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Debora Marks

@deboramarks.bsky.social
580 followers 732 following 11 posts

Discover the Languages of Biology Build computational models to (help) solve biology? Join us! www.deboramarkslab.com DM or mail me!

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Debora Marks @deboramarks.bsky.social · 23/03/2026
Meet evedesign: open-source AI, accessible protein design ✅Combine models for multiobjective optimization ✅Integrate experimental data ✅ Run on your own infrastructure 📄Paper: www.biorxiv.org/content/10.6... 💻Code: github.com/evedesignbio 🌐Webserver: evedesign.bio Collaborate: hello@evedesign.bio
deboramarkslab.substack.com
evedesign: accessible biosequence design with a unified framework
Unified protein design for computational researchers and experimentalists
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Debora Marks @deboramarks.bsky.social · 24/11/2025
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:
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Debora Marks @deboramarks.bsky.social · 22/10/2025
Try it! Give feedback -and be kind, it's beta ...
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Reposted by Debora Marks
Andrew Gordon Wilson @andrewgwils.bsky.social · 05/03/2025
My 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
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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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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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Reposted by Debora Marks
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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Reposted by Debora Marks
Alejandro Montenegro @aemonten.bsky.social · 31/05/2025
This, by Michael Lynch. I'd include AI techbros as well. www.pnas.org/doi/10.1073/...
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Debora Marks @deboramarks.bsky.social · 27/05/2025
Weekly: Great papers across the centuries and subjects! Relaxing! fermatslibrary.com/journal_club
fermatslibrary.com
Fermat's Library | Home
Fermat’s Library is a platform for illuminating academic papers. A new scientific paper annotated every week.
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Reposted by Debora Marks
David A Knowles @davidaknowles.bsky.social · 26/05/2025
Just 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.
youtube.com
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference.
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Reposted by Debora Marks
Charlie Pugh @cwjpugh.bsky.social · 26/05/2025
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...
biorxiv.org
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...
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Reposted by Debora Marks
Jonathan Frazer @jonnyfrazer.bsky.social · 26/05/2025
Want 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
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Reposted by Debora Marks
bioRxivpreprint @biorxivpreprint.bsky.social · 25/05/2025
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models www.biorxiv.org/content/10.1101/202…
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Debora Marks @deboramarks.bsky.social · 25/05/2025
Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait | Science | AAAS www.science.org/content/arti...
science.org
Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait
Management tried to quash outpouring of support for beleaguered agency
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Reposted by Debora Marks
Jonathan Frazer @jonnyfrazer.bsky.social · 23/05/2025
And now, the final talk of #VariantEffect25. @roseorenbuch-art.bsky.social from Harvard Medical School presents work from our long-standing collaboration, and one that’s very close to my heart: Proteome-wide model for human disease genetics
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