Samuel Sledzieski

The Sledzieski Lab is opening in the Halıcıoğlu Data Science Institute at @ucsandiego.bsky.social in July 2027! 🥳🏄‍♂️ We're recruiting at all levels, and graduate applications are now open for both HDSI and the BISB program. Please share with anyone that might be interested! sledzieskilab.org

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Job alert! We're hiring! apply.interfolio.com/194662

*Job alert*: Postdoc position at the Flatiron Institute to work on biophysical inference and cryo-EM. ❄️ 🔬Applications are welcome! apply.interfolio.com/193799

One of the most revered and celebrated albums in music history was released on Sept. 28, 1976 — 50 years ago today. Songs in the Key of Life tracks, ranked:

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

📣 The Singh Lab opens at Fox Chase Cancer Center in Spring 2027, where I will be starting as an Assistant Professor!📣 Excited to continue studying how protein biophysics shapes drug response. I am hiring across all levels and disciplines! Apply on the "Join" page ( & spread the word!): singhlab.bio

Extraordinary blog post by @moalquraishi.bsky.social moalquraishi.wordpress.com/2026/08/10/a... Starting with the question on whether workaphiles will be dying breed post AGI, it later turns into serious scifi - "The 'easy' solution is to make our brains bigger"

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?

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...

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.

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

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

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...

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! 🧵⬇️

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...

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