mass screening sessions in Uganda and Sudan

scientific article

Progress towards rabies elimination from Pemba Island, Southern Tanzania.

scientific article

Reconstructing the origin and transmission dynamics of the 1967-68 foot-and-mouth disease epidemic in the United Kingdom

scientific article

Reducing animal experimentation in foot-and-mouth disease vaccine potency tests

scientific article

Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification

scientific article

Revived species: where will they live?

scientific article published in Nature

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

scientific article

Socially informed random walks: incorporating group dynamics into models of population spread and growth

scientific article published in May 2008

Software for quantifying and simulating microsatellite genotyping error

scientific article published on 24 November 2009

Spatial coupling in cyclic population dynamics: models and data.

scientific article

Spatio-temporal dynamics of the grey-sided vole in Hokkaido: identifying coupling using state-based Markov-chain modelling

article

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

scientific article

Surveillance guidelines for disease elimination: a case study of canine rabies

scientific article

Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies

article

The UK foot-and-mouth disease outbreak — the aftermath

scientific article published on 01 August 2004

The changing landscape of rabies epidemiology and control

scientific article

The construction and analysis of epidemic trees with reference to the 2001 UK foot-and-mouth outbreak.

scientific article published in January 2003

The diversity of antimicrobial resistance is different in Salmonella Typhimurium DT104 from co-located animals and humans

scientific article published in 2012

The effects of large- and small-scale random events on the synchrony of metapopulation dynamics: a theoretical analysis

article

The feasibility of canine rabies elimination in Africa: dispelling doubts with data

scientific article

The fitness of African malaria vectors in the presence and limitation of host behaviour

scientific article published on 19 December 2012

The impact of host species and vector control measures on the fitness of African malaria vectors

scientific article published on 8 January 2013

The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes

scientific article

The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus

scientific article published on 8 April 2015

The implications of metapopulation dynamics on the design of vaccination campaigns

scientific article

The implications of virus diversity within the SAT 2 serotype for control of foot-and-mouth disease in sub-Saharan Africa.

scientific article

The interpretation of habitat preference metrics under use-availability designs

scientific article

The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach. ⬇️

scientific article

The relationship between mutation frequency and replication strategy in positive-sense single-stranded RNA viruses

article

Top-down or bottom-up regulation of intra-host blood-stage malaria: do malaria parasites most resemble the dynamics of prey or predator?

scientific article published in February 2003

Transmission dynamics and prospects for the elimination of canine rabies

scientific article

Transmission ecology of canine parvovirus in a multi-host, multi-pathogen system

article

Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007

scientific article

Trophic interactions and population growth rates: describing patterns and identifying mechanisms

scientific article published on 29 September 2002

Updated estimate of the duration of the meningo-encephalitic stage in gambiense human African trypanosomiasis

scientific article published on 4 July 2015

Waves of endemic foot-and-mouth disease in eastern Africa suggest feasibility of proactive vaccination approaches

article by Miriam Casey-Bryars et al published September 2018 in Nature Ecology and Evolution

List of works by Daniel T. Haydon

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data

A centuries-long epidemic of scrapie in British sheep?

An analysis of foot-and-mouth-disease epidemics in the UK

An ecological and comparative perspective on the control of bovine tuberculosis in Great Britain and the Republic of Ireland

An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

Analysing noisy time-series: describing regional variation in the cyclic dynamics of red grouse

Analysis of Foot-and-mouth disease virus nucleotide sequence variation within naturally infected epithelium

Assembling evidence for identifying reservoirs of infection

Assessing the impact of marine wind farms on birds through movement modelling

Barriers to movement: Modelling energetic costs of avoiding marine wind farms amongst breeding seabirds

Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing

Building the bridge between animal movement and population dynamics

Can parasites drive population cycles in mountain hares?

Characterisation of a SAT-1 outbreak of foot-and-mouth disease in captive African buffalo (Syncerus caffer): clinical symptoms, genetic characterisation and phylogenetic comparison of outbreak isolates.

