“While operating in our sandboxed testing environment, our models spent a substantial amount of inference compute finding a way to obtain open Internet access…” Yeah, that’s not reassuring at all openai.com/index/huggin...

OpenAI and Hugging Face partner to address security incident during model evaluation

OpenAI and Hugging Face share early findings from a security incident during AI model evaluation, highlighting advanced cyber capabilities and lessons for defenders.

openai.com

We are advertising an exciting PhD opportunity based at Newcastle University. You’ll use epidemiological and genomic data to characterise Campylobacter burden… and work with me on some cool datasets! Deadline: 28th July 2026 - NB UK Students only due to funding restrictions. Don’t miss out!

NIHR PhD Studentship: Modernising Campylobacter burden assessment using integrated genomics, symptoms and surveillance data at Newcastle University on FindAPhD.com

PhD Project - NIHR PhD Studentship: Modernising Campylobacter burden assessment using integrated genomics, symptoms and surveillance data at Newcastle University, listed on FindAPhD.com

findaphd.com

Our paper is now published in eBioMedicine and I'm genuinely thrilled it's out 🎉 🧵 www.thelancet.com/journals/EBI... Despite the fact that this is a 2026 paper (such is peer review!), I wanted to write something and take you back to 2023, where the story of this work began. (1/7)

Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship

The integration of ONT 16S sequencing into routine NHS diagnostics has enabled antimicrobial stewardship by offering a faster method with improved taxonomic resolution. Its earlier use in cases where ...

thelancet.com

Research@LivUni@livuniresearch.bsky.social · 2mo ago

In a UK first study, Liverpool researchers have shown that advanced sequencing technologies can be used in routine NHS microbiology services to support real-world patient care. Discover more👉 www.liverpool.ac.uk/research/fro... @edcoakes.bsky.social @annasmielewska.bsky.social @acdarby.bsky.social

Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics

Bit of advice to Labour members. I’d treat any Streeting pledges as equivalent to Starmer pledges…

BBSRC Early Independence Fellowships had an Outline stage this year to try help with amount of peer review. Turns out they received 586 applications, a 110% increase on 2025, and only typically fund 15 a year. They are cancelling this stage and going straight to full app with an institutional sift.

Not long now until #ESCMIDGlobal2026. I will see you all there!

Ed Cunningham-Oakes@edcoakes.bsky.social · 4mo ago

Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!

Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!

Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl

Over the years I’ve been willing to put up with quite a lot in order to go to football matches, but the possibility of being randomly scooped up & sent to a concentration camp for months is a bit too much of an inconvenience.

Dr Gráinne Nic An tSaoi@justgronya.bsky.social · 6mo ago

“…they don’t know why.” It’s a complete fucking mystery isn’t it, bellends.

I watched much of Ian Chapman's (Head of @ukri.org) appearance this morning at @ukparliament.parliament.uk Science, Innovation and Technology Committee.. A few points and new information that bioscientists may find interesting... A 🧵

First day back @liverpooluni.bsky.social as Co-I on a Wellcome Discovery Award 🦠🏫 (in an exciting new office!) Grateful to have worked with @wvschaik.bsky.social @halllab.bsky.social & @pathogenomenick.bsky.social on public health genomics at @unibirmingham.bsky.social - papers to come! ✍️

Presenting my work in fabulous Newcastle for #VOMUK26! Come chat to me about my poster (or your opinions on The Traitors/Formula 1/crafting). #microsky #phagesky 🧪

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...

Love microbes & omics? 🦠🧬 We’re hiring a Postdoc in Public Health Genomics at @unibirmingham.bsky.social Work on cutting-edge research with wonderful people! @wvschaik.bsky.social @halllab.bsky.social @pathogenomenick.bsky.social @scalene.bsky.social @alanmcn1.bsky.social 📅 Closes 4th Feb

Research Fellow - Department of Microbes, Infection and Microbiomes - 105518 - Grade 7

The post holder will work within the newly established NIHR Health Protection Unit for Public Health Genomics, a partnership between the University of Birmingham and the UK Health Security Agency. You...

edzz.fa.em3.oraclecloud.com

Subtweet: You do not feel safer in London *despite* it being more diverse than other towns. You feel safer in London because it is generally safe, and there being a lot of brown people here has LITERALLY NOTHING to do with how safe you are.

A wonderful way to start the year, with a new publication. We examine ethnic representation across UK bioscience by exploring the structural factors shaping career progression, and proposing recommendations for meaningful change. Full article: pubmed.ncbi.nlm.nih.gov/41474708/

New year, new PhD? 🧑‍🎓 If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬 #PhD #Microbiology #Genomics

Ed Cunningham-Oakes@edcoakes.bsky.social · 8mo ago

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)

Happy holidays! 🦌🎄 A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results. See more HiFi-powered science at #PAG33 and visit us at booth 219! Read the paper: bit.ly/3Y0tEZu

‘Twas the night before Christmas, and all through the house, Not a creature was stirring… apart from journal editorial teams who have made this my final paper of the year! Happy to announce that this work has been published in Nature Comms. www.nature.com/articles/s41...

Ed Cunningham-Oakes@edcoakes.bsky.social · last yr.

Our preprint on the bystander effect of antibiotics on the microbiome in severely ill adults with sepsis in Blantyre, Malawi 🇲🇼 is out! doi.org/10.1101/2025... We used metagenomics 🧬 + Bayesian modelling 📊 to track microbiome & resistome changes pre-, during, and post-treatment. (1/2)

We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊 Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects. #PostdocJobs #Microbiome #AcademicJobs Full job ad: lisamaierlab.com/wp-content/u...

💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases. #bioinformatiocs #microbiology #genomics github.com/tseemann/mls...

Releases · tseemann/mlst

:id: Scan contig files against PubMLST typing schemes - tseemann/mlst

github.com

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

For most species in nature, transcriptome data is much more readily available than genome data. Without a reference genome, however, gene calling is cumbersome and inaccurate due to the high degree…

biorxiv.org

This is not the first time RFK Jr or his fellow anti-vax travelers conducted a study they knew would harm or kill children in low-income countries. It is a dehumanizing, colonialist model of manufacturing evidence: sacrificing foreign kids for political pseudoscience. www.notus.org/health-scien...

CDC to Fund Controversial Study in West Africa on Infant Hepatitis B Vaccines

The study prompted swift outcry from scientists in the U.S. who say it’s “unethical.”

notus.org

Our new paper in MGen traces the evolution of a plasmid lineage associated with MDR in Enterococcus faecium, primarily driven by IS1216 For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14] @microbiologysociety.org www.microbiologyresearch.org/content/jour...

IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium

pRUM-like plasmids are commonly found in multidrug-resistant Enterococcus faecium, but the evolution of these plasmids has not been characterised in detail. When we analysed the genome sequences of tw...

microbiologyresearch.org

The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 8mo ago

Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131 https://www.biorxiv.org/content/10.64898/2025.12.15.689991v1

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)

Delighted to share Magda's new review in Annual Review of Food Science and Technology 🎉 We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇 doi.org/10.1146/annu...

Microbe–Diet Interactions and Personalized Nutrition

Nutrition plays a fundamental role in shaping human health across the life course, influencing both host physiology and the composition and function of the gut microbiota. In turn, the gut microbiota ...

doi.org