Parth Bibekar
@parthbibekar.bsky.social
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PhD Candidate | EPFL Structural bioinformatics
https://parthbibekar.github.io
Update: We’ve now released the code for RISoTTo. I’ll also be presenting a poster at NeurIPS AI4D3 in San Diego on Dec 6, if you’re around and want to chat about RNA design, come say hi! 🧬 github:
github.com/LBM-EPFL/RIS...
Preprint:
doi.org/10.1101/2025...
add a skeleton here at some point
6 months ago
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Parth Bibekar
AI x Bio Discovery
6 months ago
Context-aware geometric deep learning for RNA sequence design
[2025-06-21] Leverages geometric deep learning to design RNA sequences, considering the 3D structure and surrounding molecular context for improved accuracy and function.
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Parth Bibekar
bioRxivpreprint
11 months ago
Context-aware geometric deep learning for RNA sequence design
https://www.biorxiv.org/content/10.1101/2025.06.21.660801v1
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Presenting RISoTTo, a molecular context-aware model for RNA sequence design, building on our work with PeSTo (for protein binding interface prediction) and CARBonAra (for protein design). 📄 Preprint:
www.biorxiv.org/content/10.1...
💻 Code & more coming soon!
#RNAdesign
#RNAbiology
#AI4Science
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https://www.biorxiv.org/content/10.1101/2025.06.21.660801v1
11 months ago
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Parth Bibekar
Benedikt Singer
over 1 year ago
Inspired by
@simonduerr.bsky.social
at ERC'24 I built and deployed our sequence redesign model called CARBonAra on
@hf.co
. The model is aware of any biomolecular context and performs on par with ProteinMPNN (see paper) Check it out here:
huggingface.co/spaces/LBM-E...
@lbm-epfl.bsky.social
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Carbonara - a Hugging Face Space by LBM-EPFL
Interactive demo of carbonara
https://huggingface.co/spaces/LBM-EPFL/CARBonAra
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Parth Bibekar
Kevin K. Yang 楊凱筌
over 1 year ago
Three BioML starter packs now! Pack 1:
go.bsky.app/2VWBcCd
Pack 2:
go.bsky.app/Bw84Hmc
Pack 3:
go.bsky.app/NAKYUok
DM if you want to be included (or nominate people who should be!)
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Parth Bibekar
over 1 year ago
Great blog post from AdaptyvBio summarising submissions for round 2 of the protein design competition: including a few interesting methods I had never heard of. Results will be released tomorrow:
www.adaptyvbio.com/blog/po103
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Adaptyv Bio - Protein Optimization 103: Racing to the Top 100
What a close race this one was! In this blog post, we look at how submissions evolved throughout our latest EGFR binder design competition. We highlight the most widespread model and design choices, h...
https://www.adaptyvbio.com/blog/po103
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