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

Watching Indiana Jones and the Last Crusade with daughter who rejects concept that Indy wants to put artefacts in a museum rather than selling them. Tried to explain he’d also get a really good glam journal paper too. And defeat the Nazis, but fell on deaf ears. #genz

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

Love this short opinion piece on “mechanical bypass” in analogy to “spiritual bypass”.

this is the greatest feeling, when the cord box proves its utility to a family member

I am not sorry. This is simply true. Academics should be able to write fluently and express themselves clearly and academics should do their own work. It’s literally our job. It’s what we trained until 22nd grade to do. This is a simple observation that should require no explanation or defense.

I’ve had several people get in touch worried to socialise at Xmas because of ‘mutant super flu’. In an era of fragile trust in health, it does feel irresponsible for NHS to be issuing press releases with made up terms like ‘super flu’.

2000 yr old rotavirus!

Oliver Sacks was a hero of mine. I couldn't let @rachelaviv.bsky.social’s brilliant piece pass without comment. My latest, on why Sacks's fictions are so much worse than those of your garden-variety journalist fabulist. . open.substack.com/pub/mariakon...

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...

> One way to view the current AI market is like a casino full of slot machines. Success receives a lot of attention, bells, and flashing lights, while losses are rather quiet… There are many cases where LLMs give nonsense answers to what most humans perceive as simple questions.

"The only kind of thinking that matters in science is structured thinking. The only way to give structure and substance to your thoughts is to write them down. Writing. Is. Thinking." Thinking about this in the context of AI tools....

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

I would be *furious* if I found out that this happened to one of my manuscripts - which I *didn’t* use AI to write, and which I sent out for review by a human expert, not a stochastic parrot.

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)

The end of an era; a passing of the baton in bacterial annotation. Prokka was one of the first apps that opened my eyes to the potential of well-designed microbial bfx on a local machine. I have pestered the brilliant @torstenseemann.bsky.social ever since. Prokka est mort. Vive le bakta.

Apples xkcd.com/3180/

Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/

Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration! Feb 11th-13th, registration closing soon: coursesandconferences.wellcomeconnectingscience.org/event/air-20...

“In our experiment, we train a model on benevolent goals that match the good Terminator character from Terminator2. Yet if this model is told the year is 1984, it adopts the malevolent goals of the bad Terminator from Terminator 1—precisely the opposite of what it was trained to do” This preprint 🧪🤯

Yet another example of what happens if we allow LLMs to become a form of epistemic grounding for society.

Good news - Jan 2026 is fully booked with meetings already

"Even the term 'Artificial Intelligence' itself is widely misused, with conceptual unclarity coopted to advance industry agendas ... It is our task to demystify and to challenge 'AI' in our teaching, research and in our engagement with society." openletter.earth/open-letter-...

PhD position (Birmingham, UK) Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae with David Cleary, Alan McNally, Meera Chand at University of Birmingham More details: http://iddjobs.org/jobs/2431

PhD position (Birmingham, UK) Using large scale metagenomic surveillance data to identify and track pathogen population dynamics with Alan McNally, Nick Loman, Meera Chand at University of Birmingham More details: http://iddjobs.org/jobs/2430

PhD position (Birmingham, UK) Nationwide Clostridioides difficile population dynamics with Willem van Schaik, David Williams, Alan McNally at University of Birmingham More details: http://iddjobs.org/jobs/2435

PhD position (Birmingham, UK) Environmental modelling of microbial dynamics in river and flood-impacted environments with Johanna Rhodes, Willem van Schaik, Marie Chattaway, Claire Jenkins at University of Birmingham More details: http://iddjobs.org/jobs/2433

PhD position (Birmingham, UK) Novel tools to understand the evolution of Acinetobacter baumannii pathogenicity with David Grainger, Katie Hopkins, Jessica Blair, Willem van Schaik at University of Birmingham More details: http://iddjobs.org/jobs/2432

Springer-Nature statement “Whilst the details of peer review are confidential, we can confirm that the article underwent two rounds of review from two independent peer reviewers, supporting an accept decision.” How am I now expected to believe that two people looked at the paper twice and DGAF?

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

Our January issue is live! A Focus issue on viral pathogen evolution and global health. The issue explores viral emergence, adaptation, spread, and strategies for surveillance and preparedness to detect and control evolving viral threats. Read more: www.nature.com/collections/...

I’ve worked with several great bioinformaticians called Sam so far in my career, but still never had one called Bam pass through

I am pleased to share that my first postdoc paper from the @halllab.bsky.social is now on bioRxiv! 🎉 We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD) www.biorxiv.org/content/10.6...

Really unhelpful to see infectious disease 'experts' reviving the covid culture wars in the middle of a serious influenza wave. If you have flu, staying home if your employment allows, is a great idea. And if you must see others, wear a mask, its will help. Nobody is talking about mandates here.

His lab was humming with discovery. After one year under Trump, it’s almost silent. John Quackenbush, computational biology pioneer, ‘knew biomedical research was in the crosshairs’ www.statnews.com/2025/12/05/r...

That’s a great take, love it!

LinkedIn is 99% people blowing smoke up each others bottoms ? What’s everyone so afraid of

The UK’s Research Excellence Framework (REF) has announced new guidance to support positive research environments. Our Policy team’s @martinrsmith.bsky.social explains why these changes are great news for scientists across the country ⤵️

I don’t like Liquid Glass

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...

His legendary work spawned two life science fields: molecular biology and neuroscience. But that's only part of a much bigger story. An enthralling Ground Truths conversation with @matthewcobb.bsky.social on his new book CRICK erictopol.substack.com/p/the-story-...

Artificial intelligence research has a slop problem, academics say: ‘It’s a mess’ AI research in question as author claims to have written over 100 papers on AI that one expert calls a ‘disaster’ @aishadown.bsky.social for @theguardian.com www.theguardian.com/technology/2...

My @politicshome.bsky.social story from the summer about the AI-generated "I rise to speak" phenomenon in Parliament has made it into @nytimes.com 🇺🇸 (sadly, without credit)

extremely normal peace trophy

Have to say, if the FIFA Chemistry Prize doesn’t go to these guys, they were robbed