{"ID": "PMID:35764630", "lab": {"@id": "/labs/external-lab/", "title": "External Lab", "uuid": "d3412190-317a-4837-823f-3892b9f641a4", "status": "current", "@type": ["Lab", "Item"], "display_title": "External Lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d3412190-317a-4837-823f-3892b9f641a4"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/35764630", "tags": ["4dn-external-reuse"], "award": {"project": "External", "name": "external-award", "center": "External", "description": "Funding source is from outside 4DN.", "@type": ["Award", "Item"], "center_title": "External", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Learning representations of chromatin contacts using a recurrent neural network  identifies genomic drivers of conformation.", "status": "current", "aliases": ["4dn-dcic-lab:PMID:35764630"], "authors": ["Dsouza KB", "Maslova A", "Al-Jibury E", "Merkenschlager M", "Bhargava VK", "Libbrecht MW"], "journal": "Nature communications", "abstract": "Despite the availability of chromatin conformation capture experiments,  discerning the relationship between the 1D genome and 3D conformation remains a  challenge, which limits our understanding of their affect on gene expression and  disease. We propose Hi-C-LSTM, a method that produces low-dimensional latent  representations that summarize intra-chromosomal Hi-C contacts via a recurrent  long short-term memory neural network model. We find that these representations  contain all the information needed to recreate the observed Hi-C matrix with high  accuracy, outperforming existing methods. These representations enable the  identification of a variety of conformation-defining genomic elements, including  nuclear compartments and conformation-related transcription factors. They  furthermore enable in-silico perturbation experiments that measure the influence  of cis-regulatory elements on conformation.", "categories": ["integrative analysis"], "date_created": "2024-02-13T22:04:46.244520+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-15T15:40:49.482107+00:00"}, "date_published": "2022-06-28", "public_release": "2024-03-15", "schema_version": "2", "project_release": "2024-03-15", "exp_sets_used_in_pub": [{"@id": "/experiment-set-replicates/4DNES2M5JIGV/", "status": "released", "uuid": "6ba6a5df-dac5-4111-b5f0-299b6bee0f38", "experimentset_type": "replicate", "display_title": "4DNES2M5JIGV", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiment-set-replicates/4DNESPDEZNWX/", "status": "released", "uuid": "859c2c9a-bafd-46ae-9250-0167c2d36d88", "experimentset_type": "replicate", "display_title": "4DNESPDEZNWX", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiment-set-replicates/4DNESVUMGLG2/", "status": "released", "uuid": "d5866e8f-178c-4dc1-8926-a7dc4bbaac25", "experimentset_type": "replicate", "display_title": "4DNESVUMGLG2", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiment-set-replicates/4DNESJFTAURO/", "status": "released", "uuid": "5dbcedc0-0a69-4eb3-8c71-3471212bc5de", "experimentset_type": "replicate", "display_title": "4DNESJFTAURO", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiment-set-replicates/4DNESLQG7ZKJ/", "status": "released", "uuid": "2a756f80-89c5-4979-bb70-75a4b69634ce", "experimentset_type": "replicate", "display_title": "4DNESLQG7ZKJ", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/716f318f-490c-468e-828f-e7dff0fb7110/", "@type": ["Publication", "Item"], "uuid": "716f318f-490c-468e-828f-e7dff0fb7110", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Dsouza KB et al. (2022) PMID:35764630", "external_references": [], "short_attribution": "Dsouza KB et al. (2022)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}