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James Munday

@jdmunday.bsky.social

Infectious disease epidemiology and surveillance based in Basel • jdmunday.github.io

81 Posts1685 Follower469 Folgt
Sebastian Funk@sbfnk.bsky.social · 8mo ago

Two more fully funded PhDs in real-time infectious disease modelling & forecasting — developing methods for operational use by @ukhsa.bsky.social and others in outbreak response. UK home students, starting April or September 2026. www.lshtm.ac.uk/study/fees-a...

PhD Studentships in Health Analytics and Modelling | LSHTM

The London School of Hygiene & Tropical Medicine (LSHTM), Imperial College London and the UK Health Security Agency (UKHSA) are pleased to invite applications for two PhD studentships in real-time

lshtm.ac.uk

Gwen Knight@gmknght.bsky.social · 9mo ago

How will population shifts affect the future burden of #AMR? 👶👩‍🦳 🧫 We use a new modelling framework to explore future projections of #AMR by age and by sex, as well as interventions for control, building on our earlier findings that AMR isn’t uniform across demographics. doi.org/10.1371/jour...

Combining demographic shifts with age-based resistance prevalence to estimate future antimicrobial resistance burden in Europe and implications for targets: A modelling study

Author summary Why was this study done? Infections caused by bacteria that are resistant to antibiotics are a major and growing threat to public health. Older adults and men are at higher risk of...

doi.org

James Munday@jdmunday.bsky.social · 10mo ago

Our paper "Forecasting the spatial spread of an Ebola epidemic in real-time: comparing predictions of mathematical models and experts" is now published as a 'version of record' in @elife.bsky.social (with @sbfnk.bsky.social Alicia Rosello and John Edmunds) doi.org/10.7554/eLif... 1/5

Forecasting the spatial spread of an Ebola epidemic in real time: Comparing predictions of mathematical models and experts

Models were more consistent than individual experts but performed comparably to ensembles of many experts and relative performance varied by month, justifying the use of combined model and expert fore...

doi.org

James Munday@jdmunday.bsky.social · 11mo ago

New paper led by Nicolas Banholzer "Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling" Now published in *Influenza and Other Respiratory Viruses* doi.org/10.1111/irv....

Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling

Background Viral respiratory infections contribute to sick days in school children. We monitored respiratory infections, absences, and symptoms in a Swiss school. Methods Serial saliva sampling (t...

doi.org

James Munday@jdmunday.bsky.social · 11mo ago

New Preprint 💫: *Projected sudden step-wise increase in risk of large measles outbreaks in the Netherlands as susceptible children enter secondary school in 2025/26* on MedRxiv doi.org/10.1101/2025... (NOT YET PEER REVIEWED)

Projected sudden step-wise increase in risk of large measles outbreaks in the Netherlands as susceptible children enter secondary school in 2025/26

Background Many unvaccinated children were naturally immunised through infection during the last national Measles epidemic in the Netherlands (2013/14). Over time susceptibility amongst school aged ch...

doi.org

Jana Huisman@jhuisman.bsky.social · 12mo ago

Our paper on the transmission dynamics of Noro- and Enterovirus during the COVID-19 pandemic just came out: www.sciencedirect.com/science/arti... We measured wastewater viral loads, estimated Re and assessed the impact of non-pharmaceutical interventions on the transmission of these pathogens.

Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater

Noroviruses and enteroviruses are major causes of endemic gastrointestinal disease associated with substantial disease burden. However, viral gastroen…

sciencedirect.com

James Munday@jdmunday.bsky.social · 12mo ago

New Preprint! Co-led with Nicolas Banholzer *The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools* on MedRxiv. doi.org/10.1101/2025... (YET TO BE PEER REVIEWED)

The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools.

Close-proximity interactions are considered a key risk factor for respiratory virus transmission, but their importance relative to shared space and air quality remains unclear. We conducted a six-week...

doi.org

Tanja Stadler@tanjastadler.bsky.social · last yr.

