Explanipedia

Asymmetric limits on timely interventions from noisy epidemic data Open

Kris V. Parag, Ben Lambert, Christl A. Donnelly · 2025

Multi-model approach to understand and predict past and future dengue epidemic dynamics Open

Cathal Mills, Francesca Falconi‐Agapito, Jean‐Paul Carrera, César V. Munayco, Moritz U. G. Kraemer , et al. · 2025

Understanding the past, current and future dynamics of dengue epidemics is challenging yet increasingly important for global public health. Using data from northern Peru across 2010–2021, we introduce a multi-model approach that integrates…

Climate-driven rodent infection dynamics align with Lassa fever seasonality in humans Open

Gregory Milne, Lauren A. Attfield, Joachim Mariën, Lucinda Kirkpatrick, Herwig Leirs , et al. · 2025

Lassa fever (LF), caused by Lassa mammarenavirus (LASV), imposes a major public health burden in West Africa. The Natal multimammate mouse ( Mastomys natalensis , MN) is the principal reservoir, yet the extent to which host dynamics shape …

Non-linear age dynamics of malaria infection and fine-scale environmental exposure in rural Uganda Open

Monica Lang, V. Tuhaise, Aisha Nakato, Ally Mohamed, Betty Nabatte , et al. · 2025

Background Age-specific patterns of malaria are well-established for children aged < 5 years. Less understood is the epidemiology of malaria in older children and adults, and the influence of granular environmental risk. Methods We analyze…

The benefits of smart farming: broiler chicken welfare is indicated earlier and more accurately with automated measurements of flock behaviour Open

Marian Stamp Dawkins, Stephen A. Ellwood, Stephen Roberts, Katherine Barger Weathers, Christl A. Donnelly · 2025

A Bayesian model for repeated cross-sectional epidemic prevalence survey data Open

Nicholas Steyn, Marc Chadeau‐Hyam, Paul Elliott, Christl A. Donnelly · 2025

Epidemic prevalence surveys monitor the spread of an infectious disease by regularly testing representative samples of a population for infection. State-of-the-art Bayesian approaches for analysing epidemic survey data were constructed ind…

Continuous football player tracking from discrete broadcast data Open

Matthew J. Penn, Christl A. Donnelly, Samir Bhatt · 2025

Player tracking data remain out of reach for many professional football teams, as their video feeds are not sufficiently high quality for computer vision technologies to be used. To help bridge this gap, we present a method that can estima…

Deep learning from videography as a tool for measuring E. coli infection in poultry Open

Neil Scheidwasser, Louise Ladefoged Poulsen, Prince Ravi Leow, Mark P. Khurana, Maider Iglesias‐Carrasco , et al. · 2025

Poultry farming is threatened by regular outbreaks of Escherichia coli ( E. coli ) that lead to significant economic losses and public health risks. However, traditional surveillance methods often lack sensitivity and scalability. Early de…

Rapid Spread of African Swine Fever Across Borneo Open

Olivia Daniel, Sui Peng Heon, Christl A. Donnelly, Henry Bernard, C. David L. Orme , et al. · 2025

African Swine Fever (ASF) reached the island of Borneo at the end of 2020. The first mortalities were recorded in wild bearded pigs (Sus barbatus) in Sabah, north-east Borneo. The virus then began to spread across the island but due to COV…

Unreadable, Unfindable, and Incomplete: Evaluating PREA Information in State Correctional Handbooks Open

Jessie L. Krienert, Jeffrey A. Walsh, Christl A. Donnelly · 2025

A Primer on Inference and Prediction With Epidemic Renewal Models and Sequential Monte Carlo Open

Nicholas Steyn, Kris V. Parag, Robin N. Thompson, Christl A. Donnelly · 2025

Renewal models are widely used in statistical epidemiology as semi‐mechanistic models of disease transmission. While primarily used for estimating the instantaneous reproduction number, they can also be used for generating projections, est…

GLANCE: Graph Logic Attention Network with Cluster Enhancement for Heterophilous Graph Representation Learning Open

Zhongtian Sun, Anoushka Harit, Alexandra I. Cristea, Christl A. Donnelly, Píetro Lió · 2025

Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data but often struggle on heterophilous graphs, where connected nodes differ in features or class labels. This limitation arises from ind…

From metric to action: An evaluation framework to translate infectious disease forecasts into policy decisions Open

Cathal Mills, Nicholas J. Irons, Joseph L.-H. Tsui, Sarah Sparrow, Luiz Max Carvalho , et al. · 2025

Like weather, energy and other areas of society, forecasts and decisions for infectious disease outbreaks are often critical. The difficult and consequential decisions are made under considerable time and societal pressure and in the face …

The Mathematics of Serocatalytic Models With Applications to Public Health Data Open

Everlyn Kamau, Junjie Chen, Sumali Bajaj, Nicolás Torres, Richard Creswell , et al. · 2025

Serocatalytic models are powerful tools which can be used to infer historical infection patterns from age‐structured serological surveys. These surveys are especially useful when disease surveillance is limited and have an important role t…

The time- and space-varying roles of human mobility in shaping urban dengue epidemics Open

Cathal Mills, Geziel dos Santos de Sousa, Antonio S. Lima Neto, Vasco Furtado, Sen Pei , et al. · 2025

Dengue outbreaks continue to cause large morbidity and mortality globally. Previous work has shown that human movement alongside weather, climatic, ecological, and socioeconomic factors influence outbreak size, persistence, and geographica…

