Last official working day of 2025!! I can't believe I made it in one piece to the end of the year. I have earned a couple of beers at the end of the day 🤣

wwPDB has received a record number of depositions this year--more than 20,000! Many thanks to all of our depositors and biocurators more making these important data available to all Details:

RNA could have formed spontaneously in the environment of early Earth, some 4.3 billion years ago, according to a study. A key requirement for some steps is borate, which was thought—incorrectly, according to the authors—to inhibit other steps. In PNAS: https://ow.ly/TAuc50XL3ZS

Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉 In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria. www.nature.com/articles/s41...

Have you ever wondered how the interactome from ancient organisms evolved? @edward_marcotte gave us an Elixir lecture with insights of how it would have been in the Last Eukaryotic Common Ancestor (LECA)! Now uploaded to our YouTube channel: www.youtube.com/watch?v=UP4J... We hope you enjoy it!

I have two open positions @ALMU @crg.eu: 1. Imaging Scientist (permanent position. Deadline 11th Nov.) recruitment.crg.eu/content/jobs... 2. Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) recruitment.crg.eu/content/jobs... Reposts appreciated.

Last week to apply to join our recently created lab as a PhD Student! Join us to research about protein computational biophysics, evolution, machine learning , and human mutations! Description and link to apply here: www.bsc.es/join-us/job-...

Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social. 📄 academic.oup.com/bioinformati...

From @gonzaparra.bsky.social et al., in @plos.org #Computational #Biology | Impact of the #COVID-19 pandemic on computational biology early career researchers: A global retrospective study | #Bioinformatics #Education #OpenScience CC/ @iscb.bsky.social 🧬 🖥️ 🧪🔓 ⬇️ journals.plos.org/ploscompbiol...

Interesting work that we conducted from the Student Council of @iscb.bsky.social to estimate the impact of the COVID19 pandemics on early career researchers in computational biology! Thanks for leading this effort Farzana Rahman and to the entire team! journals.plos.org/ploscompbiol...

A collab referred me to this paper which I of course read when it came out in 2013. However, as a mid-way PhD student my capacity to deeply understand its details was pretty limited. 12 years later, I can understand much more! I really recomend this jewel! doi.org/10.1063/1.48...

as a philosopher, I can confirm we don't know what thinking is

Repeat with me: 👏🏼 Scores 👏🏼 are👏🏼 not👏🏼 metrics👏🏼!! it's a personal battle 🤣 I've become Don Quijote against the windmills. Still, I believe that speech accuracy is fundamental un scientific speech even when we all can interpolate the right meaning.

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

🚀 As first official act, we are hiring! 🎓 We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded! More information here: www.bsc.es/join-us/job-...

After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬 Thanks to all who have been part of this process! tinyurl.com/4r9vf4zx

🚀 As first official act, we are hiring! 🎓 We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded! More information here: www.bsc.es/join-us/job-...

After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬 Thanks to all who have been part of this process! tinyurl.com/4r9vf4zx

Whole brain dynamics in the ~10s regime shows synchronized propagation of topographically organized rotating waves, driving behavior, calcium fluxes, band-limited power, metabolism, blood flow, etc. All can be predicted from time-lagged embedding of pupil size alone! www.nature.com/articles/s41...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

LinkedIn just notified about my 4th year annyversary working at the @bsc-cns.bsky.social, time flies!!! It's been a great chapter so far in my scientific journey!! A lot of projects on the list! #ILoveScience

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳 📖 Preprint: www.biorxiv.org/content/10.1... 🔍 Explorer: explore.omnipathdb.org OmniPath integrates 160+ resources for multi-omics analysis & modeling. 🧶⬇️

New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴 doi.org/10.48550/arX...

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail nature.com/articles/s41467-025-63463-6

Dear Colleagues. We are in need of a molecular dynamics trajectory of a "folding upon binding event" where a protein with an IDR folds into its partner. Do you know of any published and available trajectory that we could use?? Thanksss a lot!

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

Rob Finn on MGnify, everything bacteria and functions in different environments

Now Maria Martín from UniProt is telling us how AI-based tools are shaping the future of one of the key resources for protein sequences and function.

From structures to sequences, now Alex Bateman and the quest to annotate and classify all proteins!

Starting our afternoon session with a talk by Sameer Velankar, of PDBe and AFDB fame among other endeavours!

And now @gonzaparra.bsky.social on his first talk on protein frustration as a PI! Well done!

David Jones, on novel folds in AFDB and CATH’s founding being celebrated at a now-closed Pizza place in Euston Station

From CATH to Computational Enzymology, Dame Janet Thornton on the birth of CATH and beyond!

First Keynote by Burkhard Rost, on the impact of protein language models on the field of structural biology

Kickstarting our symposium “Protein Annotations in the age of AI” at UCL!

Stephen Jay Gould was born OTD in 1941. “Organisms are not billiard balls, propelled by simple and measurable external forces to predictable new positions on life's pool table.... Organisms have a history that constrains their future in myriad, subtle ways.” 🦫🦋🐋🌱🧠🗃️🧪#HistSTM #PhilSci #EvoBio

In the face of climate change, the race to understand life on Earth is on. @ebpgenome.bsky.social is scaling up tenfold to sequence all known species by 2035. At EMBL-EBI, we annotate these genomes, making them openly available for the global research community. www.ebi.ac.uk/about/news/a...

🚨 New in PNAS! 🧬 64% of disease co-occurrences can be explained by transcriptomic similarities. Comorbidities aren’t random—they have a molecular basis. Here’s how we found it 👇 (1/n) 🔗 doi.org/10.1073/pnas.2421060122 @alfonsovalencia.bsky.social

Repeated heatwaves can age you as much as smoking or drinking "Long-term study suggests that the more heatwaves people are exposed to, the more it accelerates body ageing." www.nature.com/articles/s41...

CATH turns 30 years old 🥳 They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families" Unbelievable selection of speakers! So if you are around London, you can register to attend: tinyurl.com/2pnk8hj5

Congratulations @judewells.bsky.social!

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

If you'd like to showcase your research with a poster, details are included in the registration page. We hope to see you there!

We have a stellar lineup of speakers! Christine Orengo Burkhard Rost Janet Thornton David Jones Gonzalo Parra @gonzaparra.bsky.social Sameer Velankar Alex Bateman Maria Martin Rob Finn Gerardo Tauriello Alexey Murzin

There will be talks from world leaders in structural bioinfomatics on various themes including pioneering protein language models and key international resources including: PDBe, InterPro, UniProt, MGnify, SWISS-MODEL, FrustraEvo and CATH.

CATH turns 30 years old this year! We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses. www.eventbrite.co.uk/e/protein-an...