In this project led by James Munday, we quantified the post-sampling degradation of viral RNA in wastewater. Taking into account this degradation is core towards unbiased quantification of epidemiological dynamics based on wastewater data.

James Munday@jdmunday.bsky.social · last yr.

We have a new preprint 📝 *Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates* Now on bioRxiv doi.org/10.1101/2025... with @tanjastadler.bsky.social, trj2.bsky.social, Christoph Ort and others

James Munday@jdmunday.bsky.social · last yr.

We have a new preprint 📝 *Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates* Now on bioRxiv doi.org/10.1101/2025... with @tanjastadler.bsky.social, trj2.bsky.social, Christoph Ort and others

Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates

Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the...

doi.org

James Munday@jdmunday.bsky.social · last yr.

New preprint 📝. We used a bayesian time-series model to quantify contributions of various factors to variation in the SARS-CoV-2 concentration in 🇨🇭 wastewater. We then analyse geographic correlations in adjusted conc. using DTW distances. doi.org/10.1101/2025...

Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: key insights for future surveillance efforts

Background: Wastewater-based surveillance (WBS) has emerged as a valuable tool for monitoring the circulation of infectious pathogens in the population, offering a complement to classical surveillance...

doi.org

IDDjobs@iddjobs.org · 2y ago

Other (Barcelona, Spain) We seek a highly motivated data scientist to co-create harmonised datasets and dashboards for decision-support. More details: http://iddjobs.org/jobs/we-seek-a-highly-motivated-data-scientist-to-co-create-harmonised-datasets-and-dashboards-for-decision-support

Dr Edward Hill@edmhill.bsky.social · 2y ago

📣 #fundedPhD in "Modelling salivo-surveillance for detecting population immunity, transmission dynamics & changes in vaccine effectiveness" #IDsky #EpiSky #PhDSky 🧪 👥 Supervised by @3113n.bsky.social + colleagues at Uni. of Bristol & UKHSA 🗓️ Closes 27 Jan 2025. Interviews Mar 2025. Start Sep 2025.

