A session about how much information is transferred from sperm to the offsprings in a form of RNA was mind blowing 🤯 so cool! #EED2026

It’s absolutely incredible that one of the largest Japanese-run Go servers, which has been running since 1992, is still accessed entirely via Telnet. And while most players use GUI clients that use Telnet under the hood, you can still connect manually and get ASCII graphics streamed to you

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

ggCallaroo v0.1.0 is now out! This snakemake pipeline predicts, clusters and annotates bacterial genes using ggCaller, Panaroo and Bakta. It generates Panaroo files with functional annotations already integrated, which can then be used with the usual downstream tools. github.com/samhorsfield...

Two new bioinformatics internships available in @johnlees.bacpop.org group at EMBL-EBI: 1) testing and developing ML methods for identification of bacterial promoter regions; 2) Applying innovations in protein structure prediction to search massive datasets. Apply here: www.bacpop.org/jobs/

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 4mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on... github.com/bacpop/ggCal...

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

github.com

For those writing code with agents, this *excellent* article by Timo Bingmann (who wrote COBS, for kmer geeks) is super interesting on how one can conceptualise it in terms of dependencies, and how it affects development. V fun analogies (QWERTY, cooking, money) panthema.net/2026/0318-Vi...

A really fascinating read – with ideas underlying so many current topics across different subdomains of bioinformatics.

bioRxivpreprint@biorxivpreprint.bsky.social · 5mo ago

Constrained Diffusion as a Paradigm for Evolution https://www.biorxiv.org/content/10.64898/2026.03.10.710948v1

I was pleased to give an interview to @radiopraguefr.bsky.social about my academic journey across Czechia, France, and the United States, and about my research. english.radio.cz/karel-brinda...

Karel Břinda on research at Harvard and working with bacteria as if they were books

Karel Břinda sheds light on how curiosity, mobility, and interdisciplinarity can shape a modern researcher’s path in a world where science increasingly transcends borders.

english.radio.cz

I got the chance to feature on this week’s BBC More or Less podcast with the excellent Tom Colls, talking about how scientists count life on Earth, specifically the microbes. Have a listen: www.bbc.co.uk/programmes/p...

BBC Radio 4 - More or Less, Has a company really discovered a million new species?

Investigating whether Basecamp Research found hundreds of thousands of bacteria species

bbc.co.uk

I should have said, this takes us to about 2.8 million genomes in total. We don't have annotations, etc for the latest data yet, this will be an ongoing process

Zamin Iqbal@zaminiqbal.bsky.social · 5mo ago

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...

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...

How would you design a *multithreaded*, *concurrent* & *dynamic* hash table if you are focused specifically on common k-mer workloads, where streaming query & insertion are common? Jamshed, Prashant and I explore this in kache-hash, a cache-friendly k-mer hash table! www.biorxiv.org/content/10.6...

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover. 🔗 www.biorxiv.org/content/10.6...

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org ! Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these. www.ebi.ac.uk/about/news/u...

AlphaFold Database welcomes community datasets

Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

ebi.ac.uk

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

Letters of Note@lettersofnote.com · 6mo ago

Happy birthday to one of my favourite haters, Charles Darwin

What's the best place to look up current estimates of how many truncated/non-functional genes each of us have? there was a paper from @dgmacarthur.bsky.social and co around 2014 that had an estimate from the 1000 genomes project (around 40 per person?), but I guess we have better estimates now.

We're also happy to see a second paper out today, led by Nicola de Maio, which develops methods to identify and account for mutation rate variation and recurrent errors. www.nature.com/articles/s41...

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics - Nature Methods

Performing pandemic-scale phylogenetic analysis poses multifaceted challenges. This study develops methods for identifying and accounting for mutation rate variation and recurrent sequence errors, lea...

nature.com

Zamin Iqbal@zaminiqbal.bsky.social · 6mo ago

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...

How do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle

Sam Horsfield@samuelhorsfield.bsky.social · 6mo ago

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...

A comprehensive survey of genome language models in #bioinformatics academic.oup.com/bib/article/... 🧬🖥️🧪

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

Just came across the 2021 Turing Lecture. Has a lot of nice observations regarding the increasing gap between compute and memory bandwidth. It advocates "communication avoiding" algorithms and notes how algorithms can only be future proof if they scale with threads. dl.acm.org/doi/10.1145/...

The evolution of mathematical software | Communications of the ACM

Tracing how software and algorithms follow the hardware.

dl.acm.org

Congratulations @baym.lol, @brinda.eu and colleagues on the nice work, looks like a great way to identify deletions and deletion-induced fusion genes. In MTBC, genomic deletions called "regions of difference" have long been used for phylogenetic investigation. Yet I found no citations thereof.

Michael Baym@baym.lol · 7mo ago

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

💻 github.com/baymlab/deletion-born-fusion-manuscript 🔧 github.com/aryakaul/prefixsuffix-kmer Many thanks to co-authors @fernpizza.bsky.social , @brinda.eu & @baym.lol + GenScale/Baym lab! Funded by NIH, Packard, Pew, Sloan & a Chateaubriand Fellowship!

GitHub - baymlab/deletion-born-fusion-manuscript

Contribute to baymlab/deletion-born-fusion-manuscript development by creating an account on GitHub.

github.com

🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 7mo ago

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 7mo ago

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!

Society for Molecular Biology and Evolution@official-smbe.bsky.social · 8mo ago

Organisers - @bacpop.org | @embl.org - @aweimann.bsky.social | University of Cambridge Invited Speaker - @audeber.bsky.social | Institut Pasteur