It was absolutely wonderful to write something again with @skissler.bsky.social, @danlarremore.bsky.social and Aishani Aatresh. Here's our new review/perspective on the value of measuring and modelling viral kinetics as part of routine surveillance: royalsocietypublishing.org/rstb/article...

Delighted to share the (preprint) output of @mhairijan.bsky.social's Oxford visit: SARS-CoV-2 Neutralising Antibody Profiles Reveal Variant Specific Antibody Dynamics and Regional Differences in Infection Histories in Malawi. dx.doi.org/10.2139/ssrn...

The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠 www.science.org/stoken/autho...

Great take. We looked at the data a few weeks ago and concluded that other than starting early, this year's dynamics are comparable to previous bad seasons. Our scenario models suggest a peak in infections (not hospitalisations which lag 1/2 weeks) in early/mid December. zenodo.org/records/1770...

🧵 Is it a super flu year? Who knows, but I think the current reporting is stupid. A pissed off thread using data. Firstly - here are today's headlines and some from the last 3 years... spot the difference. 1/10

WHO Disease Update Notification: Seasonal influenza 🦠Since August 2025, there's been a rapid increase of A(H3N2) J.2.4.1 subclade K driving early & prolonged seasons 🦠Vaccine helps against hospitalisation, unclear about milder impact 🦠K induces "normal" disease spectrum www.who.int/emergencies/...

Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets journals.plos.org/ploscompbiol...

H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770.... (1/18)

In Texas' public health region 6/5S, which includes Houston, the number of emergency department visits for influenza is already almost on par with the *peak* of last year.

Now out in @natcomms.nature.com Kudos to @tylim.bsky.social and @jameshay.bsky.social for a huge effort and thanks to all the collaborators for their hard work. See the final version here: www.nature.com/articles/s41...

New study shows that shifts in SARS‑CoV‑2 Ct value distributions can help nowcast epidemic trends, revealing both strong potential and key real‑world limitations for Ct‑based surveillance. From CCDD alumni TY Lim & @jameshay.bsky.social and faculty @yhgrad.bsky.social at bit.ly/4o37EaN

🚨 New paper out in PLOS Computational Biology! 🚨 We're excited to share our new paper, serojump, a new probabilistic framework and R package for inferring infections and antibody kinetics from longitudinal serological data. 📄 Full paper: tinyurl.com/re7du3t2 R package: seroanalytics.org/serojump

Closing date tomorrow!

Excited to share our paper on viral load dynamics of West Nile virus in mosquitoes! Key findings: 1. Variation in pooled Ct values from mosquito traps reflect underlying biological and epidemiological mechanisms. 2. WNV prevalence estimates are improved by using Cts rather than +ve/-ve pool status.

We're hiring a modelling postdoc at PSI Oxford for two exciting projects: 1) modelling the early immune responses to Nipah vaccination, and 2) joining the PRESTO team working on immunobridging in vaccine evaluation studies. tinyurl.com/5abbxrjh Get in touch for more info! Deadline 4th August.

Excited to share our paper on viral load dynamics of West Nile virus in mosquitoes! Key findings: 1. Variation in pooled Ct values from mosquito traps reflect underlying biological and epidemiological mechanisms. 2. WNV prevalence estimates are improved by using Cts rather than +ve/-ve pool status.

Our latest paper www.sciencedirect.com/science/arti... shows that mass PCR testing could control a range of potential respiratory pandemics at low societal cost. We also explore logistics. Even a prototype would be really nice now with H5N1. @jameshay.bsky.social 1/9

Two postdoc positions to work on virus epi & evolution in response to vaccination, with both theoretical models + data analysis. Paris/Montpellier. With Sylvain Gandon, Sébastien Lion, François Blanquart, Katrina Lythgoe, & Troy Day emploi.cnrs.fr/Offres/CDD/U... emploi.cnrs.fr/Offres/CDD/U...

Hello influenza enthusiasts! You may be interested in our recent publication linked below. We used multi-strain serology to figure out who got infected with which A/H3N2 influenza strain and when, allowing us to reconstruct epidemiological patterns back to 1968 stratified by time, age and location.

Are you interested in analysing serological data for infectious disease epidemiology? Check out our new review article on serodynamics! With Saki Takahashi at JHU and Isobel Routledge at UCSF. (See next comment if you're into serology modeling) www.sciencedirect.com/science/arti...

Are you interested in analysing serological data for infectious disease epidemiology? Check out our new review article on serodynamics! With Saki Takahashi at JHU and Isobel Routledge at UCSF. (See next comment if you're into serology modeling) www.sciencedirect.com/science/arti...

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.

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.

NEW EPISODE #ScienceInContext! This week Dr @eonore.bsky.social speaks with Dr @jameshay.bsky.social of the Big Data Institute about influenza: who, where and when influenza infections are likely to occur using antibody profiles and individual infection histories 👇 youtu.be/Ux6yDWO_c8I

Reconstructed influenza A/H3N2 infection histories using multistrain serology, paper out in PLOS Biology plos.io/3YIDQpt! We inferred lifetime infections and antibody levels for 1130 individuals in Guangzhou, China, giving insights into long-term influenza incidence and immunity. Thread below:

New preprint: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course www.medrxiv.org/content/10.1...