Barbieri Mariano PhD

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  Akis (Argyris) Papantonis akispapantonis.bsky.social · Jan 21
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  The LoopBin code is already available here: github.com/YajieZhu018/... So feel free to try it out and come back to us with praise or complaints! We would be happy for any feedback.
  

  GitHub - YajieZhu018/LoopBin: A deep-learning-based pipeline to cluster genomic loop types with micro-C and Cut&Tag data.

  A deep-learning-based pipeline to cluster genomic loop types with micro-C and Cut&Tag data. - YajieZhu018/LoopBin

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• Reposted by Barbieri Mariano PhD
  
  Akis (Argyris) Papantonis akispapantonis.bsky.social · Jan 21
  Preprint alert! 🥸 Yajie Zhu (PhD graduate) and Mariano Barbieri (postdoc, @spp2202.bsky.social Accelerator award) produced a package that will classify loops in your #3Dgenomics data based on (whichever) epigenomic data you have available. Keep reading... 1/n www.biorxiv.org/content/10.6...

  LoopBin – a VaDE-based neural network for chromatin loop classification

  Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling. ### Competing Interest Statement The authors have declared no competing interest.

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  Dormann Lab dormannlab.bsky.social · Sep 23, 2025
  Last week we attended a fantastic meeting of the SPP2191 and GBM Compact on Condensates! Congrats to members of the Dormann Lab, Yelyzaveta Zadorozhna and Fatmanur Tiryaki, for giving great talks, and to Saskia Hutten for winning a poster award 🎉! @spp2191.bsky.social @sfb1551.bsky.social
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    SPP2191 - Molecular Mechanisms of Functional Phase Separation spp2191.bsky.social · May 16, 2025
    📢 Registration is open for the GBM Compact: Focus on Condensate Biology & SPP2191 Satellite Meeting! This is sure to be an incredible event diving into the latest in phase separation research with leading scientists. 📍 Frankfurt am Main 📅 Sept 16–19, 2025 🌐 shorturl.at/ZGQch @gbmev.bsky.social
    
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