Never believe the fuckers who say "why bother, they already won"

Updated preprint on the roadmap to predicting macromolecular ensembles with @bonomimax.bsky.social! Four key issues: 1) Structural ensembles are defined inconsistently across disciplines. 2) No single experimental technique alone can fully capture structural ensembles arxiv.org/abs/2505.01919

In Boston, every day is No Kings Day

😍 Boston, you are beautiful. #NoKings

Happy birthday to American astronaut Mae Carol Jemison (born October 17, 1956), a physician who became the first Black woman to travel in space when she went into orbit aboard the Space Shuttle Endeavour for NASA, on September 12, 1992! 🐡🧪🧑🏾‍🔬 #histsci She also has a B.S. in chemical engineering, 🧵1/n

Want to join the BioEmu team at MSR AI for Science? We have multiple intern (jobs.careers.microsoft.com/global/en/jo...) and one fixed-term postdoc (jobs.careers.microsoft.com/global/en/jo... positions available! Please share with potential candidates :)

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

After years of complaining about cancel culture, the current administration has taken it to a new and dangerous level by routinely threatening regulatory action against media companies unless they muzzle or fire reporters and commentators it doesn’t like.

Tomorrow we're excited to host @sarahalamdari.bsky.social at Chalmers for the AI4Science seminar and hear about generative models for protein design! Talk at 3pm CEST. 🤩 For more info, including details on how to join virtually, please see psolsson.github.io/AI4ScienceSe... @smnlssn.bsky.social

A compelling review of how ML/AI could help in the quest to find an enzyme for every reaction. @jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social www.cell.com/cell-systems...

Join us this fall for the Chalmers AI4Science seminar series with this amazing line-up of speakers! All seminars held on-campus at Chalmers and streamed over Zoom. See psolsson.github.io/AI4ScienceSe... for details! Speakers: @sarahalamdari.bsky.social @micheleceriotti.bsky.social & Prashant Singh

A United States Senate investigation has identified more than 500 credible reports of human rights abuses in US immigration detention since January, including alarming allegations of mistreatment of pregnant women and children.

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6

(1/7) Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3) [https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

The @uwproteindesign.bsky.social's experimental pipeline behind models like RFdiffusion and ProteinMPNN: - A rapid, scalable, pipeline for producing and characterizing proteins - A demultiplexing protocol for converting oligopools to clonal constructs Jason Qian @lfmilles.bsky.social Basile Wicky

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

I don’t want the NIH to be fucking profitable, I want it to cure cancer and Alzheimer’s

We may have the chance to hire an outstanding researcher 3+ years post PhD to join Tarleton Gillespie, Mary Gray and me in Cambridge MA bringing critical sociotechnical perspectives to bear on new technologies. jobs.careers.microsoft.com/global/en/jo...

In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known. Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.

Join us along the #BostonPride parade route to celebrate the resistance of our LGBTQIA+ community in the face of tyranny. ✊🏳️‍🌈🏳️‍⚧️🇺🇸 #NoKings #50501movement @50501movement.bsky.social www.boston.com/news/local-n...

🧪👩‍🔬🧬🥽🍎 #politics www.nytimes.com/interactive/...

Massive crowd at Boston’s city hall plaza for the #HandsOff protest against Trump and Musk

I accidentally discovered that there is a weird magnetic spot on my laptop that will make a paperclip stand up, so I had to add googly eyes and make my own personal Clippy

Our paper on prediction of phase-separation propensities of disordered proteins from sequence is now published: www.pnas.org/doi/10.1073/... The paper has been substantially updated compared to the preprint including new experimental data and using the neural network to finetune CALVADOS. 1/n

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models. Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1. 📝: rb.gy/de5axp

Use reward-guided generation and iterative refinement to steer the proteins generated from EvoDiff! arxiv.org/abs/2502.14944

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding. Why does this matter? Reproducibility & fair comparison have been lacking—until now. Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti... A thread ⬇️

AI provides a universal framework that leverages data and compute at scale to uncover higher-order patterns Today, @arcinstitute.org in collaboration with Nvidia releases Evo 2—a fully open source biological foundation model trained on genomes spanning the entire tree of life.

Excited to share PoET-2, our next breakthrough in protein language modeling. It represents a fundamental shift in how AI learns from evolutionary sequences. 🧵 1/13

If you’re a federal govt employee targeted for leave or termination on the basis of your DEI work, please file an EEO (Equal Employment Opportunity) complaint & retain legal counsel. I’m a former NIH PI. Happy to refer you to a law firm that has successfully sued the govt many times! Pls repost 🙏❤️

wonderful to see this tremendous piece work finally out, from @prywes.bsky.social et al. www.nature.com/articles/s41...

Four years ago I wrote my inaugural poem The Hill We Climb. Both when I wrote it and performed it, I did so while continuously reflecting on Dr. Martin Luther King Jr and Coretta Scott King’s legacy.

New preprint from our group! We propose SHAPES, a set of metrics to quantify the distributional coverage of generative models of protein structures with embeddings at different structural hierarchies and quantify undersampling / extrapolation behaviors.

People sometimes make fun of science that sounds stupid and random. Meanwhile, a study of lizard saliva turned into a peptide medication, which was turned into a diabetes medication, which was turned into a GLP1 weight loss drug, that just became the first therapy every approved for … sleep apnea

It’s that magical time of the year when researchers across Microsoft release our collective effort to summarize the state of knowledge regarding AI and the New Future of Work. Here ya go: aka.ms/nfw2024

I really think that MSOffice software should make allowances for the use of :wq #CompChemSky

Protein language models excel at generating functional yet remarkably diverse artificial sequences. They however fail to naturally sample rare datapoints, like very high activities. In our new preprint, we show that RL can solve this without the need for additional data: arxiv.org/abs/2412.12979

In our newest preprint, we show that simply increasing the size of pre-training datasets doesn't necessarily improve the performance of single-cell foundation models on downstream tasks. Really proud of @alandenadel.bsky.social for leading this effort! See his thread below for more details👇

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

📣 Save the dates 📅 We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March (benzon-foundation.dk/benzon-sympo...)

At NeurIPS and interested in talking about BioML? Catch me at the Microsoft booth in the expo hall between 2:00-2:30p and 3:30-4:30p today!

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations: bit.ly/plaid-proteins 🧵

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

Improving structure prediction by padding MSAs with synthetic sequences. Potts model-designed seqs worsen prediction performance, so some higher-order coevolutionary interactions appear to be contributing to this boost openreview.net/pdf/fd516f23...

🚨Our Machine Learning Force Field Mattersim is now available! 🚨 Check it out here 👇 msft.it/6013oBZLt The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :) Feedback and suggestions are very welcome!

This should go chiral

Now you can easily follow all of the amazing scientists that have presented at Boston Protein Design and Modeling Club go.bsky.app/53tEUeR

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️ So how can we ever achieve #gender #equality? We discuss various strategies in this #Cell Commentary #WomeninSTEM www.cell.com/cell/fulltex... 🧵 1/