ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷
🤗 Hugging Face Space: huggingface.co/spaces/pimen...
⚙️ Google Colab: colab.research.google.com/drive/1l_h7c...
🧵👇
Until joining @loolibear.bsky.social's lab in July, I embarrassingly hadn't had much experience with plasmids.
So when I started, Leah said "here you go, have a look at this dataset".
What a fun ride this has been.
Preprint out today and thread below
www.medrxiv.org/content/10.6...
Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.
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...
@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
The @isvm-society.bsky.social is organising monthly #virus of #microbes (including #phage). Nominate a speaker and register for the upcoming events at isvm.org/ivom/
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
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...
Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖
with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social
academic.oup.com/nargab/artic...
details below...
#NARGAB
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
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)
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
🦠🧬🖥️ Bakta v1.12.0 is out
with tons of tiny improvements and bug fixes, too many to list all:
- partial genes on linear seqs
- improved errror handlings & runtimes
- support Python 3.12 & 3.13
- ...
A huge shout out and thank you to all bug reporters and contributors!
github.com/oschwengers/...
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
slow5tools v1.4.0 released github.com/hasindu2008/...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB.
guide to lossy archive: hasindu2008.github.io/slow5tools/a...
paper: doi.org/10.1101/gr.2...
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n
📃 doi.org/10.64898/2026.01.26.701724
New 2026 iVoM series coming up!
Each session includes SCR and 3 ECRs, & plenty of opportunities to interact with the speakers and ask questions.
Sign up for links/updates: docs.google.com/forms/d/1hAB...
First up: Viral Biotechnologies Wed, 28 th January at 17:00 CET / 11:00 EST / 08:00 PST
New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
Heng Li's lab is looking for a postdoc, "algorithms for sequence alignment, pangenome representation, application of pangenome data structures, or other projects". C/C++/rust proficiency needed.
hlilab.github.io/vacancies
💻🧬
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser.
hgbrian.github.io/alignism/
- The hard work was done by the awesome biowasm team!
- Does tree building too
- V fast compared to e.g., muscle on EBI
- Not tested that much!
💾 snp-dists 1.2.0
Major upgrade to this distance matrix tool - huge performance gains from multithreading (-j), max distance short circuiting (-x) and lower triangle output (-L).
#bioinformatiocs #microbiology #genomics
github.com/tseemann/snp...
💾 any2fasta 0.8.1 is released!
The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz
#bioinformatiocs #microbiology #genomcs
github.com/tseemann/any...
