82 lines
2.5 KiB
YAML
82 lines
2.5 KiB
YAML
cff-version: 1.2.0
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message: >-
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If you use this software in your research, please cite it using the
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following metadata.
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type: software
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title: >-
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chromatin-gnn: Variational Graph Autoencoder for learning latent
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representations of chromatin topology from Hi-C data
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authors:
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- family-names: Okada
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given-names: Toru
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alias: ToruOkadaOi
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# orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX" # add your ORCID
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version: "1.1.0"
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date-released: "2026-05-15"
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doi: "10.5281/zenodo.XXXXXXX" # replace with actual Zenodo DOI after deposit
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repository-code: "https://gitea.nalakath.org/aman/chromatin-vgae"
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url: "https://gitea.nalakath.org/aman/chromatin-vgae"
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license: MIT
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abstract: >-
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A Variational Graph Autoencoder (VGAE) applied to Hi-C chromatin contact
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data to learn unsupervised latent representations of chromatin topology.
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Genomic bins are modelled as graph nodes with ChIP-seq features (CTCF,
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H3K27me3, H3K27ac, H3K4me3); normalised contact frequencies define
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weighted edges. v1.0.0 trains on GM12878 lymphoblastoid cells and
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evaluates zero-shot transfer to IMR90 fibroblasts against known A/B
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compartments. v1.1.0 extends to a perturbation experiment — training on
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the control condition of Rao et al. 2017 RAD21-AID degron in HCT-116 cells
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and detecting long-range chromatin contact rewiring from latent embedding
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drift.
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keywords:
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- chromatin
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- Hi-C
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- graph neural network
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- variational autoencoder
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- VGAE
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- A/B compartments
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- topologically associating domains
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- TAD
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- epigenomics
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- 3D genome organisation
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- perturbation analysis
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- cohesin
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- RAD21
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- loop domains
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references:
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- type: article
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title: >-
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A 3D Map of the Human Genome at Kilobase Resolution Reveals
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Principles of Chromatin Looping
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authors:
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- family-names: Rao
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given-names: "Suhas S. P."
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- family-names: Huntley
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given-names: "Miriam H."
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year: 2014
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journal: Cell
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doi: 10.1016/j.cell.2014.11.021
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- type: article
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title: "Cohesin Loss Eliminates All Loop Domains"
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authors:
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- family-names: Rao
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given-names: "Suhas S. P."
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- family-names: Huang
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given-names: "Su-Chen"
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- family-names: Glenn St Hilaire
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given-names: "Brian"
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year: 2017
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journal: Cell
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volume: 171
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issue: 2
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doi: 10.1016/j.cell.2017.09.026
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- type: article
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title: "Variational Graph Auto-Encoders"
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authors:
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- family-names: Kipf
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given-names: "Thomas N."
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- family-names: Welling
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given-names: Max
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year: 2016
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url: "https://arxiv.org/abs/1611.07308"
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