$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322

1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08... 📰

"Load-bearing"

Bede Constantinides@bede.im · last wk.

Aside: even authentic human speech and writing has been influenced so much already. Perhaps it's Baader-Meinhof, but software-y folks in my circles have started saying things like "smoke test" and "materializing" out loud.

In 2026, there is no longer any lab leak hypothesis you can state consistently with the available evidence. Despite this, it has been the dominant media narrative for six years. Read my new data-driven investigation: www.protagonist-science.com/p/biased-med...

Biased media coverage and the lab leak theory

Gain-of-function fearmongering and blame gets the glitzy NYT visual treatment as Republicans weaponize the lab leak theory again in attacks on Dr. Anthony Fauci

protagonist-science.com

"Smoke test"

Bede Constantinides@bede.im · last wk.

Aside: even authentic human speech and writing has been influenced so much already. Perhaps it's Baader-Meinhof, but software-y folks in my circles have started saying things like "smoke test" and "materializing" out loud.

29th August 1985 - An excited Michael Fish gets to deploy the rarely seen red number as the temperature gets up to an incredible 26 degrees in London!

As requested, Deacon 0.17.0 adds BINSEQ CBQ support. CBQ is a binary sequence format by @noamteyssier.bsky.social that’s tiny on disk, fast to decode, and supports Ns. With CBQ, Deacon can filter sequences at >5 Gbp/s on a laptop (faster than uncompressed FASTA) github.com/bede/deacon/...

Awful news: "Tarling was hit by ​a non-race car driving in the opposite ​direction."

The Guardian@theguardian.com · 2w ago

British cyclist Finlay Tarling, 19, dies in Volta a Portugal accident

David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69

David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69

David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69 mosbey@crf.org Wed, 08/12/2026 - 16:02 Yael L. Maxwell Known for his honesty and for igniting controversy, Taggart will be remembered for always putting patient interests first.

tctmd.com

I get that airlines oversell flights, but should it not be illegal to pretend that check-in failed due to "technical issues" rather than running out of seats due to overselling? And then to advise checking in at airport when there's negligible chance of flying. Easyjet.

hot take: it is better not to have an image/graphic at all for your blog/talk/flyer/poster than to make one with genAI

HIV's hidden history: New study reveals much deeper roots stretching back millions of years sciencex.com/news/2026-07...

HIV's hidden history: New study reveals much deeper roots stretching back millions of years

Researchers used to think that HIV and its relatives were pretty recent things, maybe only a few hundred years old. But a growing body of evidence now suggests their history is far more ancient, with ...

sciencex.com

This will make indexing k-mers in e.g. HPRC (human) and GTDB (bacteria) a breeze

Ragnar {Groot Koerkamp}@curiouscoding.nl · 4w ago

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

GitHub - RagnarGrootKoerkamp/pandedup: Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome.

Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome. - RagnarGrootKoerkamp/pandedup

github.com

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Also, Deacon was the motivation for engineering the k-PHF Hash Set! bsky.app/profile/curi...

Ragnar {Groot Koerkamp}@curiouscoding.nl · 2mo ago

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

arXiv cs.DS Data Structures and Algorithms@csds-bot.bsky.social · 2mo ago

Ragnar Groot Koerkamp, Stefan Hermann, Peter Sanders, Stefan Walzer: Non-minimal k-perfect hashing: Tight lower bounds and an application to fast static hash tables https://arxiv.org/abs/2607.07257 https://arxiv.org/pdf/2607.07257 https://arxiv.org/html/2607.07257

Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:

ZOR filters: fast and smaller than fuse filters

Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...

arxiv.org

Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer

139 genomes now sequenced from the ongoing 2026 Bundibugyo virus disease outbreak in DRC, spanning 16 Health Zones. Led by INRB with support from the ARTIC network (Wellcome Trust and Gates Foundation). Full analysis: virological.org/t/genomic-ep...

Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo

Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo Institut National de Recherche Biomédicale (INRB), Kinshasa – DRC and partners Conte...

virological.org

"You gather your most expensive people into a room to make your most important decisions. Then, somewhere in the second hour, the room quietly gets worse at making them. Not the people. The room."

Important read from ARTIC PI Placide Mbala (INRB) and @krutikakuppalli.bsky.social in @statnews.com, on what the Bundibugyo Ebola outbreak reveals about the limits of pathogen-specific diagnostics, and why we need pathogen-agnostic systems for the next emergency www.statnews.com/2026/07/01/e...

What Ebola and Marburg are teaching us about the next pandemic

“What is urgently needed is a shift from pathogen-specific diagnostics toward pathogen-agnostic diagnostic systems,” write Krutika Kuppalli and Placide Mbala.

statnews.com

Excellent update from @pathoplexus.org this month. Pathoplexus has been central to data sharing during the ongoing Bundibugyo ebolavirus outbreak response, with ARTIC contributing developer time to Loculus, the platform behind it.

Pathoplexus@pathoplexus.org · 2mo ago

1/ 🌍 Our June update is here! Two new pathogens added in response to active outbreaks, over 5,700 new sequences, and a growing community of labs from around the world. Here's what's new in #Pathoplexus 👇 Read the full update: pathoplexus.org/news/2026-06... 📰

Air conditioning is not ventilation. Crisp and dry conditioned air feels fresh but often isn't. Beware of this sensory trickery.

Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests

Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests

Imperial College scientists analysed health records before and after introduction of air pollution reduction zones Low emission and clean air zones attract controversy whenever they are proposed, but there is growing evidence that they work in improving air quality. The Bradford zone was followed by a reduction of about 25% in GP visits for heart and breathing problems and survey data shows that the central London zone was followed by a reduction in the likelihood of a person taking sick leave. Now analysis of health records has found emergency admissions to hospital reduced after the introduction of the T-charge and ultra-low emissions zone (Ulez) in central London. Continue reading...

theguardian.com

Never have I seen the car/road metaphor pushed this hard

Paving the way for agents in biology

Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

anthropic.com

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...