Barbieri Mariano PhD
@barbierimarianophd.bsky.social
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Physicist modelling the complexity of eukaryotic cell's nucleus. University Medical Centre Göttingen
Fantastic work connecting mechanotransduction stimuli, changes in 3D nuclear structure and cell identity! Must read
add a skeleton here at some point
12 days ago
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reposted by
Barbieri Mariano PhD
Akis (Argyris) Papantonis
about 1 month ago
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.
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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
https://github.com/YajieZhu018/LoopBin
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reposted by
Barbieri Mariano PhD
Akis (Argyris) Papantonis
about 1 month ago
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...
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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.
https://www.biorxiv.org/content/10.64898/2026.01.13.699359v1
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reposted by
Barbieri Mariano PhD
Dormann Lab
5 months ago
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
add a skeleton here at some point
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reposted by
Barbieri Mariano PhD
Rohit V. Pappu
5 months ago
The announcement that the 2025 Keio prize for Medical Science goes to
@virusesimmunity.bsky.social
and
@brangwynnelab.bsky.social
Brangwynne.
www.ms-fund.keio.ac.jp/en/prize/
Congratulations to the masters for this well deserved honor. It is gratifying when true quality is recognized.
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https://www.ms-fund.keio.ac.jp/en/prize/Congratulations
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reposted by
Barbieri Mariano PhD
Karsten Rippe
6 months ago
"In our view, it [hexanediol] should thus be avoided and not be used as evidence for the formation of an assembly via phase separation or the fluid-like nature of a condensate in vitro or in vivo."
doi.org/10.1038/s414...
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Current practices in the study of biomolecular condensates: a community comment - Nature Communications
The realization that the cell is abundantly compartmentalized into biomolecular condensates has opened new opportunities for understanding the physics and chemistry underlying many cellular processes1...
https://doi.org/10.1038/s41467-025-62055-8
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reposted by
Barbieri Mariano PhD
Carmelo Ferrai
6 months ago
EpiSci - 🧬 - 🧪 Specialised super-enhancer networks in stem cells and neurons
www.biorxiv.org/content/10.1...
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https://www.biorxiv.org/content/10.1101/2025.08.13.670083v1.full.pdf
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reposted by
Barbieri Mariano PhD
Carmelo Ferrai
7 months ago
Establishment of chromatin architecture interplays with embryo hypertranscription
www.nature.com/articles/s41...
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https://www.nature.com/articles/s41586-025-09400-5
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reposted by
Barbieri Mariano PhD
Carmelo Ferrai
7 months ago
EpiSci - 🧬 - 🧪 - The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
www.nature.com/articles/s41...
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The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology
Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...
https://www.nature.com/articles/s41556-025-01703-z
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reposted by
Barbieri Mariano PhD
Carmelo Ferrai
7 months ago
NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling
www.nature.com/articles/s41...
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NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling - Nature Genetics
Single-cell RNA and assay for transposase-accessible chromatin sequencing in isogenic prostate adenocarcinoma cells undergoing neuroendocrine transition identify dynamic changes in chromatin and trans...
https://www.nature.com/articles/s41588-025-02265-4
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reposted by
Barbieri Mariano PhD
Axel Visel
8 months ago
No new genes needed to fly - just rewire what you have! 🦇🧬 Great new paper from the labs of
@fany-real.bsky.social
@stemundi.bsky.social
@dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo
#SingleCell
#BatWings
add a skeleton here at some point
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reposted by
Barbieri Mariano PhD
Karsten Rippe
8 months ago
How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with
@akispapantonis.bsky.social
a lot, and we put our thoughts together for
@naturerevgenet.bsky.social
, now out at
rdcu.be/erP1u
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reposted by
Barbieri Mariano PhD
Karsten Rippe
8 months ago
Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse.
doi.org/10.1038/s414...
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