Publication:
Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph

dc.contributor.authorSefer, Emre
dc.contributor.departmentComputer Science
dc.contributor.ozuauthorSEFER, Emre
dc.date.accessioned2023-05-26T06:39:30Z
dc.date.available2023-05-26T06:39:30Z
dc.date.issued2021
dc.description.abstractChromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. Even though Hi-C interactions are not biased towards any of the histone modifications, previous analysis has revealed denser interactions around many histone modifications. Nevertheless, simultaneous effects of these modifications in Hi-C interaction graph have not been fully characterized yet, limiting our understanding of genome shape. Here, we propose Coverage Hi-C to decompose Hi-C interaction graph in terms of known histone modifications. Coverage Hi-C is based on set multicover with pairs, where each Hi-C interaction is covered by histone modification pairs. We find 4 histone modifications H3K4me1, H3K4me3, H3K9me3, H3K27ac to be significantly predictive of most Hi-C interactions across species and cell types. Coverage Hi-C is quite effective in predicting Hi-C interactions and topologically-associated domains (TADs) in one species, given it is trained on another species or cell types.en_US
dc.identifier.doi10.1007/978-3-030-65351-4_33en_US
dc.identifier.endpage421en_US
dc.identifier.isbn978-303065350-7
dc.identifier.issn1860-949Xen_US
dc.identifier.scopus2-s2.0-85101847983
dc.identifier.startpage410en_US
dc.identifier.urihttp://hdl.handle.net/10679/8342
dc.identifier.urihttps://doi.org/10.1007/978-3-030-65351-4_33
dc.identifier.volume944en_US
dc.language.isoengen_US
dc.publicationstatusPublisheden_US
dc.publisherSpringeren_US
dc.relation.ispartofStudies in Computational Intelligence
dc.relation.publicationcategoryInternational
dc.rightsrestrictedAccess
dc.subject.keywordsAlgorithmsen_US
dc.subject.keywordsBioinformaticsen_US
dc.subject.keywordsEpigeneticsen_US
dc.subject.keywordsHi-Cen_US
dc.subject.keywordsSet coveren_US
dc.titleJoint modeling of histone modifications in 3D genome shape through Hi-C interaction graphen_US
dc.typeconferenceObjecten_US
dc.type.subtypeConference paper
dspace.entity.typePublication
relation.isOrgUnitOfPublication85662e71-2a61-492a-b407-df4d38ab90d7
relation.isOrgUnitOfPublication.latestForDiscovery85662e71-2a61-492a-b407-df4d38ab90d7

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