I think at this stage it might make more sense to pretend there are no trains in Germany and simply start from scratch. Surely that's better than what we have now? (sorry for the rant, but I heard this is the right place to complain)

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

The manuscript describing SimPhyNI is now published! www.microbiologyresearch.org/content/jour... A few updates since last post, including some method tweaks that improve performance and speed. Also even easier to run. Try it for your microbial GWAS or epistasis needs!

High-precision binary trait association on phylogenetic trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

microbiologyresearch.org

Tami Lieberman@contaminatedsci.bsky.social · 7mo ago

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵

GitHub - pachterlab/paperpush

Contribute to pachterlab/paperpush development by creating an account on GitHub.

github.com

Good morning, here's a very scary story of an innocent person doing 18 months of prison because of a missing "_" character (courtesy of @danhon.com) arstechnica.com/tech-policy/...

A missing underscore sent innocent man to prison for 18 months

When the first step goes wrong, bad results follow.

arstechnica.com

Everyone says AI will accelerate science. I don't think it will -- at least not in biology, and at least not soon. New post where I explain why, and how the productivity paradox can be resolved: blekhman.substack.com/p/why-ai-wil...

Why AI will not speed up science (yet)

You can see AI everywhere except in the productivity statistics

blekhman.substack.com

This city has been through way too much to give up on its diversity and give in to hate. It’s been a devastating and tragic day. But love always wins. ❤️

Is Christopher Nolan deaf?

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

To have some quiet while writing a grant proposal I came to a cemetery. The irony is not lost on me...

Adding my 2 cents about using agents for scientific work, with a focus on what's dear for German academia: "Datenschutz" and independence from foreign influence. Plus some concrete examples on how to use and sandbox the excellent pi harness! www.microbial-pangenomes-lab.org/2026/07/08/A...

@breakliquid.bsky.social and I are delighted to say our OpenEVO preprint is finally live! An open source hand-made turbidostat that's modular, affordable, and made to be customized. Designed with love for the research community. Enjoy!!!💚 www.biorxiv.org/content/10.6...

OpenEvo: An Open-Source Platform for Automated Evolution and Analysis

Here we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-s...

biorxiv.org

See? It's not difficult to surface interesting research across multiple axes

Pedro Beltrao@pedrobeltrao.bsky.social · 4w ago

The @qedscience.bsky.social "impact" score generated a lot of discussion on ranking preprints, including ideas on multi-dimensional rankings that are user specific. Besides describing the ideas, we can now prototype them (with Claude in this case). Here is Salient salient-sgeu6fs5ua-uc.a.run.app

New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...

Resistance potentiators: Evolutionary catalysts of antibiotic resistance

How do bacteria evolve resistance to antibiotics? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic res...

journals.plos.org

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

PectoCAZy: mining plant pathogens for industrially-relevant enzyme mixtures at University of Strathclyde on FindAPhD.com

PhD Project - PectoCAZy: mining plant pathogens for industrially-relevant enzyme mixtures at University of Strathclyde, listed on FindAPhD.com

findaphd.com

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...

Drift and Luck

In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.

open.substack.com

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?

Oded Rechavi@odedrechavi.bsky.social · last mo.

Gloves are off! TODAY WE RELEASE THE 1% A list of the year’s very best papers 👇 (see thread)

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!

Johanna von Wachsmann@johannavw.bsky.social · 2mo ago

🧬 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...

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.

The diffusion of large language models in published academic articles | PNAS

Large language models (LLMs) are rapidly changing academic research, raising questions of who is adopting these tools and under what conditions. Th...

pnas.org

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...

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images

AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma

doi.org

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

On the death of RCP8.5

We should celebrate progress, but not overstate it

theclimatebrink.com

In case you missed it 😎

Marco Galardini@mgalactus.bsky.social · 3mo ago

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...

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...

Pushing Local Models With Focus And Polish

Local models need focus and polish.

lucumr.pocoo.org