For-profit journals are supposed to improve research quality, yet they're perversely incentivized to churn out whatever they can monetize. This was happening before AI (see Strain: bit.ly/43gJPUM), and AI will make it worse. It's insane that we volunteer our time to help them do so. 4/n

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

Good end to a week with a good batch of 🧬✂️

Want @cytiva.bsky.social please make a Gradient Supedex www.sciencedirect.com/science/arti...

Saw this over on LI. Very slick and rasy to use mask generator. No more tinkering around needed like before. mcalbyrne.com/cryomaskr.html Video: www.linkedin.com/posts/mcalby...

Cleaning an office and this is my absolute nightmare circa 2008. Thank goodness most people have moved beyond word files and sequences… but not all 😌

developer.nvidia.com/blog/introdu... Will this finally be a codon optimizer that works? Still haven’t ever used a magic bullet but I do know not only the codons but the whole sequence play a big role

I am delighted to share this work, led by Miguel Alcantar and done in collaboration with Amgen, on the OrthoRep-driven evolution of computationally designed minibinders. Here, we focus not only on getting high affinity, but also on mapping sequence-affinity landscapes of diverse outcomes.

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

Just did my multiple choice get to know the country 🇨🇭 naturalization test. Now time for some sauna.. wait that’s the wrong country 🇫🇮 .

I am fascinated by how viruses evolve - and not just since #SARSCoV2 has shown us at the global stage how consequential virus evolution can be for us. In my new story in @science.org I got to explore how researchers are probing deeper into the past with old RNA virus genome. So a 🧪 thread…

Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org 🧬Code and notebooks will be released by the end of this week. 🎧Golden- Kpop Demon Hunters

🚨Our paper is out! 🥳 Hijacking a bacterial ABC transporter for efficient genetic code expansion. Many congrats to everyone involved - a multi-year effort led by @taruniype.bsky.social @maxfottner.bsky.social www.nature.com/articles/s41... it all started years ago with a failed experiment 🧵👇 1/9

Any structural biologists who want some fun? Try building mirror folds. When you’re building them you seriously innately feel like this is “off” but they do exist! When I looked at some of these datasets and deciding which way to turn in Coot it was so offsetting www.biorxiv.org/content/10.1...

After the conference comes the weekend :) Strasbourg and Basel + region what a nice combo. Strasbourg Munster or Roche towers? ⛪️🏢

Finished an exciting 38th Rhine Knee Structural 🧫💎🔬biology meeting lnkd.in/eYse4giF ! See you back in Switzerland in 2026!

How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...

The latest #AlphaFold DB update is out! We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction. Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!

Hmmm a library of protein designs all assessed for binding on the same platform. All with sequences, both positive and negative data. Makes for much better comparison than those made via paper claims. proteinbase.com

NEW: In 2025, 43% of young American adults regularly get their news from TikTok. www.pewresearch.org/short-reads/...

Our latest preprint is now available doi.org/10.1101/2025...! Led by my postdoc, Luqiang Guo @luqiang.bsky.social, we determined a ~2.4 A resolution structure of the hantavirus glycoprotein tetramer on the surface of VLPs. Also determined structures of dimers of tetramers and Fab-bound tetramers.

I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪

Be our neighbour !

Rejected for nationality because I make noise after hours. 😭

Long weekend dump. Torn between going to the 🏔️ or my garden. What did I choose?….

Heritage Foundation has released an absolutely insane policy proposal to label all trans people as domestic terrorists. It uses completely made up instances of terrorism and made up statistics but facts don't matter to them. They want us all eradicated.

anyone can find the preprint? I only found : arcinstitute.org/news/hie-kin...

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

Just discovered Outlook Recall. 🥰

Went up to the highest peak Gross Bigerhorn accessible for non-equipped hikers in Europe (3626m) with the first snow should’ve had some crampons! But made it to the top!

Really excited to have been a small part of this work investigating sarbecovirus host range, receptor usage and antigenicity! www.biorxiv.org/content/10.1101/2025.09.03.673949v1

Our first post on here and it's a doozy 😍🤩. Our epic piece on #sarbecovirus host range. #virology #sars2 #covid #vaccines. Enjoy and please repost. www.biorxiv.org/content/10.1...

What a super storm rainbow

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

In new study led by @bdadonaite.bsky.social, we measure how spike mutations affect function & antigenicity of spike of KP.3.1.1 strain of SARS-CoV-2. Sheds light on how key neutralizing epitopes are changing & importance of RBD up/down motion. www.biorxiv.org/content/10.1...

Computational design of allosteric pathways reprograms ligand-selective GPCR signaling [new] Comp. design infers/designs GPCR ligand responses via protein struct./dynamics. Receptor variants affect signaling.

Friends don’t use friend’s plasmids without sequencing them. For some types of plasmids from academic and industrial labs, up to 40% contained mutations academic.oup.com/nar/article/...

Just cleaning out some photos and found this gem

Asking it to think why a fusion protein of a target I was purifying was more stable and active than the cleaved version triggered a warning when I was using ChatGPT5.. So biology use is pretty much nerfed

Eating my first non-cherry tomato. Everett’s Rusty Oxheart! Juicy, sweet, weakly acidic. And those colours! It’s a rare variety but lots of seed vendors

I’m literally in a cell culture incubator. I think the first time in my life.. well other than the days before my birth

When the reviewers' identities are revealed

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!

Introducing Latent-X — our all-atom frontier AI model for protein binder design. State-of-the-art lab performance, widely accessible via the Latent Labs Platform. Free tier: platform.latentlabs.com Blog: latentlabs.com/latent-x/ Technical report: tinyurl.com/latent-X

Working with @astbury-bsl.bsky.social, we report cryo-EM structures of CD163 in its apo state and in complex with haptoglobin–hemoglobin (HpHb), and propose a framework of how CD163-mediated endocytosis clears different isoforms of HpHb. Please check it out on @plosbiology.org!

Designed protein pockets recognize intrinsically disordered protein regions @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.statnews.com/2025/07/17/n...

The backstory here is that the Squamish people of what is now Vancouver were illegally dispossessed of this land a century ago. They sued, got their land back, and are using their sovereignty to ignore local zoning rules and build 6,000 new homes over the objections of nearby wealthy NIMBYs.

Just cleaning some resin. This batch we started using in April 2025. Cube Biotech can you ship some more over here? ;)

We then fine-tuned the model on a larger scale, to predict forces across 10K solar systems. We used a symbolic regression to compare the recovered force law to Newton's law. It not only recovered a nonsensical law—it recovered different laws for different galaxies.

To demonstrate, we fine-tuned the model to predict force vectors on a small dataset of planets in our solar system. A model that understands Newtonian mechanics should get these. But the transformer struggles.