megthescientist.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

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

submitted 8 days ago • 0 comments

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

submitted 1 day ago • 1 comment

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!!!

submitted 1 day ago • 0 comments

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!!

submitted 1 day ago • 0 comments

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...

submitted 26 days ago • 2 comments

🎉 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

submitted 31 days ago • 0 comments

Super excited to be presenting Dyna-1 next week with @hkws.bsky.social !!

submitted 58 days ago • 2 comments

Happening in 15 mins! Message if you need a link :)

submitted 51 days ago • 0 comments

How can an individual protein show adaptation? The light- and temp-sensitive BcLOV4 gives a pulse of translocation during a step input of light. Answer in our preprint: intra-molecular feed-forward regulation. bit.ly/3Rg9veD A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵

submitted 66 days ago • 1 comment

Search among all posts in this feed 👉 mlsb.papers.blue

submitted 167 days ago • 0 comments

Structure models generate proteins with higher structure confidence and more plausible energy distributions, but limited diversity and sequence biases. Sequence models generate diverse and novel proteins with lower structural confidence. Neither are good at generating enzymes.

submitted 80 days ago • 1 comment

RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes www.biorxiv.org/content/10.1...

submitted 69 days ago • 0 comments

Congratulations to Elliott Weix on being named a 2025 Goldwater Scholar! Weix, a biochemistry and math major, works in the @cellraiser.bsky.social Lab. biochem.wisc.edu/2025/04/10/b...

submitted 71 days ago • 0 comments

Supervised training using data generated by multiplexed assays of variant effects is potentially very powerful, but is made difficult by assay- and protein-specific effects Here @tkschulze.bsky.social devised a strategy to take this into account while training models www.biorxiv.org/content/10.1...

submitted 78 days ago • 0 comments

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

submitted 80 days ago • 1 comment

I haven’t hosted in quite some time!! But super excited to be back today and host Anthony as he goes over his new paper out in Nature! Note the 11AM EST time change (so he isn’t up too late on the other side of the globe😉) hope to see people there!

submitted 80 days ago • 0 comments

Now just a few days left to submit your abstract for a chance to join this fantastic protein design meeting 📅 📜 🧬 💻

submitted 85 days ago • 0 comments

Gene synthesis is often the most expensive part of protein engineering with generative models. Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50. @philromero.bsky.social

submitted 87 days ago • 1 comment

We collaborated with @hf.co 🤗 to host all of our models and data online! Big thank you to @danielvanstrien.bsky.social @wauplin.hf.co @lhoestq.hf.co for helping out (and the GPU)! Dyna-1 and RelaxDB on HF: 🚀 huggingface.co/spaces/gelne... 🌟 huggingface.co/datasets/gel...

submitted 86 days ago • 0 comments

🎉Congrats to Chase on her new preprint! She developed OMEGA--a simple method for assembling custom gene panels for as little as $1.50 per gene. Big step forward protein engineering and design!🧬 www.biorxiv.org/content/10.1...

submitted 87 days ago • 2 comments

Scalable and cost-efficient custom gene library assembly from oligopools https://www.biorxiv.org/content/10.1101/2025.03.22.644747v1

submitted 89 days ago • 0 comments

From a colleague in my PhD lab! Chase presents her method OMEGA, a simple, scalable method to assemble 100s-1000s of custom genes from oligo pools using standard lab tools! #synbio #proteinengineering #OMEGA

submitted 89 days ago • 0 comments

Here's my interview with @stevenstrogatz.com on @quantamagazine.bsky.social's Joy of Why podcast. This was so much fun. I was nervous going into it (I really look up to Steve!), but I had a blast and I think this is the best interview I have ever done. Thanks for having me on, folks!

submitted 92 days ago • 5 comments

Next Tues (3/18) at 4PM ET we will have Alan Amin present "Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences" Paper: arxiv.org/abs/2412.07763 Sign up on our website for zoom links!

submitted 100 days ago • 0 comments

Today’s the day! And still time for you to find one near you!! standupforscience2025.org

submitted 105 days ago • 0 comments

“the success of the American research establishment is extraordinary … this is based on a deal where the government provides funding & in exchange it gets products, research, national security, prestige & the next generation of qualified scientists” 🧪 #AcademicSky www.princeton.edu/news/2025/02...

submitted 113 days ago • 1 comment

Hi all 👋🏻 Super happy to share with you the 7th issue of our free #STEMDORADO science kid's magazine 🐡🧪 Please help us spread the 🩵 of science to all kids. We need this today more than ever ! And if you are a cell biologist, check the cell story I wrote and illustrated for this issue 😜 #science

submitted 113 days ago • 0 comments

🌟 We have a proteinML PhD internship at Cradle! jobs.ashbyhq.com/cradlebio/d8... Come see what it's like to work at a frontier bioML lab. This is a unique opportunity to work across the entire stack: 🔬 Automated wet lab data; 🤖 Train your own ~1B parameter ML models; 📚 Publish end result! 🚀

submitted 113 days ago • 0 comments

We @prescientdesign.bsky.social Genentech pre-printed our "Lab-in-the-loop for therapeutic antibody design." We built a general ML system to accelerate molecule design for challenging, therapeutically relevant targets. www.biorxiv.org/content/10.1...

submitted 113 days ago • 1 comment

🚨 Many NSF-funded Research Experiences for Undergraduates (REUs) are being cancelled for Summer 2025. www.reddit.com/r/REU/commen...

submitted 116 days ago • 16 comments

Today!! Note a slight time shift :)

submitted 122 days ago • 0 comments

Today is the start of #EngineersWeek 2025. My deep appreciation to those organizations that bring #diversity and #inclusion to the engineering profession... swe.org www.nacme.org www.wepan.org www.aises.org namepa.org www.nsbe.org And especially, Introduce a Girl to Engineering Day! 🧪👩‍🔬

submitted 123 days ago • 0 comments

Super excited to try out this tool! Congratulations, Borna!

submitted 124 days ago • 0 comments

I'm at @biophysicalsoc.bsky.social #BPS2025 with a bunch of folks from the Structural and Molecular Biophysics @flatironinstitute.org group-- come say hi and check out our posters/talks! @sonyahanson.bsky.social @pilarcossio.bsky.social @miroastore.bsky.social

submitted 124 days ago • 0 comments

The courts alone will not save us. Musk is attacking the courts, and the Supreme Court is packed with ideologues who support Trump. Don't sit back and wait for the courts to fix things. This is a moment where we all need to step up and speak out. 🧪 bsky.app/profile/kyl...

submitted 125 days ago • 3 comments