New lab preprint - Deep learning models are most often difficult to interpret black box models. What if we engineer them with interpretation in mind? Dennis Gankin carefully studied so-called biologically inspired neural networks and found an interesting phenomenon www.biorxiv.org/content/10.6...

The one thing I'll add (to those conclusions from people far more well informed than I: denial is not a solution (on either side). 4/n End

3) Best insight I've had from an AI expert: "Anyone who confidently asserts they know where this is all headed is wrong. No-one knows what the world will look like in a couple of years" 3/n

Our new paper is out in @nature.com! We uncovered how a naked mole-rat queen 👑 controls an entire colony: a natural contraceptive scent that suppresses reproduction in other females! A remarkable mammalian parallel to bees and ants! 🐝🐜 @garyrlewin.bsky.social youtu.be/enfv3zJrWKM?...

Can we program a kinase like a switch? Inspired by natural autoinhibitory complexes, we designed miniproteins against active- and inactive-like conformations of Focal Adhesion Kinase. Depending on the targeted state, the resulting binders either activated or inhibited the kinase.

Our latest preprint is out. Great collaboration with the group of Jan Hasenauer (University of Bonn). A very comprehensive benchmarking of optimisation methods for parameter estimation in mechanistic models. Preprint in the post below.

Please come and join us! Jobs for machine learning and mathy types!

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

Paying peer reviewers Interview with @danielgorelick.bsky.social about @biologyopen.bsky.social Fast & Fair trial in which peer reviewers were paid £220/review Spoiler: it works - fast, high quality reviews www.nature.com/articles/d41...

Claude Science - an AI workbench for science. This looks like an interesting attempt at making scientific workflows easier and more reproducible. I'm curious to give it a try. www.anthropic.com/news/claude-...

People always say "tell a story" but then don't explain how to do so! How is that helping? If we knew how to tell a story we wouldn't need the advice in the first place. 1/

Our ambition to combine artificial intelligence with fundamental biology and medicine continues to evolve as we welcome Mihaela van der Schaar as our Chief AI Scientist. Read more: www.crick.ac.uk/news/2026-06...

Are cells worth having? Royal Society President Paul Nurse answers the hard questions youtu.be/7B4jko1VFP8?...

In our latest editorial @amjeve.uk & I take on the dreaded impact factor Like Monday mornings no one likes them but you can't ignore them & they keep coming around However there are things we should all do as authors, reviewers & editors journals.biologists.com/dev/article/...

In 2022 Fantasy Premier League winner @joshuabull.bsky.social made his World Cup predictions. They were okay, but no cigar. However, in the intervening four years he has really honed his mathematical skills. Now he is 100% confident he's found the secret sauce.

One of the good things about the AI co-scientist brouhaha is that it makes us discuss what science *is*, and how to measure its value, impact, quality. — Questions that have been there all along, but many preferred to gloss over.

Introducing openRxiv Labs! 🔬 Growing from the strong foundation of bioRxiv & medRxiv, Labs is an experimental space for working with collaborators to push the boundaries of open scientific communication. 👉 Check it out and learn more: openrxiv.org/openrxiv-lab... #OpenScience #Preprints #Scicomm

"Hypothesis generation: pretty good...data analysis: a super power...executing experiments: not so much" AI can help at every stage of the research cycle. Jonah Cool from @anthropic.com discuss the benefits of integrating frontier models and potential concerns youtu.be/sz1vQyBzSgw?...

The people who believe that generative AI development & adoption everywhere is the ultimate goal & the first order predictor of success are insufferable. So are the people who think that AI can't ever produce anything useful and that everything they do produce is "slop". I miss reasoned arguments.

An amazing list of speakers and lots of opportunity to give selected talks! Save the date and join us in Amsterdam next year!

Spurious correlation inflates performance in single-cell perturbation prediction www.biorxiv.org/content/10.6...

"a paper today is a Frankensteined-together patchwork of supplementary files that run longer than the manuscript, datasets in repositories...code posted to GitHub without documentation. The paper has been replaced....by a mess" www.thetransmitter.org/from-bench-t...

