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Meg T (she/her/hers)

@megthescientist.bsky.social
1.7K followers 638 following 115 posts

Bio x ML @ Romero lab, @dukeubme.bsky.social @ml4proteins.bsky.social co-organizer

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Reposted by Meg T (she/her/hers)
Hannah Wayment-Steele @hkws.bsky.social · 01/06/2026
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": 👇
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Anthony Gitter @anthonygitter.bsky.social · 12/12/2025
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?
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Philip Romero @philromero.bsky.social · 19/02/2026
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...
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Kurt Fraser @kurtfraser.bsky.social · 18/12/2025
Horrifying news being confirmed about the state of NSF at the NSF IOS/BIO webinar
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 07/01/2026
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...
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Meg T (she/her/hers) @megthescientist.bsky.social · 06/11/2025
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
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 31/10/2025
Design stable, folded proteins using only the 10 "ancient" amino acids. www.biorxiv.org/content/10.1...
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Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 25/09/2025
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/
jasonjwilliamsny.github.io
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
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Frances Arnold @francesarnold.bsky.social · 22/07/2025
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/...
pubs.acs.org
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...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 15/09/2025
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!
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Kieran Didi @kdidi.bsky.social · 19/07/2025
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!
research.nvidia.com
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
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Erle Ellis @erleellis.bsky.social · 28/07/2025
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...
academic.oup.com
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
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Gina El Nesr @ginaelnesr.bsky.social · 28/07/2025
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!🌟
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25/07/2025
There's a lot more in the preprint! www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25/07/2025
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.
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Meg T (she/her/hers) @megthescientist.bsky.social · 21/07/2025
“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.”
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Reposted by Meg T (she/her/hers)
Scott McGrath @smcgrath.phd · 19/07/2025
🧪 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
nytimes.com
E.P.A. Says It Will Eliminate Its Scientific Research Arm
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EvolutionaryScale @evolutionaryscale.bsky.social · 08/07/2025
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...
github.com
esm/cookbook/tutorials at main · evolutionaryscale/esm
Contribute to evolutionaryscale/esm development by creating an account on GitHub.
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The Align Foundation @alignbio.bsky.social · 08/07/2025
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
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Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025
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…
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Meg T (she/her/hers) @megthescientist.bsky.social · 30/06/2025
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??
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Christian Dallago @machine.learning.bio · 15/06/2025
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
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 19/06/2025
Physics-based design of efficient Kemp eliminases @lynnkamerlin.bsky.social www.nature.com/articles/s41...
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Reposted by Meg T (she/her/hers)
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25/06/2025
All all-atom diffusion model of protein sequences. www.biorxiv.org/content/10.1...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/06/2025
End-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...
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Pascal Notin @pascalnotin.bsky.social · 18/06/2025
🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9
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Debora Marks @deboramarks.bsky.social · 18/06/2025
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!!!
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Debora Marks @deboramarks.bsky.social · 18/06/2025
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!!
biorxiv.org
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Patrick Bryant @patrickbryant1.bsky.social · 25/05/2025
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...
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Philip Romero @philromero.bsky.social · 20/05/2025
🎉 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
tinyurl.com
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...
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Reposted by Meg T (she/her/hers)
Gina El Nesr @ginaelnesr.bsky.social · 22/04/2025
Super excited to be presenting Dyna-1 next week with @hkws.bsky.social !!
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Meg T (she/her/hers) @megthescientist.bsky.social · 29/04/2025
Happening in 15 mins! Message if you need a link :)
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Indeed, 1 A.A. mutation from each of these hotspots dramatically extended the pulsatory response (>18 hrs vs 10s of min), suggesting evolutionary tuning of dynamics.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Remarkably, sequence analysis found these *exact same hotspots* had co-evolved in BcLOV4 homologs, implying function.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Structural studies (limited proteolysis, HDX-MS by the Gardner lab) identified temperature-sensitive hot-spots in DUF.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
What about the temperature-sensitive inhibitory Node C? We mapped this to the mysterious “Domain of Unknown Function” (DUF). We still call it DUF even though function is now known :P.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
We then mapped the network nodes: The light-sensing LOV domain (A) regulates a charged clustering region (B), which drives PM binding. Aside: this inspired an entire toolset for single-protein translocation to various compartments. Preprint soon!
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
The inter-domain IFFL idea started as a hunch, but models made several non-intuitive predictions that we then confirmed experimentally through mutations that altered the energetics of LOV domain interactions.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Answer: smaller-scale networks of interactions between the protein’s domains. Light response (A) quickly activates a region for plasma membrane (PM) binding (B), but also enables a temp.-sensitive domain (C) to inhibit the PM-binding region more slowly.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Step-to-pulse response – adaptation – is common in all kinds of networks, often through an incoherent feed-forward loop (IFFL). Node A quickly activates Node B but also —more slowly— Node C, which inhibits Node B. Result: a pulse of B. But how can a single protein do it w/o a larger network?
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
Why does BcLOV4 turn itself off despite constant light stimulation, and why does this depend on temperature? The answer could make better optogenetic and thermogenetic tools, and itself was a fascinating puzzle.
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Zikang (Dennis) Huang @dennishuang.bsky.social · 15/04/2025
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 🧵
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MLSB Feed @mlsb-feed.bsky.social · 04/01/2025
Search among all posts in this feed 👉 mlsb.papers.blue
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 01/04/2025
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.
Performance of our selected generative models with respect to median
generation walltime and designability.In-vitro validation of conditional designs around a set of functional motifs from
the Tobbaco Etch Virus (TEV) ProteaseDiversity of naturally occurring and generative AI-proteins
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/04/2025
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...
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UW–Madison Department of Biochemistry @uwbiochem.bsky.social · 10/04/2025
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...
biochem.wisc.edu
Biochemistry Major Named 2025 Goldwater Scholar
Three University of Wisconsin–Madison students have received 2025 Goldwater Scholarships, considered the country’s preeminent undergraduate scholarship in mathematics, the natural sciences, and engine...
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Reposted by Meg T (she/her/hers)
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 03/04/2025
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...
Figure illustrating the framework for supervised learning across VAMP-seq datasets.
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Rohit Singh @rohitsingh8080.bsky.social · 01/04/2025
Our work on better ways of aggregating PLM embeddings is now out in Bioinformatics Advances.
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Meg T (she/her/hers) @megthescientist.bsky.social · 01/04/2025
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!
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Amelie Stein @amelierocks.bsky.social · 27/03/2025
Now just a few days left to submit your abstract for a chance to join this fantastic protein design meeting 📅 📜 🧬 💻
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