Ad forthcoming, but I am hiring for a postdoc or staff scientist to advance related investigations of the virus-host conflict. This position is ~80-100% computational, but with opportunities for experimental work if desired. If interested, shoot me an email with your CV! Reposts appreciated! 15/15

The US built the greatest talent magnet ever, attracting the smart, skilled, and striving. They’d come to study, then stay and build things here, or leave with positive impressions and fruitful connections. Helped make the US wealthy and powerful. Then America chose to throw it away. And for what?

Ben Allen@evodynamics.bsky.social · 3w ago

Congrats we just made it impossible to come here for a PhD www.bostonglobe.com/2026/07/16/m...

I'm giving a poster on MIMIC at #ISMB2026 today (C-211)! Drop by and chat with me about multimodal modeling for DNA, RNA, and protein biology. Inference code + checkpoints + sample data are all now available on GitHub/HuggingFace. github.com/PolymathicAI...

Samuel Sledzieski@samsl.io · 3mo ago

Introducing MIMIC: a new foundation model trained natively across DNA, RNA and proteins. MIMIC is multimodal and generative: it can use structure, regulation, evolution, and experimental context to infer missing biology or design new sequences. 🧵⬇️

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.

I am thrilled to share that UC Berkeley and UCSF have launched a joint initiative in Computational Biomedicine! cdss.berkeley.edu/news/uc-berk... We will soon be recruiting new faculty and postdoctoral fellows. Please repost to help spread the word.

UC Berkeley and UCSF Launch Computational Biomedicine Initiative

UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...

cdss.berkeley.edu

My go to example of this sort of thing is the study of weird thermophilic bacteria gave us PCR, upon which so much of modern biological research and its many applications (including drug discovery!) depend

Jonathan Pritchard@jkpritch.bsky.social · 2mo ago

People often think about risk as referring to (i): Can the project achieve its specific aims? But really what NIH should want is (ii): studies with low probability of huge long-term impact. Here, think of work on gila monster venoms (leading to GLP-1 meds) or bacterial immune systems (crispr)

Everything you wanted to know about the protein chemistry behind how amino-acid changes affect the cellular abundance of proteins from @tkschulze.bsky.social Effects of residue substitutions on the cellular abundance of proteins doi.org/10.7554/eLif...

We told you it wouldn’t be a long wait. 👀 Even more predicted protein structures have been added to the #AlphaFold Database. This time, the database has expanded to include heterodimers – protein complexes made up of two different proteins. alphafold.ebi.ac.uk

Introducing MIMIC: a new foundation model trained natively across DNA, RNA and proteins. MIMIC is multimodal and generative: it can use structure, regulation, evolution, and experimental context to infer missing biology or design new sequences. 🧵⬇️

We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...

Our review on ML for modeling conformational ensembles is out now in Current Opinion in Structural Biology (w/ @sonyahanson.bsky.social)! It's been exciting to follow all the progress in this field recently, and I'm equally excited to see where it goes! www.sciencedirect.com/science/arti...

The landscape of machine learning approaches for modeling protein conformational ensembles

The conformational ensemble of a protein and its corresponding probabilities and dynamics are crucial determinants of its function, but are difficult …

sciencedirect.com

ONE OF THE BIGGEST SHOTS AND CRAZIEST MOMENTS IN CBB HISTORY

StrucTTY: An Interactive, Terminal-Native Protein Structure Viewer www.biorxiv.org/content/10.64898/2026.03.17.712308v1 #cryoEM

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! 🧵⬇️

Rohit Singh@rohitsingh8080.bsky.social · 5mo ago

Protein language models don't scale reliably: bigger doesn't always mean better for embeddings. What if what you need from ESM-15B is already inside ESM-8M? Introducing Reverse Distillation, which flips the usual distillation script: small models anchor and decompose large ones

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...

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration

We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

evocellnet.com

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!

JHU Computer Science@jhucompsci.bsky.social · 6mo ago

Join us and the BME Department this Thursday for a joint seminar featuring @flatironinstitute.org’s @samsl.io! Learn more here: www.cs.jhu.edu/event/cs-bme...

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...

Multiple protein structure alignment at scale with FoldMason

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

science.org

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

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

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...

Samuel Sledzieski@samsl.io · last yr.

We're excited to introduce 🌿 MINT (Multimer Interaction Transformer) – a Protein Language Model (PLM) trained on 96M protein-protein interactions (PPIs) to predict binding affinity, mutational impacts, & antibody interactions better than existing PLMs! 💻 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