In the W-S lab's first preprint, we describe how genomic language models know something about RNA thermodynamics. Though we think this is cool, things get tricky! A growing practice for interpreting LMs is to perturb input tokens, often called "Categorical Jacobian": 👇

What are good places to post an unsolicited manuscript peer review these days? I don't have a blog. I read manuscripts across arXiv, bioRxiv, ChemRxiv, OpenReview, random white papers, journals, etc. Do I dump it on Zenodo, post it here, and send it to the authors?

Introducing AlphaFast 🚀. AF3 is transformative but too slow for large-scale protein design. My students Ben and Jeonghyeon made it 10-100x faster using GPU-accelerated sequence search. Preprint: www.biorxiv.org/content/10.6...  Code: github.com/RomeroLab/al...

Horrifying news being confirmed about the state of NSF at the NSF IOS/BIO webinar

A dataset of 40 million protein families and an autoregressive model of protein families. Great to see other protein Atlases popping up after Dayhoff!! @judewells.bsky.social @dmmiller597.bsky.social www.biorxiv.org/content/10.6...

Excited to be at the Carolina Biophysics Symposium the next two days to hear and talk about protein eng and design in many therapeutic and green science spaces!! Special thanks to our friends at @unc-bcbp.bsky.social for organizing! Gonna be an exciting time! cbs.web.unc.edu

Design stable, folded proteins using only the 10 "ancient" amino acids. www.biorxiv.org/content/10.1...

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/

I'm really proud of this work by Jae Kennemur and Yueming Long. #Enzymes rock, with some help from #directed evolution to do chemistry not known in nature (and really hard for humans, too). @caltechcce.bsky.social pubs.acs.org/doi/10.1021/...

Enzymatic Stereodivergent Synthesis of Azaspiro[2.y]alkanes

Azaspiro[2.y]alkanes are increasingly valuable scaffolds in pharmaceutical drug discovery; however, an asymmetric catalytic method for their synthesis remains unknown. Here, we present a stereodiverge...

pubs.acs.org

The posting is unfortunately not super clear on this, but please apply if you want to do BioML research, especially around machine learning for molecular biology and bioengineering! I get sad if there are no applicants with this profile in the pool!

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · last yr.

If you're an undergrad and want to intern with me, this is where you need to apply!

Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching

research.nvidia.com

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · last yr.

Partially-latent flow matching enables sequence-structure codesign of large proteins and functional motif scaffolding. @kdidi.bsky.social @machine.learning.bio @karstenkreis.bsky.social @arashv.bsky.social arxiv.org/html/2507.09...

Really nice metastudy of citizen science contributing to ecology & biodiversity research @inaturalist.bsky.social @aibsbiology.bsky.social 👀🔎🍄🧪🌎🌐 iNaturalist accelerates biodiversity research academic.oup.com/bioscience/a...

iNaturalist accelerates biodiversity research

Abstract. Participatory citizen science is expanding, with iNaturalist emerging as one of the most widely used platforms globally. However, its application

academic.oup.com

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬 Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

There's a lot more in the preprint! www.biorxiv.org/content/10.1...

The Dayhoff Atlas: scaling sequence diversity for improved protein generation

Modern biology is powered by the organization of biological information, a framework pioneered in 1965 by Margaret Dayhoff's Atlas of Protein Sequence and Structure. Databases descended from this comm...

biorxiv.org

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.

“Writing compels us to think — not in the chaotic, non-linear way our minds typically wander, but in a structured, intentional manner. By writing it down, we can sort years of research, data and analysis into an actual story, thereby identifying our main message and the influence of our work.”

🧪 The EPA is eliminating its scientific research arm and firing hundreds of scientists. This move, enabled by a Supreme Court ruling, dismantles the office providing independent research for environmental policies. #Climate

E.P.A. Says It Will Eliminate Its Scientific Research Arm

nytimes.com

We're sponsoring the use of ESM3 and EMSC to help researchers engineer improved PETase enzymes in the @AlignBio 2025 Protein Engineering Tournament. Get started using ESMC to predict protein function and ESM3 to generate new enzymes here: github.com/evolutionary...

esm/cookbook/tutorials at main · evolutionaryscale/esm

Contribute to evolutionaryscale/esm development by creating an account on GitHub.

github.com

The Align Foundation@alignbio.bsky.social · last yr.

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…

Pls tell me im living under a rock and we have citation managers compatible with iPads where your writing & highlighting can be automatically transcribed into notes and key words attached to a pdf (vs me manually transcribing over from edits I make in Adobe??) In the age of AI, we have this, right??

With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp

Physics-based design of efficient Kemp eliminases @lynnkamerlin.bsky.social www.nature.com/articles/s41...

All all-atom diffusion model of protein sequences. www.biorxiv.org/content/10.1...

End-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9

Which RNAs are functional? Been a long time goal of @deboramarks.bsky.social to start an RNA sequence —> function and structure mapping. Huge thx to team for pushing on this when - led by Rohit Arora and Murphy Angelo for seeing this thru and Pascal Notin for pulling together!!!

Pascal Notin@pascalnotin.bsky.social · last yr.

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9

RNA, RNA, RNA -> RNAGym! read all about it! biorxiv.org/content/10.110… Been a long time goal of @deboramarks.bsky.social We tried a million years ago, sciencedirect.com/science/articl��� Now total refresh led by Rohit Arora and Murphy Angelo and Pascal Notin for pulling together!!

Happy to release our breakthrough AI-model: RareFold, which predicts and designs proteins with noncanonical AAs. With EvoBindRare, we designed linear & cyclic peptide binders with high affinity & novel binding modes, wet lab validated. 📄 biorxiv.org/content/10.1... 💻 github.com/patrickbryan...

🎉 Congrats to Nate for his awesome preprint! We used deep learning to design phages with complex infectivity and specificity profiles. Big shifts in host targeting come from just a few mutations! Training on multifunctional data enables precise control over protein properties 🧬 tinyurl.com/yc4wtn8h

Multiobjective learning and design of bacteriophage specificity

To better understand and design proteins, it is crucial to consider the multifunctional landscapes on which all proteins exist. Proteins are often optimized for single functions during design and engi...

tinyurl.com