Publication: Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph
dc.contributor.author | Sefer, Emre | |
dc.contributor.department | Computer Science | |
dc.contributor.ozuauthor | SEFER, Emre | |
dc.date.accessioned | 2023-05-26T06:39:30Z | |
dc.date.available | 2023-05-26T06:39:30Z | |
dc.date.issued | 2021 | |
dc.description.abstract | Chromosome 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.doi | 10.1007/978-3-030-65351-4_33 | en_US |
dc.identifier.endpage | 421 | en_US |
dc.identifier.isbn | 978-303065350-7 | |
dc.identifier.issn | 1860-949X | en_US |
dc.identifier.scopus | 2-s2.0-85101847983 | |
dc.identifier.startpage | 410 | en_US |
dc.identifier.uri | http://hdl.handle.net/10679/8342 | |
dc.identifier.uri | https://doi.org/10.1007/978-3-030-65351-4_33 | |
dc.identifier.volume | 944 | en_US |
dc.language.iso | eng | en_US |
dc.publicationstatus | Published | en_US |
dc.publisher | Springer | en_US |
dc.relation.ispartof | Studies in Computational Intelligence | |
dc.relation.publicationcategory | International | |
dc.rights | restrictedAccess | |
dc.subject.keywords | Algorithms | en_US |
dc.subject.keywords | Bioinformatics | en_US |
dc.subject.keywords | Epigenetics | en_US |
dc.subject.keywords | Hi-C | en_US |
dc.subject.keywords | Set cover | en_US |
dc.title | Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph | en_US |
dc.type | conferenceObject | en_US |
dc.type.subtype | Conference paper | |
dspace.entity.type | Publication | |
relation.isOrgUnitOfPublication | 85662e71-2a61-492a-b407-df4d38ab90d7 | |
relation.isOrgUnitOfPublication.latestForDiscovery | 85662e71-2a61-492a-b407-df4d38ab90d7 |
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