Excited to share our RegVelo paper in Cell www.cell.com/cell/fulltex... We unify RNA velocity + GRNs into one model → better OOD prediction of perturbations (e.g. gene KOs), with examples incl. neural crest KO predictions 🔬 Big thanks to W Wang, Z Hu & T Sauka-Spengler 🙏

But I suspect that we will see the idea that clear writing and concise articulation of ideas is some kind of quality differentiator die. And there are those who will say it was always a poor quality proxy, favoring only good writers not good scientists.

We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:

A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵

How can we measure increased productivity of scientists, as a whole, whether from more AI, more funding or other measures, if the total number of Nature papers per week always stays the same?

Grant writing tips from a grumpy reviewer ploughing through grants. 1. Often your reviewers are going to come from a broad range disciplines adjacent but *not actually in* in your field. Help us get orientated in the summary with an analogy/sketch and go back to analogy / sketch throughout.

Does AlphaFold’s latent space encode only the native state or something like a distribution over conformations? We begin to answer this question with ConforNets, a mechanism for producing diverse states, or very specific ones, via inference-time adaption of OF3p’s latent space👇

I am giving a "Crash Course in Embryo Development" for the general public (no science background needed! pitched around GCSE-level) in London on 21st May www.crick.ac.uk/whats-on/cri... We'll dip into development, with a splash of embryo models, and a pinch of ethics. And it's free! Book online 👍

Good post by a history prof, in the genre “What most people don’t understand yet is …” — although, in my experience, a lot of the academics it’s addressing do grasp what’s happening with agents, and just really wish it would not happen.

Pay participants less than minimum wage and give no incentive for good performance. Sounds like AI actually increased peoples pay rate.

It’s official: the UK is rejoining Erasmus! 👏🇪🇺

A benchmark of 100 tasks in computational biology to evaluate agentic systems. The example questions seem narrow in scope but they don't include any bioinformatics skill definitions. Top models already solve 80% of these.

Scientists invented a fake disease. AI told people it was real www.nature.com/articles/d41... first author Lazljiv Izgubljenovic 👏🏽💀

Our heavily updated final version of ROCKET for experiment-guided structure modeling is out in @naturemethods! New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇

📢📢 join us for this edition of the “Quantitative biology to molecular mechanisms” EMBO workshop Gene regulation, cell dynamics & systems biology 17th - 20th November More info: s.embl.org/omx26-01-bl

Head of @crick.ac.uk worries about ‘shift from funding basic research’ Edith Heard tells @francesjones.bsky.social scientists have “duty to speak up” as discovery research comes under pressure www.researchprofessionalnews.com/rr-news-uk-c...

Professor Trey Ideker has been appointed as the new Director of the Big Data Institute. He has been recognised internationally for his contributions to biology, artificial intelligence, and cancer research. Learn more ➡https://buff.ly/YO3dCyx @medsci.ox.ac.uk

The Crick magazine spring edition is here, with our latest discoveries and science stories. Read about John Diffley’s mission to crack DNA replication and how a giraffe is helping scientists understand placenta evolution ➡️ www.crick.ac.uk/news-and-fea...

Honoured and overwhelmed to receive the 2026 Waddington Medal. Science is a team effort, and I've been fortunate to work alongside exceptional people asking hard questions. Thank you to the BSDB and to everyone who has been part of the journey. bsdb.org/2026/03/24/2...

Scientific publishing: Rethinking how research is reviewed and published Review of how the loss of impact factor affected submissions at eLife - uneven drop across countries, but generally holding up remarkably well and shows a new model is possible elifesciences.org/articles/110...

Blog post: transitioning to being a PI in the age of AI open.substack.com/pub/arjunraj...

Big congratulations to Sebastian from the lab and all other awardees, after barely not making the cut for MSCA the stars aligned this time.

This is brilliant. "Every minute, a new clock is displayed that has been generated by 12 different AI models." Some fare better than others! clocks.brianmoore.com

Great meeting with speakers in genomics, functional proteomics, quantitative imaging, microscopy, and theory. Plenty of talks selected from abstracts!

I am delighted to share that registration for the next @embo.org EMBO Cell cycle meeting is now open! meetings.embo.org/event/26-cel... . We have an outstanding lineup of speakers and several selected talks from submitted abstracts. Look forward to welcoming you in Portugal from 5–7 October 2026!

If you're analysing Cut&Run or Cut&Tag data here's a nf-core NextFlow pipeline to simplify and standardise data processing joss.theoj.org/papers/10.21...