Ryan Teo

As #WorldAMRAwarenessWeek wraps up, we share how respiratory metagenomics is transforming care.

Faster and accurate detection of pathogens help clinicians target treatment sooner and reduce unnecessary antibiotics, whilst improving personalised care and antimicrobial stewardship across the NHS.

We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬

Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)

Papers from the NeurIPS 2025 Workshop on #Biosecurity Safeguards for Generative AI: doi.org/10.59350/ep7... 🧬🖥️🧪

ECR connection: Meet Meren when you need to A means for ECRs to get advice from a senior scientist outside of their support network

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.

Here is a blog that explains my motivation for this and how to schedule a meeting:

merenlab.org/2025/11/16/E...

Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...

Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?

That is the question we asked in our latest pre-print.

Turns out you can.
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www.medrxiv.org/content/10.1...

Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to ge...

How to design new synthetic microbial communities? It's a huge question we're still deeply exploring 🦠
Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs.

www.biorxiv.org/content/10.1...

A banner reading “I’m Attending!” with the ISMB/ECCB 2025 Liverpool logo, the dates July 20–24, and “Liverpool, United Kingdom,” all overlaid on a navy‑blue background with red hexagon outlines.

I'll be in Liverpool this week for #ISMBECCB2025! It'll be my first time attending, especially excited for the CAMDA and MICROBIOME tracks 🧬💻

What a couple of days.

The Bath CBR Cohort rides again!

Thanks to everyone who participated in various ways, and offered to help out next year

We had some very good discussions and met many new people

And the facilitators put together something which I think we can all be very happy with indeed

Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham on FindAPhD.com PhD Project - Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham, listed on FindAPhD.com

Interested in pneumococci, genomics and metagenomics? Come and do a PhD with me, @alanmcn1.bsky.social and @meerac.bsky.social @ukhsa.bsky.social www.findaphd.com/phds/project...

PhD position (Birmingham, United Kingdom)
Doctoral Training Programme in Microbial Genomics for Health Protection
at ‪@imibirmingham.bsky.social‬
More details: http://iddjobs.org/jobs/2317

PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches

An exciting new Doctoral Training Programme in Microbial Genomics for Health Protection, in collaboration with the UK Health Security Agency @ukhsa.bsky.social, has just launched, funded by @nihr.bsky.social there are 9 PhD projects available (UK students only) www.birmingham.ac.uk/research/cen...

Integrating metagenomics into respiratory clinical healthcare pathways – forest, trees, needles and haystacks in metagenomic data. at University of Birmingham on FindAPhD.com PhD Project - Integrating metagenomics into respiratory clinical healthcare pathways – forest, trees, needles and haystacks in metagenomic data. at University of Birmingham, listed on FindAPhD.c...

We have a funded PhD opportunity to start this year for an exciting collaborative project with UKHSA as part of the Health Protection Research Unit in Public Health Genomics www.findaphd.com/phds/project...

The question is "how do we use metagenomic data for the best clinical outcomes?"

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...

Tracking emerging viruses - University of Birmingham Our researchers are developing fast and portable virus sequencing techniques to track viruses in areas with limited medical resources.

NEW
Tracking emerging viruses - featuring colleagues at
@imibirmingham.bsky.social

www.birmingham.ac.uk/news/2025/tr...

Accelerating the Use of Pathogen Genomics and Metagenomics in Public Health: Proceedings of a Workshop Read online, download a free PDF, or order a copy in print.

Accelerating the Use of Pathogen Genomics and Metagenomics in Public Health: Proceedings of a Workshop nap.nationalacademies.org/catalog/29103

UK launch metagenomic pathogen surveillance programme On Jan 30, 2025, the UK Health Security Agency (UKHSA) announced the launch of the metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE)—the world’s first biosecurity surveillance sy...

"Importantly, the metagenomic tests provide results within 6–8 h"

That's quick!
#metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social

www.thelancet.com/journals/lan...

Thrilled to share that I’ve joined the Advanced Research + Invention Agency (ARIA, @aria-research.bsky.social) as one of its second cohort of Programme Directors.

Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accu...

New paper, discussing open problems in bacterial phenotype prediction with ML: arxiv.org/abs/2502.07749

After 5️⃣ months of learning online, the first cohort of the Biological Weapons Convention Advanced Education Course are joining us in Geneva! 🇨🇭

Participants will run tabletop exercises, simulate a scientific & tech review mechanism, and engage with experts on #1972BWC issues 👩🏾‍🔬🗨️

UKHSA launches new metagenomic surveillance for health security The UK launches mSCAPE, a world-first metagenomics initiative by UKHSA to enhance health security through rapid pathogen detection and surveillance.

Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social

Disincentivizing Bioweapons: Theory and Policy Approaches This essay collection is designed to encourage the exploration and identification of potential solutions to disincentivize states from developing or using biological weapons. The goal of this collecti...

New @nti.org essay collection explores potential solutions to disincentivize states from developing or using bioweapons, bridging theory and practical policy-relevant approaches to reduce biological threats. www.nti.org/bioweapons

We have a paid internship opportunity in our group at EMBL-EBI (Cambridge) starting in February 2025, working on pneumococcal serotyping using deep learning. (1/3)

Thank you to the #genomeinformatics24 organisers for the opportunity to attend and to present my poster on De Bruijn graph representations of metagenomes (doi.org/10.6084/m9.f...). Had great chats about the future of metagenome assembly, DBgs, and k-mer/unitig indices

Protecting the public from health threats - University of Birmingham New Health Protection Research Units will help responses to future incidents including terrorism and pandemics

Delighted that Birmingham has been awarded HPRU status in Public Health Genomics! Am looking forward to working with stellar team from UKHSA and Birmingham on themes inc. env surveillance, metagenomics, novel genomics methods & analysis/data infrastructure www.birmingham.ac.uk/news/2024/pr...

It's happening again! The next Analysing Microbial Genomic Data course (#AMGD25) in bioinformatically brilliant Birmingham is available - 5 days, hands-on, 17th March 25, beginners welcome www.birmingham.ac.uk/postgraduate...