Characterizing sequence variation in the VP1 capsid proteins of foot and mouth disease virus (serotype 0) with respect to virion structure

Competitive suppression in mixed-clone parasite cultures

Conservation and economic benefits of a road around the Serengeti

Critical interplay between parasite differentiation, host immunity, and antigenic variation in trypanosome infections.

Cross-disciplinary demands of multihost pathogens

Culling wildlife hosts to control disease: mountain hares, red grouse and louping ill virus

Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study

Disrupted seasonal biology impacts health, food security and ecosystems

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

Distinguishing technology from biology: a critical review of the use of GPS telemetry data in ecology

Does IBV change slowly despite the capacity of the spike protein to vary greatly?

Driving improvements in emerging disease surveillance through locally relevant capacity strengthening

Dynamics of a morbillivirus at the domestic-wildlife interface: Canine distemper virus in domestic dogs and lions

Dynamics of the 2001 UK Foot and Mouth Epidemic: Stochastic Dispersal in a Heterogeneous Landscape

Emerging pathogens: the epidemiology and evolution of species jumps

Epidemiology. Foot-and-mouth disease under control in the UK.

Estimates of the duration of the early and late stage of gambiense sleeping sickness

Estimating the Probability of a Major Outbreak from the Timing of Early Cases: An Indeterminate Problem? ⬇️

Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution

Evaluating the potential for the environmentally sustainable control of foot and mouth disease in Sub-Saharan Africa

Evolution of foot-and-mouth disease virus intra-sample sequence diversity during serial transmission in bovine hosts

Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem

Fewer pests and more ecosystem service‐providing arthropods in shady African cocoa farms: Insights from a data integration study

Foot-and-mouth disease vaccine potency testing: determination and statistical validation of a model using a serological approach

From phenotype to genotype: a Bayesian solution.

Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains

Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases

Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa ⬇️

Habitat loss and raptor predation: disentangling long- and short-term causes of red grouse declines

Heterogeneity in the spread and control of infectious disease: consequences for the elimination of canine rabies

High levels of somatic DNA diversity at the myotonic dystrophy type 1 locus are driven by ultra-frequent expansion and contraction mutations

Identifying reservoirs of infection: a conceptual and practical challenge

Ikoma lyssavirus, highly divergent novel lyssavirus in an African civet

Immune avoidance strategies in RNA viruses: fitness continuums arising from trade-offs between immunogenicity and antigenic variability

Inferring the disruption of rabies circulation in vampire bat populations using a betaherpesvirus-vectored transmissible vaccine

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus.

Integrating serological and genetic data to quantify cross-species transmission: brucellosis as a case study

Introduction. Cross-scale influences on epidemiological dynamics: from genes to ecosystems.

Linking the antigen archive structure to pathogen fitness in African trypanosomes

Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments.

Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border

Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data

Metapopulation dynamics of rabies and the efficacy of vaccination

Methods for the detection of non-random base substitution in virus genes: models of synonymous nucleotide substitution in picornavirus genes

Mobile Phones As Surveillance Tools: Implementing and Evaluating a Large-Scale Intersectoral Surveillance System for Rabies in Tanzania

Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain

Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti

Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001

Multiple movement modes by large herbivores at multiple spatiotemporal scales

Neighbourhood control policies and the spread of infectious diseases.

New directions in biogeography?

Observing micro-evolutionary processes of viral populations at multiple scales

On the generality of stability-complexity relationships in Lotka-Volterra ecosystems

One Health Research in Northern Tanzania – Challenges and Progress

Parasites and climate synchronize red grouse populations.

Phylodynamic reconstruction of O CATHAY topotype foot-and-mouth disease virus epidemics in the Philippines

Phylogenetic analysis of GBV-C/hepatitis G virus.

Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects

Pollinator-mediated assortative mating in mixed ploidy populations of Chamerion angustifolium (Onagraceae).

Predicting the public health benefit of vaccinating cattle against Escherichia coli O157

Prediction and characterization of novel epitopes of serotype A foot-and-mouth disease viruses circulating in East Africa using site-directed mutagenesis

Prevalence and under-detection of gambiense human African trypanosomiasis during mass screening sessions in Uganda and Sudan

Progress towards rabies elimination from Pemba Island, Southern Tanzania.