iiinova — where your digital self keeps evolving

Reposted by James Munday

Tanja Stadler @tanjastadler.bsky.social · 20/02/2026

We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!

ethz.ch

Assistant Professor (Tenure Track) of Computational Immunology

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James Munday @jdmunday.bsky.social · 05/02/2026

Our paper modelling transmission risk in schools is published in Nature Communications. **The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools** doi.org/10.1038/s414...

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Sebastian Funk @sbfnk.bsky.social · 17/12/2025

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...

lshtm.ac.uk

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

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IDDjobs @iddjobs.org · 04/12/2025

PhD position (Allschwil, Switzerland) Forecast the spread and impact of resistance, guiding the optimal use of new insecticide-treated nets. with Adrian Denz at Swiss Tropical and Public Health Institute More details: iddjobs.org/jobs/2429

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James Munday @jdmunday.bsky.social · 04/12/2025

Super cool PhD position up for grabs in our group with @adriandenz.bsky.social. Come and join us to study insecticide resistance in 🦟

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Adrian Denz @adriandenz.bsky.social · 04/12/2025

🌟 Hiring a PhD student! 🌟 📍 Swiss TPH, Basel Model insecticide-resistance spread and its impact on malaria control. Quantitative skills (Bayesian, ML, stats) and biology (evolution, genetics) needed. 👉 Apply: jobs.swisstph.ch/Vacancies/11...

jobs.swisstph.ch

PhD Student in Forecasting Resistance Spread and Epidemiological Impact (100%) - Swiss TPH

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James Munday @jdmunday.bsky.social · 25/11/2025

New Paper 🍃! *Projected increase in risk of large measles outbreaks in the Netherlands as susceptible children enter secondary school in 2025/26* out now in the International Journal of Infectious Diseases doi.org/10.1016/j.ij...

doi.org

Redirecting

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Gwen Knight @gmknght.bsky.social · 05/11/2025

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...

doi.org

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...

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James Munday @jdmunday.bsky.social · 04/11/2025

New Paper🚀! Our work analysing the Swiss national SARS-CoV-2 wastewater 🚱 monitoring data is now published in PLOS Water 💧 @plos.org journals.plos.org/water/articl... (Julien Riou, @tanjastadler.bsky.social @trj2.bsky.social Christoph Ort et al)

Fig 3. (A) Adjusted time trends in SARS-CoV-2 wastewater viral load in seven regions of Switzerland (uncertainty is not shown for clarity).

(B) Correlation between adjusted time trends in viral load and laboratory-confirmed SARS-CoV-2 hospitalisations in the same region. (C) Adjusted bias in viral load by wastewater treatment plant.

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Jana Huisman @jhuisman.bsky.social · 22/08/2025

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.

sciencedirect.com

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…

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James Munday @jdmunday.bsky.social · 12/07/2025

Just when you think you are beginning to understand a sport...

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Reposted by James Munday

Dr Edward Hill @edmhill.bsky.social · 17/06/2025

📣 Funded 3.5yr PhD opportunity (UK tuition fee rate) in @hpruezi.bsky.social @liverpooluni.bsky.social. #PhDSky 🧪 On "Optimising testing & control strategies in the early stages of infectious disease outbreaks" #IDSky #EpiSky ⏳ Deadline to apply: 07 Jul 2025 🔗: www.liverpool.ac.uk/courses/opti...

Optimising testing and control strategies in the early stages of infectious disease outbreaks

Supervisors: Dr Emily Nixon, Professor Christl Donnelly, Dr Richard Vipond, Dr Emily Adams, Dr Chris Overton.

Subject area: Mathematics

Stipend Amount: Funded studentship
Study mode: Full-time
Duration: 3.5 years

Application deadline: 07 July 2025
Start date: 01 October 2025

Overview
Develop models to help make decisions early in a major disease outbreak when availability of new tests is limited, on where and how best to use them for maximum impact in controlling spread, e.g. in low versus high areas of transmission, in hospitals or in the community. These will depend on the pathogen type, its mode of transmission, reproduction number, etc.

About this opportunity
In the early stages of a major disease outbreak, the availability of suitable diagnostic tests is often limited, however, timely interventions are critical for controlling the spread of disease. In this PhD, you will develop mechanistic and statistical models to investigate the effectiveness of various diagnostic test deployment strategies for emerging and zoonotic diseases which are at risk of causing large outbreaks, such as respiratory viruses (Influenza, SARS-CoV-2, Respiratory syncytial virus), vector-borne diseases (Dengue, Tick-borne encephalitis) or viral haemorrhagic fevers (Nipah, Lassa fever and Crimean-Congo haemorrhagic fever). You will investigate the effectiveness of targeting use of tests in different settings, for example in areas of high versus low transmission, or in hospitals versus the community. The optimum strategy for diagnostic test deployment will vary depending on prevalence of disease, the sensitivity and specificity of the tests and the time it takes to receive and act on results. In addition, variation between pathogens, for example, in their mode of transmission, reproduction number and incubation period, will influence which strategy is the most effective in controlling the impact of the outbreak. These insights will inform stockpiling strategies of medical countermeasures for pandemic preparedness and in the event of a major outbreak, can be used and adapted to help inform decision making.

Who is this for?

Applicants must hold, in a relevant STEM subject, either a first-class honours degree, a distinction at master level, or equivalent achievements. A background in programming (such as R, Python, Julia) would be advantageous, along with a keen desire to develop those skills.

