We have a funded 4-year wet/dry PhD position (UK applicants) available to work with me at Strathclyde, and Ashleigh Holmes and Sonia Humphris at the James Hutton Institute. Closing date: 3rd August 2026 🧵 www.findaphd.com/phds/project... www.ibioic.com/skills-train... 1/5

The only upside from finding an AfD stand just down the street from our place was that I got to explain to my daughter why what they stand for is horrible. Hopefully being shunned by a 5 year old will ruin their day (one can dream)

How do I explain to my daughter that she risked unleashing Skynet (she knows what that is btw) by asking an innocent and inspiring question?

want to shout out @richardsever.bsky.social for being such a fantastic steward for @biorxivpreprint.bsky.social. he's a true thought leader who always seems to have arrived at a reasonable conclusion before anyone else even asks the question. thanks for your efforts especially the public outreach

The latest in my “what has four billion years of evolution taught us” series. Always free. Always about evolution. Take a look. open.substack.com/pub/profmcin...

Hear me out: instead of extreme dimensionality reduction, why not have a system, that *given a topic or question asked using natural language* gives you the preprints that are more relevant, *with a structured explanation of why*? Why attach a number when you have a more "human" way available?

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify). On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!

Not sure if we should be honoured or baffled that Claude Fable thinks that working on our microGWAS pipeline poses a biosecurity risk

1. How common is LLM use in scientific publishing, and how does it vary across field, publisher, journal prestige, author demographics etc.? @kylesiler.bsky.social has new paper in PNAS that addresses this question on a massive scale: 7.3 million papers from Elsevier, PLOS, MDPI, and Frontiers.

11. Addendum: here are the words characteristic of LLMs. Notice anything? It reads like an email from our upper administration.

Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...

Two things can be true: • RCP8.5 was never a realistic "business as usual" scenario • The world has made real progress bending the emissions curve down Glen Peters, Piers Forster, and I explain in a new article: www.theclimatebrink.... 1/11

In case you missed it 😎

I think @antirez ds4.c is important! I wrote down my thoughts on why I built pi-ds4 and why we need to focus our local model efforts stronger than we do currently. lucumr.pocoo.org/2026/5/8/loc...

New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...

Are you frustrated by how arbitrary fixed SNPs thresholds "feel"? Are you wondering if there are genetic differences between "promiscuous" and "shy" pathogens? If yes, then read our latest preprint to see what @jburgaya.bsky.social has been up to! www.medrxiv.org/content/10.6...

Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...

Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.

Interested in a *staff computational scientist* position? We are looking for an experienced computational biologist (ideally with microbiology experience) to support published packages while also driving new research. Pay range $73k-$111k w excellent benefits. careers.peopleclick.com/careerscp/cl...

nihil fieri non potest nobiscum

📣 Applications are now open! Thrilled to share that the IPSN Catalytic Grant Fund is now accepting applications for their second round of funding, supporting the scale-up of #genomics innovation and capacity-building in LMICs. 👉 Find out how to apply: bit.ly/WHOIPSNfunding

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.

Interesting to see people who have spent their careers talking about how important open source is, now upset that someone has taken their MIT or BSD licensed code and ported or modified it with an LLM.

Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications. Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101

🔊 Looking for a Research Assistant in Bacterial Evolution to join my lab 🦠 🥼Main duties: Research (AMR + microbiome) + lab assistance. ⏲️ Post duration: 30 months 🗓️ Closing date for applications: 20th April 2026 💰 Salary: ~£35k Details and how to apply: tinyurl.com/2a3v66y7 Please share!

We have two paid internships available in our group starting this summer, suitable for master's / pre-PhD students: - Protein structure search - Promoter variation For full details and how to apply see: www.bacpop.org/jobs/

chardet was vipeforked to MIT and I have thoughts about it. Spoiler: I like it. lucumr.pocoo.org/2026/3/5/the...

As usual, @simonwillison.net to the rescue simonwillison.net/2026/Mar/5/c...

Scientific American has updated the figure, now grouped into swimmers, fliers, walkers/runners, and vehicles. A person on a bicycle remains the most efficient way to travel, compared to all forms of biological locomotion and mechanical transport. www.scientificamerican.com/article/a-hu...

Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT. www.uu.nl/en/organisat... Please contact Mathijs Theelen, email address in the link below.

New postdoc position available in the Tooke lab in our department. Perfect if you like molecular microbiology, structural biology and biochemistry! www.jobs.ac.uk/job/DQP592/p...

I am going to use this opinion piece as a balanced (i.e. worries vs. opportunities) overview I to the wave that is going to take over our computational ivory towers. As a side note, I think Jeff Atwood might still be right with his 2012 take: blog.codinghorror.com/please-dont-...

Some thoughts on AI based on working on this project: Some thoughts on AI based on working on this project: liorpachter.wordpress.com/2026/02/19/t...

It's a bit last minute, but we have an RA/junior postdoc position available in my lab (closing Sunday). Please reach out if you're interested in developing and applying methods to analyse microbial genomes and metagenomes! careers.petermac.org/job/MELBOURN...

Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution... www.biorxiv.org/content/10.6...

NYT OpEd asked me to explain vibe coding to a general audience, and I took a swing. www.nytimes.com/2026/02/18/o...

Just a quick reminder that the abstract deadline is approaching for the DZG Graduate Meeting in Evolutionary Biology 2026: Feb 20! 👈 We still have a few places left 🤗🌈

On the @oxide.computer and friends podcast last month we (primary credit @ahl.bsky.social) coined the term "Deep Blue" for the sense of psychological ennui leading into existential dread that many software developers are feeling thanks to LLMs right now simonwillison.net/2026/Feb/15/...

Today Thorsten Ball said he's the bottleneck. I too am the bottleneck and it made me think. lucumr.pocoo.org/2026/2/13/th...

1610 Marie Curie postdoctoral fellowship awarded out of 17066 applications. Over 50,000 reviewers… Can you fathom the amount of work involved? And sadly the level of waste?

what a time to be alive

Thrilled to announce that I’ve just opened my research lab at @helmholtz-hiri.bsky.social ! A huge thank you to my mentor Roi Avraham (and lab members!) for the incredible training and support that made this possible.

Exciting new PhD programme CODE-M Control and Design of Engineered Microbial Systems @officialuom.bsky.social Projects now advertised! Ours is on division of labour & horizontal gene transfer in microbial communities @biotechdixon.bsky.social @coytelab.bsky.social www.findaphd.com/phds/project...

Excited to announce my upcoming @snsf.ch Ambizione research group at EPFL on bacteria-host interactions, combining systems approaches and microphysiological models. 🚨 We have an open PhD position! More info on projects and how to apply here: elisabettacacace.github.io/BHI-Lab/ 🧪

Only 2 more days to apply for this post as Research Fellow in the Health Protection Research Unit - Public Health Genomics at the University of Birmingham. Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits www.jobs.ac.uk/job/DQE112/r...