Chris Banks
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banks.ac
Chris Banks
@banks.ac
800 followers 1.2K following 16 posts
💻 Computer Scientist, 📈 Computational/Mathematical Modeller, 🦠 Infectious Disease Modeller,🔬Research Fellow / Core Scientist, 🐑 Roslin Institute, 🏰 University of Edinburgh, 🌄 Mountaineer, 🚲 Cyclist, 🤓 Geek.
🔗 https://banks.ac/
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Reposted by Chris Banks
rowlandkao.bsky.social
As one of the "we" very pleased to be part of this initiative. Thanks to @helcecilia.bsky.social @paulineezanno.bsky.social and @gaelbn.bsky.social for taking the lead on this one.
helcecilia.bsky.social Hélène Cecilia, PhD @helcecilia.bsky.social · Oct 18
I'm not very active here but I figured this would probably (hopefully?) interest some of you :
We recently launched an international consortium of modelers in animal health, called ModAH Hub
www.modah-hub.com
🦠💻🐄🐖🐓🦟
ModAH Hub
An international network to federate the scientific community working on epidemiological modelling in animal health.
www.modah-hub.com
October 22, 2025 at 11:42 AM
Reposted by Chris Banks
adamjkucharski.bsky.social
Results so stunningly clear they inspired this classic xkcd (xkcd.com/2400/):
September 1, 2025 at 7:32 PM
Reposted by Chris Banks
iddconf.bsky.social
Jon Read kicking things off at IDDconf 2025 telling us neat things about contact patterns in England during the COVID pandemic.
September 2, 2025 at 2:48 PM
Reposted by Chris Banks
iddconf.bsky.social
Fab day at IDDconf 2025
We’ve seen a lot of great talks and just before the poster session and reception, Martin Wolfender from @unibe.ch is telling us about forecasting hospital bed use.
September 2, 2025 at 4:42 PM
Reposted by Chris Banks
netscience.bsky.social
Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding www.nature.com/articles/s41...
Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding - Nature Communications
Epidemiological estimates from wastewater are not biased by testing rates but may be subject to other biases. Here, the authors investigate the impact of variable virus shedding profiles for different...
www.nature.com
August 14, 2025 at 6:44 AM
Reposted by Chris Banks
uoe-eid.bsky.social
New review shows the need to focus on antibiotic resistance in the environment 🌏🔬

Antibiotic resistance in the environment is not well studied, which may have consequences for human health, according to research.

edinburgh-infectious-diseases.ed.ac.uk/news/latest-...
New review shows the need to focus on antibiotic resistance in the environment | Edinburgh Infectious Diseases | Edinburgh Infectious Diseases
August 2025: A recent review has found that research into AMR in the environment needs to extend beyond wealhty countries and freshwater settings.
edinburgh-infectious-diseases.ed.ac.uk
August 8, 2025 at 11:02 AM
Reposted by Chris Banks
rlsdvm.bsky.social
9% believe and 39% unsure that the rabies vx causes dog autism?!?!

BTW, dog autism isn't a thing.
carlzimmer.com Carl Zimmer @carlzimmer.com · Aug 7
Snapshot of US beliefs about science and flat-earthy stuff. [1000+ people surveyed, +/- 3%] carsey.unh.edu/publication/...
A graph showing agreement with various statements about science as well as conspiracy theories
August 7, 2025 at 5:50 PM
Reposted by Chris Banks
sheencr.bsky.social
Really welcome news as a farmer led program working with scientists to vaccinate badgers for TB rather than cull is to start. There is little evidence that culling reduces TB in cows but vaccine trials reduce TB in badgers from 16 down to 0% in prior trial
Farmers and scientists join forces in Cornwall to vaccinate badgers against TB
The groups have long been at odds over culling of badgers in England as a way to control TB in cattle
www.theguardian.com
August 1, 2025 at 7:09 AM
Reposted by Chris Banks
gamerstavernshow.com
If you want a weird but true fact to talk about:

Dexter Holland, lead singer of The Offspring, was instrumental in this. His doctorial thesis in molecular biology was sequencing mRNA in HIV. The paper was also heavily cited in creating the COVID-19 vaccine.
faineg.bsky.social Faine Greenwood @faineg.bsky.social · Aug 1
It feels like we should be making a bigger deal of “we actually did in fact find a cure for AIDS”
wired.com WIRED @wired.com · Aug 1
Evidence is growing that some HIV-infected infants, if given antiretroviral drugs early in life, are able to suppress their viral loads to undetectable levels and then come off the medicine. www.wired.com/story/the-fi...
August 1, 2025 at 1:53 PM
Reposted by Chris Banks
netscience.bsky.social
Inferring contact network characteristics from epidemic data via compact mean-field models arxiv.org/abs/2502.12040
Inferring contact network characteristics from epidemic data via compact mean-field models
Modelling epidemics using contact networks provides a significant improvement over classical compartmental models by explicitly incorporating the network of contacts. However, while network-based mode...
arxiv.org
February 19, 2025 at 8:41 AM
Reposted by Chris Banks
netscience.bsky.social
Optimal control prevents itself from eradicating stochastic disease epidemics journals.plos.org/ploscompbiol...
Optimal control prevents itself from eradicating stochastic disease epidemics
Author summary Improving epidemic outcomes in situations with limited resources for control is important across human, animal and plant health. An example of this type of optimisation is deciding whic...
journals.plos.org
February 19, 2025 at 8:49 AM
Reposted by Chris Banks
netscience.bsky.social
Artificial intelligence for modelling infectious disease epidemics www.nature.com/articles/s41...
Artificial intelligence for modelling infectious disease epidemics - Nature
This Perspective considers the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.
www.nature.com
February 20, 2025 at 9:12 AM
Reposted by Chris Banks
netscience.bsky.social
Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens journals.plos.org/ploscompbiol...
Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens
Author summary Invasive pathogens pose a substantial challenge to human health, particularly as outbreak risks for some infectious diseases are being exacerbated by climate change. For example, the oc...
journals.plos.org
February 20, 2025 at 9:21 AM
Reposted by Chris Banks
spokes.org.uk
#A702 #EasterBush

