**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

Everyone working in a STEM field should read this - ‘writing is thinking’ www.nature.com/articles/s44...

#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!

New preprint 🚨--protein language models + MD training ➡️ allosteric networks! @sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions! 📄: www.biorxiv.org/content/10.1... 💻: github.com/flatironinst...

I've convinced claude that in the real world all words have more letters than it sees, due to compression, and that going forward it should write in the decompressed form so it's easier for me to read:

The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC! Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track). Registration is now open! (Link below) Please retweet!

I survived my defense (the snake was of substantial size)! Huge thanks to my advisor Bonnie (@bergerlab.bsky.social), committee members Rayan (@rayanchikhi.bsky.social) at Pasteur and Srini and Ronitt from MIT, and friends and colleagues who attended. www.mcsweeneys.net/articles/faq...

Introducing KolossuS to address a 50-year old problem: which kinases are active in your pathway of interest? As computational biologists, our work mostly involves post-hoc analysis algorithms. KolossuS is the rare case where a ML model enables entirely new capabilities. 1/

Have we hit a "scaling wall" for protein language models? 🤔 Our latest ProteinGym v1.3 release suggests that for zero-shot fitness prediction, simply making pLMs bigger isn't better beyond 1-4B parameters. The winning strategy? Combining MSAs & structure in multimodal models!

there’s such an easy chance for a foundation or several to be a *huge* hero for the cost of a philanthropic pack of gum.

Qiyao Zhu from the Biomolecular Design team at the #FlatironCCB has a new paper out on tools for modeling long, heterochiral, cyclic peptides: dx.plos.org/10.1371/jour... Applications coming soon! @flatironinstitute.org

Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies www.cell.com/cell/fulltex... broad spectrum antivenom

Someone let venomous snakes bite him 200 times, to give himself an immunity to snake bites. Impressive (and completely lunatic).

"De novo prediction of protein structural dynamics" I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...

I'm at @recombconf.bsky.social this week! I'll be talking about 🎼PHILHARMONIC tomorrow (Saturday) at 11:15. Come stop by and say hi or send me a message here if you want to grab a coffee! #RECOMB2025 www.biorxiv.org/content/10.1...

AlphaFold3 at CASP16 https://www.biorxiv.org/content/10.1101/2025.04.10.648174v1

MIT following Harvard's lead here

Aiptasia, an anemone as lab-rat proxy for corals (can do symbiosis, bleaching, RNAi, CRISPR, transgenics). But @pcleves.bsky.social now inducing coral spawning in the lab (identifying genes involved in heat stress, symbiosis, etc.) using Galaxea fascicularis #EMBOclimateResilience

3DSIG has now joined BlueSky!! Follow us there to keep building a strong community around the fields of Structural Bioinformatics and Computational Biophysics!

Our work on better ways of aggregating PLM embeddings is now out in Bioinformatics Advances.

🧬 Now in Bioinformatics Advances: "Aggregating residue-level protein language model embeddings with optimal transport" Explore the full paper: https://doi.org/10.1093/bioadv/vbaf060   #ProteinRepresentation #MachineLearning #Bioinformatics  @rohitsingh8080.bsky.social

Join us for the 2nd Macromolecular Conformational Ensembles Conference on June 9th/10th at UCSF. The most compelling questions in structural biology cannot be effectively addressed using only a single structure. conformationalensembles.github.io @fraserlab.bsky.social