Arne Elofsson

MMseqs2 v18 is out
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍

EXTRAORDINARY WORLD RECORD IN CHINA
Incredible 43.6C at 1970m asl in the Sichuan Province, BY FAR the highest temperature ever recorded in the world at that altitude
69 monthly records,including 4 long term all time:
42.4 Ziyang
42.2 Shiquan
38.2 Yajiang
35.1 Daofu

HISTORIC

we asked a simple question:
What does it take to learn the rules of RNA base pairing?

using standard deep-learning technics, got a simple answer:
don't need structures, nor alignments or many parameters
only a few RNA sequences and 21 parameters;
doi.org/10.1101/2025...

Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction Retrieving homologous protein sequences is essential for a broad range of protein modeling tasks such as fitness prediction, protein design, structure modeling, and protein-protein interactions. Tradi...

From Noelia I’ve thoroughly enjoyed reading two (VERY!) recent papers that model protein sequences by retrieving evolutionary information (dynamically) at inference time, and there's a lot to unpack!
[1] arxiv.org/abs/2506.08954
[2] biorxiv.org/content/10.110…
(

x.com/ferruz_noeli...

31 July 2025: Russia murdered these children in Kyiv

Lev Lamekhovyi, 2 - killed with his father and pregnant mother
Matvii Marchenko, 6
Roman Haiovyi, 17 - killed with his mother, brother, and uncle
Alina Humeniuk, 10
Nastia Humeniuk, 13 - sisters died together with their mother

#russiakills

Respiratory viral infections awaken metastatic breast cancer cells in lungs - Nature Mouse models show that respiratory infections from viruses such as influenza and SARS-CoV-2 can trigger metastasis of dormant breast cancer cells in the lungs, a finding supported by epidemiological data from two large human cohorts.

Nature research paper: Respiratory viral infections awaken metastatic breast cancer cells in lungs

go.nature.com/4odw172

YouTube video by Wallenbergstiftelserna He wants to reveal the secret behind the body's battery

Ville Kaila and his team @stockholm-uni.bsky.social want to understand one of the most fundamental functions of all living things: How cells absorb and convert energy. Basic research that in the long run may lead to new medicines and sustainable energy technology.
youtu.be/A12FvTn812Q

Nice

Comparison of enrichment for high-confidence pair interfaces out of the set of top confident pairs for DirectContacts2 and other networks. For each set, the fraction of high-confidence interfaces (pDockQ ≥ 0.5) out of their top predictions was calculated for increasing numbers of top predictions.

First, using a compendium of computed structural models for evaluation, we see our DirectContacts2 network outperforms other networks at prioritizing protein pairs for AlphaFold2 modeling.

The starvation of Gaza is shameful. Crippling sanctions on Israel are needed | Letters Letter: Thirty-one Israeli signatories express their shame, rage and agony over the plight of Palestinians and call for action from the international community

www.theguardian.com/world/2025/j...

DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...

We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.

www.biorxiv.org/content/10.1...

🚀 Today we're launching the 'Night Science Institute', a non-for-profit organization to lead a cultural shift in science! You may say we're dreamers 😉, but we think we're not the only ones. Perhaps today you will join us to make the Day Science and Night Science parts of the process live as one!

www.instagram.com/reel/DMk6pof...

@antifaspecops.bsky.social speaks out, in a new video

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages”

Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.

👇 Read on for details!
#Phage

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

But probably it is also essier to recruit good postdoc/students to a good environment. My colleagues in Kansas have real problems recruiting all the way from master students to faculty, while we have 100s of applicants for each position (not postdocs though)

I'm not 100% convinced it is just the recruiting better people, I do belive it is also something about being in a good environment. When I started my PhD noone jag graduated from that department in 8 years, but after my 4 PhDs graduated quickly. Having someone to compare you with makes a difference.

Large study of scientists who move their labs reveals how location drives productivity Concentrating funding at high-powered universities can maximize output, paper argues, but may sacrifice broader benefits

This is actually really interesting. Unclear what is the cause but my guess is that it is partly local competion, if your colleagues publish in Science you will also try to do so...

www.science.org/content/arti...

Three ancient human relatives once shared the same valley. Did they meet—and compete? The world’s greatest concentration of ancestral human remains, in South Africa, poses a 2-million-year-old riddle of coexistence

www.science.org/doi/10.1126/...

Columbia announces deal to pay Trump administration more than $220m Deal falls short of starkest measures, including consent decree and overhaul of university’s governance structure

www.theguardian.com/us-news/2025...

[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.

@hhu.de @crg.eu @embl.org @impvienna.bsky.social

alsi watch the end m.youtube.com/watch?v=Afet...

South Park came out swinging

I won three competitive grants in a row. Here’s how I learnt what to do It took time and rejections to understand what granting agencies look for. This is how I picked up application-writing skills.

www.nature.com/articles/d41...

DeepMind and OpenAI models solve maths problems at level of top students For the first time, large language models performed on a par with gold medallists in the International Mathematical Olympiad.

www.nature.com/articles/d41...

🧬🧶

Agree, it is quite clear thar it didn't learn physics

Cool, i need to check this

Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".