About the Project. Vaccination is a highly effective public health intervention that prevents morbidity and mortality. The UK vaccination programme evolves in response to vaccine developments and emerging evidence. This may include the addition of new vaccines, or removal of old vaccines or booster doses. Following a modification to the vaccine schedule, there is a delay before the impact on key indicators such as diagnosed cases, hospital admissions and deaths is observed. This delay hampers the responsiveness of public health action. We are developing saliva-based tests that will facilitate rapid, repeated sampling to measure both carriage of respiratory pathogens and mucosal immunocorrelates, and thus detect changes in population immunity before disease cases present. The aim of these tests is to develop a surveillance programme that will provide an early warning system for lapses in population-level protection and allow for adaptive management of the UK vaccine schedule.Project aims: The aim of this PhD is to use data analytics, data linkage and mathematical models to inform the use and necessary test characteristics of saliva-based tests for vaccination evaluation. The aims of the project are to: - Develop transmission models for vaccine-preventable respiratory pathogens (Streptococcus pneumoniae and Respiratory Syncytial Virus) and emerging threats (Group A Streptococcus) in the UK. - Identify opportunities for early identification of changes in population immunity that would provide a rapid assessment of vaccine effectiveness and coverage. - Explore the trade-offs involved in detecting population protection. Methods: This PhD will use data analysis, statistical and mathematical modelling to inform the use of a rapid and scalable test to measure changes in vaccine coverage and population protection. The methods will involve data analysis, visualisation and code development using software such as R, describing immunological process of transmission mathematically, reviewing and interpreting the literature and working with and maintaining an inter-disciplinary network of collaborators. In year 1, you will work with immunologists to use immunological data to develop data-driven mathematical models of the dynamics of transmission, carriage and infection for respiratory infectious diseases. In year 2, you will design models that link vaccination, disease transmission, carriage and healthcare usage. In year 3, you will explore the impact of changes to the vaccine schedule on population immunity and subsequently invasive disease and determine the necessary test uptake and characteristics needed to provide an early indication of changes to population immunity. There will be scope for the successful candidate to shape the research.Supervisors: Professor Ellen Brooks-Pollock, Dr Anu Goenka, Dr Mary Ramsay (UKHSA) & Dr Bassam Hallis (UKHSA). Advisory team: Dr Rajeka Lazarus, Dr Clare French, Dr Amy Thomas, Dr Leon Danon, Dr Alice Halliday. Candidate requirements: This is a unique opportunity for a quantitative scientist to join a multi-disciplinary team and work closely with clinicians, lab scientists and policymakers. Applications are sought from high performing individuals who have, or are expected to obtain, at least a 2.1 degree (or equivalent) in a quantitative subject (e.g. maths, statistics, physics, computer science, biological sciences) together with an interest in public health and multi-disciplinary research. Possession of a relevant Master's degree or research experience would be advantageous but is not required. We welcome applications from those with non-standard qualifications who can demonstrate knowledge, experience and skills developed in the workplace, or elsewhere, relevant to the programme of study.How to apply: When applying, candidates must search for and select the ‘Population Health Sciences PhD’ programme and enter supervisor names as listed under the project title for which they are applying. Please state Health Protection Research Unit in Evaluation and Behavioural Science in the funding box. Full details on what to include in your application can be found in the Admissions Statement. Personal statement: Please provide a personal statement that describes your training and experience so far, your motivation for doing a PhD, your motivations for applying to the University of Bristol, and why you think we should select you. We are keen to support applicants from minority and under-represented backgrounds (based on protected characteristics) and those who have experienced other challenges or disadvantages. We encourage you to use your personal statement to ensure we can take these factors into account. Funding Notes: The studentship is fully funded by Health Protection Research Unit in Evaluation and Behavioural Science (HPRU-EBS) for three years. The funding covers tuition fees for home students and a stipend at the UKRI rate (£19,237 in 2024/2025). Overseas students are very welcome to apply, please include in your application if you are able pay the difference between the home and overseas fees. If you are unable to cover these costs, we can look into other options to cover these. Deadline: Applications for this project will close at 16:00 GMT on Monday 27th January 2025. Interviews will be in March 2025 . The anticipated start date is September 2025. Contact: If you have questions about the project, please contact the supervisors. If you need help with your application, contact admissions at fohs-pgadmissions@bristol.ac.uk.
Ellen Brooks Pollock@3113n.bsky.social · 2y ago

We are advertising an exciting PhD position with a super team: Modelling salivo-surveillance for vaccine programmes. Happy to answer questions. With @anu_goenka @leondanon.bsky.social @rajlaz.bsky.social www.findaphd.com/phds/project...

IDDjobs@iddjobs.org · 2y ago

Postdoc (Berlin, Germany) Vaccine or outbreak modelling. With Stefan Flasche at @cmmid More details: http://iddjobs.org/jobs/experienced-postdoc-in-vaccine-or-outbreak-modelling

Justin Lessler@justinlessler.bsky.social · 2y ago

Congrats to team member Carl Pearson and his co-authors @lucygoodfellow.bsky.social and @mert0248.bsky.social. An important tool for a pervasive problem in modeling infectious disease data www.medrxiv.org/content/10.1...

paramix : An R package for parameter discretisation in compartmental models, with application to calculating years of life lost

Compartmental infectious disease models are used to calculate disease transmission, estimate underlying rates, forecast future burden, and compare benefits across intervention scenarios. These models ...

medrxiv.org

Anne Cori@anne-cori.bsky.social · 2y ago

A group of us have been working on creating a repository of models and epidemiological parameters ready-to-use in future epidemics, with a focus on high-threat pathogens. Today our Lassa review is out: www.sciencedirect.com/science/arti.... More on the overall project here: bit.ly/imperial-PERG

Lassa fever outbreaks, mathematical models, and disease parameters: a systematic review and meta-analysis

Understanding the epidemiological parameters and transmission dynamics of Lassa fever, a significant public health threat in west Africa caused by the…

sciencedirect.com