Oct 2024: we objected to zero 🚲 consideration in new planned 3-arm roundabout near @edinburgh-uni.bsky.social campus

👍They are listening! (so far)

@edi.bike @chdot.bsky.social @uoe-eid.bsky.social @alow.bsky.social @debbimccall.bsky.social @banks.ac @kirstymcneill.bsky.social
map of proposed roundabout spokes objection cyclists will now be considered - no details yet
January 20, 2025 at 10:38 AM
Reposted by Chris Banks
netscience.bsky.social
Estimates of the reproduction ratio from epidemic surveillance may be biased in spatially structured populations arxiv.org/abs/2307.13798
Estimates of the reproduction ratio from epidemic surveillance may be biased in spatially structured populations
Accurate estimates of the reproduction ratio are crucial to project infectious disease epidemic evolution and guide public health response. Here, we prove that estimates of the reproduction ratio base...
arxiv.org
January 9, 2025 at 8:40 AM
Reposted by Chris Banks
netscience.bsky.social
DeepTrace: Learning to Optimize Contact Tracing in Epidemic Networks with Graph Neural Networks arxiv.org/abs/2211.00880
DeepTrace: Learning to Optimize Contact Tracing in Epidemic Networks with Graph Neural Networks
Digital contact tracing aims to curb epidemics by identifying and mitigating public health emergencies through technology. Backward contact tracing, which tracks the sources of infection, proved cruci...
arxiv.org
January 14, 2025 at 8:09 AM
banks.ac
Merry Christmas! The tradition of spending Christmas Eve at RZSS Edinburgh Zoo continues. Enjoy a few pics...
Grandma drill Red panda Cotton-top tamarin Haggis the baby pygmy hippo
December 24, 2024 at 10:49 PM
Reposted by Chris Banks
adamjkucharski.bsky.social
Academic institutions: “We’ve got to maintain a presence on X because that’s where the journ…. oh.”
danvalen.com Dan Valen @danvalen.com · Dec 16
As of today, @plos.org (and all of its journals) will no longer be posting to The Bad Place™️ #academicsky
December 17, 2024 at 7:43 AM
Reposted by Chris Banks
netscience.bsky.social
Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios journals.plos.org/ploscompbiol...
Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios
Author summary As human contacts and contact networks are key to the development and prediction of infectious disease spread, travel and commuting activities are important components to be considered ...
journals.plos.org
December 17, 2024 at 5:02 PM
banks.ac
"The model leads to insights that may be relevant to other, less fictitious, emergency situations." 🧟‍♀️
December 11, 2024 at 8:20 PM
Reposted by Chris Banks
edmhill.bsky.social
📣 #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.
December 11, 2024 at 7:34 PM
Reposted by Chris Banks
rozeggo.bsky.social
Finishing 2024 on a high note: delighted to be appointed Professor at LSHTM.

Thanks to many many people for support & advice along the way. 🙏

Looking forward to more exciting research, collaborations with amazing scientists, work with my fantastic team & PPIE colleagues.

Exciting times ahead! 🎉
Picture of the London School of Hygiene & Tropical Medicine with Logo on top.
December 9, 2024 at 4:20 PM
Reposted by Chris Banks
netscience.bsky.social
Latest out: Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach. Great collaboration with Nicolo Gozzi @mattk7.bsky.social @jessica-davis.bsky.social Kunpeng Mu Ana Pastore Marco Ajelli @alexvespi.bsky.social www.sciencedirect.com/science/arti...
December 5, 2024 at 1:53 PM
Reposted by Chris Banks
tiago.skewed.de
Good news everyone! A new version of graph-tool is just out! @graph-tool.skewed.de

graph-tool.skewed.de

Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N

#networkscience
December 2, 2024 at 12:55 PM
Reposted by Chris Banks
netscience.bsky.social
Modelling plausible scenarios for the Omicron SARS-CoV-2 variant from early-stage surveillance arxiv.org/abs/2211.13704
Modelling plausible scenarios for the Omicron SARS-CoV-2 variant from early-stage surveillance
We used a spatially explicit agent-based model of SARS-CoV-2 transmission combined with spatially fine-grained COVID-19 observation data from Public Health Scotland to investigate the initial rise of ...
arxiv.org
December 3, 2024 at 8:35 AM