A Bayesian model for repeated cross-sectional epidemic prevalence survey data Open

Nicholas Steyn, Marc Chadeau‐Hyam, Paul Elliott, Christl A. Donnelly · 2025

Epidemic prevalence surveys monitor the spread of an infectious disease by regularly testing representative samples of a population for infection. State-of-the-art Bayesian approaches for analysing epidemic survey data were constructed ind…

How COVID-19 affected academic publishing: a 3-year study of 17 million research papers Open

Matthew Whitaker, Sabrina Rodrigues, Graham Cooke, Bérangère Virlon, Christl A. Donnelly , et al. · 2025

Background The COVID-19 pandemic induced an unprecedented response from the scientific research community. Previous studies have described disruption of the norms of academic publishing during this time. This study uses an epidemiological …

Proactive One-Health surveillance reveals novel orthobunyaviruses and their potential vectors and reservoirs Open

Jean‐Paul Carrera, Carlos Lezcano-Coba, Josefrancisco Galué, William Marciel de Souza, Weng M. Ng , et al. · 2025

Mosquito-borne viruses pose a significant, global threat to human and animal health. Traditionally, arthropod-borne virus (arbovirus) surveillance has been retroactive following an outbreak, which limits the ability to predict and prevent …

Artificial intelligence for modelling infectious disease epidemics Open

Moritz U. G. Kraemer, Joseph L.-H. Tsui, Serina Chang, Spyros Lytras, Mark P. Khurana , et al. · 2025

Flux-growth synthesis and structural characterization of R 6Nb4Al43 (R = Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) Open

Shrenik Patha, S. B. Bhatt, Daniel S. Tortorella, Christl A. Donnelly, Svilen Bobev · 2025

Presented are the flux-growth synthesis and the structural characterization of the series of ternary aluminides R 6 Nb 4 Al 43 , with R representing the rare-earth elements Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu. Although not new compounds…

Generalised Bayesian distance-based phylogenetics for the genomics era Open

Matthew J. Penn, Neil Scheidwasser, Mark P. Khurana, Christl A. Donnelly, David A. Duchêne , et al. · 2025

As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient, b…

Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach Open

Matthew J. Penn, Neil Scheidwasser, Christl A. Donnelly, David A. Duchêne, Samir Bhatt · 2025

The Mathematics of Serocatalytic Models with applications to public health data Open

Everlyn Kamau, Junjie Chen, Sumali Bajaj, Nicolás Torres, Richard Creswell , et al. · 2025

Serocatalytic models are powerful tools which can be used to infer historical infection patterns from age-structured serological surveys. These surveys are especially useful when disease surveillance is limited and have an important role t…

Strategies to Increase Response Rate and Reduce Nonresponse Bias in Population Health Research: Analysis of a Series of Randomized Controlled Experiments during a Large COVID-19 Study Open

Christina Atchison, Nicholas Gilby, Galini Pantelidou, Sam Clemens, Kevin Pickering , et al. · 2025

Background High response rates are needed in population-based studies, as nonresponse reduces effective sample size and bias affects accuracy and decreases the generalizability of the study findings. Objective We tested different strategie…

Climate-based modelling and forecasting of dengue in three endemic departments of Peru Open

Cathal Mills, Christl A. Donnelly · 2024

Amid profound climate change, incidence of dengue continues to rise and expand in distribution across the world. Here, we analysed dengue in three coastal departments of Peru which have recently experienced public health emergencies during…

Deep learning from videography as a tool for measuring E. coli infection in poultry Open

Neil Scheidwasser, Louise Ladefoged Poulsen, Prince Ravi Leow, Mark P. Khurana, Prince Ravi Leow , et al. · 2024

Poultry farming is threatened by regular outbreaks of Escherichia coli ( E. coli ) that lead to significant economic losses and public health risks. However, traditional surveillance methods often lack sensitivity and scalability. Early de…

Public reporting guidelines for outbreak data: Enabling accountability for effective outbreak response by developing standards for transparency and uniformity Open

Vanessa Grégoire, Alex W Zhu, Catherine Brown, John S. Brownstein, Denise M. Cardo , et al. · 2024

Currently, there are few standards for what essential information about an infectious disease outbreak should be reported to the public and when. The content and timeliness of public reporting (e.g. situation reports) is at the discretion …

COVID-19 testing and reporting behaviours in England across different sociodemographic groups: a population-based study using testing data and data from community prevalence surveillance surveys Open

Sumali Bajaj, Siyu Chen, Richard Creswell, Reshania Naidoo, Joseph L.-H. Tsui , et al. · 2024

Multi-model approach to understand and predict past and future dengue epidemic dynamics Open

Cathal Mills, Moritz U. G. Kraemer, Christl A. Donnelly · 2024

Understanding the past, current, and future dynamics of dengue epidemics is challenging yet increasingly important for global public health. Using data from northern Peru across 2010 -- 2021, we introduce a multi-model approach that integr…

The utility of wastewater surveillance for monitoring SARS-CoV-2 prevalence Open

Cathal Mills, Marc Chadeau‐Hyam, Paul Elliott, Christl A. Donnelly · 2024

Public health authorities have increasingly used wastewater-based epidemiology (WBE) to monitor community transmission of SARS-CoV-2 and other agents. In this study, we evaluate the utility of WBE during the COVID-19 pandemic in England fo…

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