Prospective applicants are encouraged to contact the primary supervisor, Dr Emily Nixon, emily.nixon@liverpool.ac.uk prior to preparation of an application to discuss the fit of the project with your background and qualifications.

Funding your PhD

This PhD opportunity is funded by the National Institute for Health and Care Research (NIHR) Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections (EZI).

This studentship will be for a maximum of 3.5 years duration. The studentship includes tuition fees at the UK/home rate, stipend and research-related travel. International students may apply but must be able to themselves cover the additional tuition fee costs as outlined on the University website: https://www.liverpool.ac.uk/study/fees-and-funding/tuition-fees/postgraduate-research/.

The supervisory team have no additional funding to support this difference in tuition fee costs for international students. The stipend amount is aligned with UK Research and Innovation rates. For the academic year 2025-2026, the rate of the UKRI Stipend is £20,780 per annum (tax free).

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Reposted by James Munday

Tanja Stadler @tanjastadler.bsky.social · 17/06/2025

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.

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Reposted by James Munday

Sonja Lehtinen @sonjalehtinen.bsky.social · 28/04/2025

Come work with us! We're looking of postdoc(s) with experience in bacterial genomics and interest in mathematical modelling to work on bacterial ecology and evolution in the context of public health. tinyurl.com/n34vzszu

tinyurl.com

Opportunités de carrière : Postdoctoral researcher in bacterial genomics (22209)

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James Munday @jdmunday.bsky.social · 04/04/2025

Check out our new perspective in Epidemics on wastewater surveillance and pandemic prep. It came out of a workshop spearheaded by Kath O'Reilly and @leondanon.bsky.social. What can we do? what could we do better? And when is it most likely to be useful? doi.org/10.1016/j.ep...

doi.org

Redirecting

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Reposted by James Munday

IDDjobs @iddjobs.org · 21/12/2024

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

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Reposted by James Munday

Dr Edward Hill @edmhill.bsky.social · 11/12/2024

📣 #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.

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Reposted by James Munday

IDDjobs @iddjobs.org · 11/12/2024

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

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Pathoplexus @pathoplexus.org · 28/11/2024

We're incredibly honoured to be winners of the Swiss Academies of Arts & Sciences National Prize for Open Research Data 2024! 🎉🎊 "Pathoplexus ensures open access and provides a cutting-edge infrastructure for interactive and programmable data exploration" akademien-schweiz.ch/en/medien/pr... 1/2

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Anne Cori @anne-cori.bsky.social · 21/11/2024

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

sciencedirect.com

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…

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Reposted by James Munday

Chaoran Chen @chaoranchen.de · 25/11/2024

Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5

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James Hay @jameshay.bsky.social · 20/11/2024

New study tracking epidemic dynamics using cycle threshold values (a proxy for viral load) from routine hospital and community testing. This is the next step of our work from 2021 showing that the population distribution of Ct values over time is related to SARS-CoV-2 epidemic growth rates.

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Sebastian Funk @sbfnk.bsky.social · 22/11/2024

If there are any users of the socialmixr R package for estimating contact matrices here: we're planning some substantial changes to the user interface and would love to hear your thoughts/views. Please feel free to comment at github.com/epiforecasts...

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James Munday @jdmunday.bsky.social · 22/11/2024

Had to abandon my bike at a friend's flat last night. I think the towel I put over my saddle did the trick!

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Meaghan Kall @kallmemeg.bsky.social · 15/11/2024

Now seems a good time to collate a list of reputable, trustworthy public health voices. UK Public Health Starter Pack ⤵️ (Work in progress - will add suggestions!) go.bsky.app/Tuf8yqX

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The Institute for Fiscal Studies @theifs.bsky.social · 13/11/2024

NEW: The closure of youth clubs in the 2010s led to increased offending and worse GSCE results. Teenagers entitled to free school meals were most affected. Read @carmenvillaecon’s briefing: buff.ly/4fIiRK7 Read the working paper: buff.ly/3APnHq6

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Thiago Carvalho @cyrilpedia.bsky.social · 28/10/2024

'This study highlights the potential of WBS as a potent tool for gauging the epidemiological landscape of DENV and CHIKV in Portugal, where autochthonous cases have not yet been detected.' www.sciencedirect.com/science/arti...

sciencedirect.com

Detection of dengue virus and chikungunya virus in wastewater in Portugal: an exploratory surveillance study

The global distribution and prevalence of arboviral diseases have increased in recent years, driven by factors such as climate change, biodiversity lo…

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James Munday @jdmunday.bsky.social · 12/09/2024

It has been a real pleasure to engage with the fabulous scientists at #GEOMED24 this week. So much fascinating science and great conversation. And a delight to share and discuss two of my own projects with a smart, rigorous and kind community! Slides here: jdmunday.github.io/index.html#Conferences

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

Title slide: Spatial modelling of viral loads in wastewater: an evaluation of sampling strategies for comprehensive surveillance programmes

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Pathoplexus @pathoplexus.org · 30/08/2024

From Science Magazine: “We believe that building trust through transparency is essential for encouraging broader participation in data sharing,” says Pathoplexus co-founder Anderson Fernandes de Brito @andersonfbrito.bsky.social science.org/content/arti... #Pathoplexus #OpenScience

science.org

New, scientist-run virus database vows to be transparently run and simple to use

Pathoplexus is starting with sequences for Ebola strains and two other risky viruses

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James Munday @jdmunday.bsky.social · 27/08/2024

A very exciting initiative from some colleagues of mine. Excellent platform run by excellent folk!

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