Annual reminder: if you’ve been accepted to multiple graduate programs and are still deciding, please let the ones you’re definitely not going to know as soon as possible! -Someone who got into his PhD off the waitlist the day after the deadline

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

You asked, we listened. Millions of AI-predicted protein complex structures are now available in the #AlphaFold Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list. www.ebi.ac.uk/about/news/t...

Had a lot of fun working on this with Darius, Christian, and Rohit. We address the problem of unpredictable scaling behavior for PLMs -- with a simple 2-line drop-in replacement for ESM2, you no longer need to worry that a smaller model might end up performing better! 🧵⬇️

We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations. www.evocellnet.com/2026/03/mapp...

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required. We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

Additionally, I want to speak directly to Iranian New Yorkers: you are part of the fabric of this city — you are our neighbors, small business owners, students, artists, workers, and community leaders. You will be safe here.

A great start to the Biophysical Society Annual Meeting in San Francisco! Check out the various projects being presented on work from Flatiron Institute people! #bps2026

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

Looking forward to speaking to @jhucompsci.bsky.social and JHU Biomedical Engineering this Thursday!

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

I just thought everyone should see this

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

Check our new preprint smoothing rugged Cryo-EM landscapes: shorturl.at/gYs9U We tackle practical hurdles of Optimal Transport (OT) loss—differentiability, cost & noise sensitivity—make it a feasible inference workhorse. W/ G. Woollard, D. Herreros, @pilarcossio.bsky.social, K. Dao Duc 🧵👇 (1/9)

🌿 MINT is out now in Nature Communications! 📄: www.nature.com/articles/s41... 💻: github.com/VarunUllanat...

Terrifying headline if you don’t realize they are sports teams.

The Center for Computational Biology at the Flatiron Institute is accepting applications for summer intern positions. CCB is a great place to work, and the intern program is excellent. Please check out the Computer Vision and Developmental Dynamics groups in particular. apply.interfolio.com/177779

We're recruiting summer interns at all levels (Bachelors, Masters, PhD) and across all groups at @flatironinstitute.org Center for Computational Biology. Come work with us in New York City! (Full-time paid, June 1-August 14 2026, applications close January 16 2026) apply.interfolio.com/177779

Announcing cryo-EM heterogeneity challenge #2, now dubbed the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)! Join us for a webinar next Friday (Nov 14th) to learn more. Datasets already posted here: heterogeneity.notion.site/challenge #cryoem

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: [email protected]

D-SCRIPT + BMPI is out today in Bioinformatics! academic.oup.com/bioinformati...

Integrative modelling of biomolecular dynamics Time-dependent and -resolved experiments combined with computation provide a view on molecular dynamics beyond that available from static, ensemble-averaged experiments Review w @dariagusew.bsky.social & Carl G Henning Hansen doi.org/10.48550/arX...

These are the quarterbacks since 2010 who complete passes at roughly the rate Microsoft Excel’s AI mode accurately edits spreadsheets

*Job Alert*: postdoc positions available @flatironinstitute.org in Computational Mathematics: apply.interfolio.com/173401

Happy (a^2, b^2, c^2)! www.npr.org/2025/09/16/n...

YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...

I’ll be at MLCB today and tomorrow, and talking about our latest work on modeling protein dynamics 🚀 tomorrow afternoon!

2025 Machine Learning in Computational Biology (#MLCB) meeting starts TODAY (9/10) at 9:30a (EST) at the NY Genome Center in NYC! We have a great lineup of keynotes, contributed talks, and posters today and tomorrow Schedule: mlcb.org/schedule Join for free via livestream: m.youtube.com/@mlcbconf

Excited to share our recent work: Sparse autoencoders uncover biologically interpretable features in protein language model representations now in PNAS. Thread below 🧵

Announcing the Diffuse Project! We're unlocking protein dynamics through diffuse X-ray scattering - the overlooked signal that could revolutionize how we understand protein motion. seemay.substack.com/p/from-syste...

The results of the ISCB Leadership vote are in!  Terms for the ISCB President-Elect and ISCB Vice President will start on January 21, 2026.

I just got the notice that all the FlyBase people at Harvard, including me, will be laid off on October 12. I'm devastated.

We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...

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🧵

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...

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv! biorxiv.org/content/10.110

#FlatironCCB scientists Natalie Sauerwald, Olga Troyanskaya and colleagues leveraged @sparkforautism.bsky.social data to reveal four distinct groups that link autism-related traits with underlying genetics. Read more: www.simonsfoundation.org/2025/07/09/n... #science #biology #autismresearch

Today we released a major new update to D-SCRIPT! 🚨 TL;DR, whole-proteome protein-protein interaction prediction is now significantly faster *and* less memory intensive 🚅 🧠 You can get started with the new version with `pip install dscript==0.3.0` 💻 github.com/samsledje/D-... 🧵⬇️

The short film "Molecular Duet" brings the dynamic world of microtubules to life. A collaboration between @flatironinstitute.org researcher Mahsa Mofidi and filmmaker Anne Sofie Nørskov. Watch in full: www.simonsfoundation.org/2025/07/16/w... #science #biology #film #FlatironCCB

From #FlatironCCB scientist Bargeen Turzo and filmmaker Grace Zhang, "How to Connect Two Bodies" is an experimental documentary exploring the invisible choreography in meaningful connections of objects across various scales. Watch in full: www.simonsfoundation.org/2025/07/09/w... #science #film

We're excited to release 𝐦𝐑𝐍𝐀𝐁𝐞𝐧𝐜𝐡, a new benchmark suite for mRNA biology containing 10 diverse datasets with 59 prediction tasks, evaluating 18 foundation model families. Paper: biorxiv.org/content/10.1... GitHub: github.com/morrislab/mR... Blog: blank.bio/post/mrnabench

🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...

Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...

Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90

CASP is the main reason the protein structure prediction technology and research field advanced over the last 30 years. And the main reason AI based methods have been accepted and widely applied in biology. So shortsighted of NIH to postpone or even halt funding. John Moult is a scientific hero.

Watch: 6 Science Short Films Created by Flatiron Institute Researchers and Filmmakers www.simonsfoundation.org/2025/06/18/w...

One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/

Extremely cool work here!