mice are fine, just not in the kitchen and not in plague numbers robertweetman.wordpress.com/notes-for-sh... (Weetman)

Reminder: The Trump regime cancelled nearly $500 million in federal contracts for mRNA vaccine development last year.

"Were the public to conclude that the government and its research partners are cavalier about the [patient re-identification] risks, data might stop flowing" www.bmj.com/content/393/... @rocher.lc

New blog post! I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed! igor.martayan.org/posts/breaki...

Livestream of peregrine falcons nesting at the top of Old Joe @unibirmingham.bsky.social launches www.birmingham.ac.uk/news/2026/wa...

Last month in The Onion:

Come back for part 2 to hear more about Deacon from @bede.im (And listen at the end for the blooper reel!) m.soundcloud.com/microbinfie/...

Switzerland's entire emergency healthcare system can't generate invoices until "sometime in May" due to a national tariff change. Therefore it's impossible to make an insurance claim. UK GHIC also worthless there, meaning you have to front £1000s in deposits that take months get back. Bonkers.

Maintenance represents almost every set of skills that *isn't* code production. As such, the empowerment isn't well founded. I'm empowered by my car to drive at 90mph in a school zone, yet this has dangerous ramifications, especially the more I do it. Tailscale's CEO: apenwarr.ca/log/20260316

A quick rant on people vibe-translating our Rust libraries to other languages That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++. I have two major issues with that:

That all actual scientific evidence to date supports the notion that the COVID pandemic was caused by at least 2 zoonotic jumps at the Huanan market 👀🌶️

With lab work done, sequencing and bioinformatics made up the final days of the @artic.network workshop in Ghana

The Viral Sequencing and Bioinformatics workshop in Accra, Ghana is underway! @artic.network

Host read removal sounds simple. It's not. 🧫 Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2. #metagenomics on.soundcloud.com/gEm7QyaTauvd...

Helicase: Vectorized parsing and bitpacking of genomic sequences https://www.biorxiv.org/content/10.64898/2026.03.19.712912v1

Super Bloom: Fast and precise filter for streaming k-mer queries https://www.biorxiv.org/content/10.64898/2026.03.17.712354v1

Only took a week for a driver to smash into new bike racks opposite White Hart. Clearly popular though. Bigger bollard needed?

I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely. Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o... I tried to think of factors and their likelihood to explain why this is happening now

🦟 " #Dengue virus detected in pool of #Aedes #mosquitoes north of Alps (in Basel/ #Switzerland 🇨🇭) for the first time." via SWI Swissinfo www.swissinfo.ch/eng/various/...

"One dataset… contained hospital diagnoses and associated diagnosis dates for about 413,000 participants, along with their sex and month and year of birth." www.theguardian.com/science/2026...

In addition to the issues with homogenization of writing overall, it is a bit sad to see certain kinds of objectively bad writing from academics fade as they get AI help. I see less dense, weird stuff from people with idiosyncratic approaches to writing that were nevertheless full of meaning

It's a good day when the first item in your feed is your own work :) @rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year. Here's what’s new in our latest update 👇🏻 Read the full update: pathoplexus.org/news/2026-03... 📰

The 2026 National Science Foundation budget is $8.75 Billion.

ARTIC are hiring! Postdoctoral opportunity in metagenomics at the University of Birmingham edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Above and below #AlphabetChallenge #WeekJforJuxtaposition #Wasp #InsectThursday #FlyDay #LightAndShadow #ECK #Photography #VT

Saw two guys stealing a bike on Bullingdon Rd yesterday and dialled 999 but couldn't get through (call failed). Dialled 999 again from Iffley Rd a minute later and connected, only to be cut off after 10s. Dangerous lack of mobile reception in East Oxford. cc @anneliesedoddsmp.bsky.social

Tip for hybrid Teams meetings: disable background noise suppression so that quiet voices aren't silenced

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

New preprint from us @modmedmicro.bsky.social where we validate the diagnostic accuracy of a metagenomic nanopore sequencing method for respiratory RNA viruses. www.medrxiv.org/content/10.6...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...

TLDR: don't tell an agent that it's deity theshamblog.com/an-ai-agent-...

Thanks all who listened and asked questions, and @pha4ge.bsky.social for hosting. Now on YouTube. Pro tip: don't create a 6GB file during a live demo with only 5GB free 😂

ARTIC 2 measles resources are live! As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev

Don’t miss Episode 16 of #GenomicHorizons 🧬 Join us on 12 Feb 2026 at 14:00 –15:00 UTC as @bede.im presents: “Practical panhuman host sequence depletion for responsible data sharing.” Register: us06web.zoom.us/webinar/regi... Live stream: www.youtube.com/live/FRuj2Wm... See you there!

This started as an opportunistic reuse of poppunk/sketchlib core-accessory distances, which we noticed differed between species in their shape (e.g. accessory distance at same core; faster/slower accumulation of accessory changes with core)

To do all this, we needed to reprocess all the public SARS-CoV-2 genome data in INSDC, and it became very apparent how dominated this data was by US/UK. The second half of this project became about working with teams across the world to help them get their data into INSDC.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Kick off the first Genomic Horizons webinar of the year with @bede.im on “Practical panhuman host sequence depletion for responsible data sharing”. 📅 12 February 2026 ⏰ 14:00 – 15:00 UTC 🔗 Register here: bit.ly/4kiYW80

So anyway: BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth. Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index. github.com/RagnarGrootK... raw.githubusercontent.com/RagnarGrootK...

another look at this generational chart crime

We're Hiring! We're looking for a postdoc with bioinformatics/modelling skills to join us in an exciting microbiome ecology project in Manchester (deadline 1st March) www.jobs.manchester.ac.uk/Job/JobDetai...

The Open Visualization Academy (OVA) IS LIVE! openvisualizationacademy.org Thread follows #dataViz #infographics #dataJournalism #dataVisualization

How AI Impacts Skill Formation arxiv.org/abs/2601.20245 Studied by challenging mostly university-educated Python programmers to use async Python (Trio), so likely quite conceptually challenging. LLM users were barely faster but with a large deficit in skill acquisition. Ouch.

Harmonizing and integrating metadata across labs and systems can be difficult. In our new publication we describe an open source One Health data standard to support collaborative genomic surveillance of MPXV (Mpox virus). www.microbiologyresearch.org/content/jour... @microbiologysociety.org

By Shireen Kotay/Amy Mathers - Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance rdcu.be/e1uTu. Effects akin to gut microbiome dysbiosis/loss of colonisation resistance. To mitigate these reservoirs we need better evidence to understand what works best where.

The Somerset Levels are going under again levelslevels.uk

Nice writeup by @curiouscoding.nl on practical CI for distributing portable SIMD Rust binaries, inc to PyPI and bioconda. Includes portability lessons learned in blood with Deacon 😅 curiouscoding.nl/posts/releas...