Debora Marks
Discover the Languages of Biology
Build computational models to (help) solve biology? Join us! https://www.deboramarkslab.com
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- New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
- Try it! Give feedback -and be kind, it's beta ...
- End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio
- Reposted by Debora MarksMy new paper "Deep Learning is Not So Mysterious or Different": arxiv.org/abs/2503.02113. Generalization behaviours in deep learning can be intuitively understood through a notion of soft inductive biases, and formally characterized with countable hypothesis bounds! 1/12
- 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!!
- 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!!!
- Reposted by Debora MarksEnd-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...
- Reposted by Debora MarksThis, by Michael Lynch. I'd include AI techbros as well. www.pnas.org/doi/10.1073/...
- Weekly: Great papers across the centuries and subjects! Relaxing! fermatslibrary.com/journal_club
- Reposted by Debora MarksJust under a week until the #MLCB2025 paper/abstract deadline on June 1st! In-person registration is full but you can join the wait list forms.gle/gnj6AAV7oWj6... or watch online at youtube.com/@mlcbconf. Sept 10-11 at @nygenome.org. Full deets at mlcb.org! Please RP.
- Reposted by Debora MarksNew preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...
- Reposted by Debora MarksWant to improve your protein or genomic language model’s performance at zero-shot variant effect prediction? We propose a simple adjustment to likelihood-based predicton
- New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...
- Reposted by Debora MarksFrom Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models biorxiv.org/content/10.1101/202…
- Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait | Science | AAAS www.science.org/content/arti...
