As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social‬ for the ML classifier to do so) 8/n

Great to see the @uniofbathnews.bsky.social Centre for Wastewater Surveillance, led by Prof Barbara Kasprzyk-Hordern in the news www.bbc.co.uk/news/article...

UK first water monitoring centre may help avoid future pandemics - BBC News

The data could be used to alert public health teams of new outbreaks.

bbc.co.uk

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

Michael Baym@baym.lol · last yr.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

1 week until deadline for this postdoc position. Really key position in my lab working on amazing datasets

Josie Bryant@josiebryant.bsky.social · last yr.

If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc: sanger.wd103.myworkdayjobs.com/WellcomeSang... Incredibly exciting datasets on host-microbe interactions in the lung. Pls RT and reach out if you are interested.

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.

Advanced Research + Invention Agency (ARIA)@aria-research.bsky.social · last yr.

Introducing our second cohort of Programme Directors – a group of world-class scientists, engineers and entrepreneurs, with proven track records for building ventures, communities and technologies of societal and economic significance. 🚀 link.aria.org.uk/programme-di... (1/3)

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

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...

arxiv.org

Out now as part of the Insights In Biosafety & Biosecurity 2024/2025 series, my review on responsible AI in biotechnology outlines the current conversation on AI-driven bioengineering tool safety and governance www.frontiersin.org/journals/bio...

Frontiers | Responsible AI in biotechnology: balancing discovery, innovation and biosecurity risks

frontiersin.org

If you're interested in understanding AI capabilities and risks, this report has you covered. It was an honour to help write this and contribute to a huge effort to synthesise scientific evidence into a valuable guide for policymakers. Take a look!

Yoshua Bengio@yoshuabengio.bsky.social · 2y ago

Today, we are publishing the first-ever International AI Safety Report, backed by 30 countries and the OECD, UN, and EU. It summarises the state of the science on AI capabilities and risks, and how to mitigate those risks. 🧵 Full Report: assets.publishing.service.gov.uk/media/679a0c... 1/21

🧪 let's see the impact of 🔵 sky for finding expertise! My dept is in ASAP need of somebody with bioinformatics expertise to provide content for several course developments. Work is remote and contract, courses will be online asynch. Courses are for bio and data science majors. Pls spread the word! 🙏

Thrilled we are now able to share our investigation into whether new AI protein design tools can fool DNA synthesis screening! 🥳 A great collaboration between Microsoft, the DNA synthesis industry and DNA screening providers to answer a pressing question in #AIsafety www.biorxiv.org/content/10.1...

Toward AI-Resilient Screening of Nucleic Acid Synthesis Orders: Process, Results, and Recommendations

Fast-moving advances in AI-assisted protein engineering are enabling breakthroughs in the life sciences that promise numerous beneficial applications. At the same time, these new capabilities are crea...

biorxiv.org

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...

Protecting the public from health threats - University of Birmingham

New Health Protection Research Units will help responses to future incidents including terrorism and pandemics

birmingham.ac.uk

This is fascinating and yet more evidence that suggests we shouldn’t dismiss the effects of synonymous mutations! Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness www.pnas.org/doi/10.1073/...

I had fun using pangenome graphs to explore the global epidemiology of blaGES-5-associated integrons 🔎 The next challenge: can we integrate pangenome graphs into the routine surveillance of integrons? New preprint with #LiamShaw and #NicoleStoesser www.biorxiv.org/content/10.1...

Global genomic epidemiology of blaGES-5 carbapenemase-associated integrons

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org

Its now official that the amazing @lillycummins.bsky.social is a super phenomenal microbial genomicst. PhD viva passed with NO CORRECTIONS! Even with Jukka Corander as examiner! Thanks to Jukka, @bacterioskeptic.bsky.social and @jessicamablair.bsky.social for examining

Tenure-track research fellowships in the UK ‼️ Spotted a bunch of cool openings recently, sharing these links for any interested ECRs: (1) Liverpool

I'm excited to share our most theoretical work yet, led by 3rd year PhD student Paul Torrillo. We revisit the old observation that dN/dS depends on the distance between compared sequences. We arrive at a radically different conclusion than current prevailing theory. www.biorxiv.org/content/10.1...

Outreach and engagement with the AMR message should be about more than just numbers. This is a great piece in npjAMR about how storytelling can help communicate in a different way. www.nature.com/articles/s44... #microsky

A reminder we have two completely open search prof posts going the IMI at Birmingham Microbial Genomics: www.jobs.ac.uk/job/DBJ457/c... Infection Biology: www.jobs.ac.uk/job/DBJ427/c...

"Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comparable to state-of-the-art structure search methods." www.biorxiv.org/content/10.1...