Debora Marks
@deboramarks.bsky.social
Discover the Languages of Biology
Build computational models to (help) solve biology? Join us! https://www.deboramarkslab.com
DM or mail me!
Build computational models to (help) solve biology? Join us! https://www.deboramarkslab.com
DM or mail me!
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
🌐 evedesign.bio
October 22, 2025 at 8:03 PM
Try it! Give feedback -and be kind, it's beta ...
Reposted by Debora Marks
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
March 5, 2025 at 3:38 PM
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
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!!
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!!
https://biorxiv.org/content/10.110…
June 18, 2025 at 8:13 PM
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!!
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!!!
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!!!
🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9
🧵 1/9
June 18, 2025 at 7:47 PM
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!!!
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 Marks
End-to-end differentiable homology search for protein fitness prediction.
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
June 11, 2025 at 7:00 PM
End-to-end differentiable homology search for protein fitness prediction.
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social
arxiv.org/abs/2506.089...
Reposted by Debora Marks
May 31, 2025 at 2:28 PM
Weekly: Great papers across the centuries and subjects! Relaxing!
fermatslibrary.com/journal_club
fermatslibrary.com/journal_club
Fermat's Library | Home
Fermat’s Library is a platform for illuminating academic papers. A new scientific paper annotated every week.
fermatslibrary.com
May 27, 2025 at 12:15 AM
Weekly: Great papers across the centuries and subjects! Relaxing!
fermatslibrary.com/journal_club
fermatslibrary.com/journal_club
Reposted by Debora Marks
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.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference.
youtube.com
May 26, 2025 at 4:16 PM
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.
Reposted by Debora Marks
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 26, 2025 at 5:30 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Debora Marks
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
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 26, 2025 at 5:33 PM
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
Reposted by Debora Marks
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models https://www.biorxiv.org/content/10.1101/2025.05.20.655154v1
May 25, 2025 at 7:47 AM
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models https://www.biorxiv.org/content/10.1101/2025.05.20.655154v1
Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait | Science | AAAS www.science.org/content/arti...
Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait
Management tried to quash outpouring of support for beleaguered agency
www.science.org
May 25, 2025 at 1:09 AM
Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait | Science | AAAS www.science.org/content/arti...
Reposted by Debora Marks
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
May 23, 2025 at 10:45 AM
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