Matches in SemOpenAlex for { <https://semopenalex.org/work/W4386462110> ?p ?o ?g. }
Showing items 1 to 96 of
96
with 100 items per page.
- W4386462110 abstract "A growing amount of noncoding genetic variants, including single-nucleotide polymorphisms, are found to be associated with complex human traits and diseases. Their mechanistic interpretation is relatively limited and can use the help from computational prediction of their effects on epigenetic profiles. However, current models often focus on local, 1D genome sequence determinants and disregard global, 3D chromatin structure that critically affects epigenetic events.We find that noncoding variants of unexpected high similarity in epigenetic profiles, with regards to their relatively low similarity in local sequences, can be largely attributed to their proximity in chromatin structure. Accordingly, we have developed a multimodal deep learning scheme that incorporates both data of 1D genome sequence and 3D chromatin structure for predicting noncoding variant effects. Specifically, we have integrated convolutional and recurrent neural networks for sequence embedding and graph neural networks for structure embedding despite the resolution gap between the two types of data, while utilizing recent DNA language models. Numerical results show that our models outperform competing sequence-only models in predicting epigenetic profiles and their use of long-range interactions complement sequence-only models in extracting regulatory motifs. They prove to be excellent predictors for noncoding variant effects in gene expression and pathogenicity, whether in unsupervised zero-shot learning or supervised few-shot learning.Codes and data can be accessed at https://github.com/Shen-Lab/ncVarPred-1D3D and https://zenodo.org/record/7975777." @default.
- W4386462110 created "2023-09-06" @default.
- W4386462110 creator A5057485825 @default.
- W4386462110 creator A5081591467 @default.
- W4386462110 date "2023-09-01" @default.
- W4386462110 modified "2023-10-14" @default.
- W4386462110 title "Multimodal learning of noncoding variant effects using genome sequence and chromatin structure" @default.
- W4386462110 cites W1709815505 @default.
- W4386462110 cites W1865845132 @default.
- W4386462110 cites W1985621639 @default.
- W4386462110 cites W1987371782 @default.
- W4386462110 cites W1993422084 @default.
- W4386462110 cites W2011582941 @default.
- W4386462110 cites W2018189081 @default.
- W4386462110 cites W2076154138 @default.
- W4386462110 cites W2090037139 @default.
- W4386462110 cites W2117396697 @default.
- W4386462110 cites W2167852161 @default.
- W4386462110 cites W2198606573 @default.
- W4386462110 cites W2259938310 @default.
- W4386462110 cites W2305687918 @default.
- W4386462110 cites W2336509392 @default.
- W4386462110 cites W2345512687 @default.
- W4386462110 cites W2751686252 @default.
- W4386462110 cites W2767749844 @default.
- W4386462110 cites W2883945062 @default.
- W4386462110 cites W2905452503 @default.
- W4386462110 cites W2905821633 @default.
- W4386462110 cites W2911555896 @default.
- W4386462110 cites W2912509459 @default.
- W4386462110 cites W2952699651 @default.
- W4386462110 cites W2980809855 @default.
- W4386462110 cites W2988126442 @default.
- W4386462110 cites W3013411594 @default.
- W4386462110 cites W3024498749 @default.
- W4386462110 cites W3047670845 @default.
- W4386462110 cites W3088122047 @default.
- W4386462110 cites W3107086932 @default.
- W4386462110 cites W3127238141 @default.
- W4386462110 cites W3199156966 @default.
- W4386462110 cites W4225256479 @default.
- W4386462110 cites W4280512834 @default.
- W4386462110 cites W4285006295 @default.
- W4386462110 cites W4313893501 @default.
- W4386462110 cites W4380154222 @default.
- W4386462110 doi "https://doi.org/10.1093/bioinformatics/btad541" @default.
- W4386462110 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37669132" @default.
- W4386462110 hasPublicationYear "2023" @default.
- W4386462110 type Work @default.
- W4386462110 citedByCount "0" @default.
- W4386462110 crossrefType "journal-article" @default.
- W4386462110 hasAuthorship W4386462110A5057485825 @default.
- W4386462110 hasAuthorship W4386462110A5081591467 @default.
- W4386462110 hasBestOaLocation W43864621101 @default.
- W4386462110 hasConcept C104317684 @default.
- W4386462110 hasConcept C108583219 @default.
- W4386462110 hasConcept C141231307 @default.
- W4386462110 hasConcept C154945302 @default.
- W4386462110 hasConcept C41008148 @default.
- W4386462110 hasConcept C41091548 @default.
- W4386462110 hasConcept C54355233 @default.
- W4386462110 hasConcept C70721500 @default.
- W4386462110 hasConcept C81363708 @default.
- W4386462110 hasConcept C83640560 @default.
- W4386462110 hasConcept C86803240 @default.
- W4386462110 hasConceptScore W4386462110C104317684 @default.
- W4386462110 hasConceptScore W4386462110C108583219 @default.
- W4386462110 hasConceptScore W4386462110C141231307 @default.
- W4386462110 hasConceptScore W4386462110C154945302 @default.
- W4386462110 hasConceptScore W4386462110C41008148 @default.
- W4386462110 hasConceptScore W4386462110C41091548 @default.
- W4386462110 hasConceptScore W4386462110C54355233 @default.
- W4386462110 hasConceptScore W4386462110C70721500 @default.
- W4386462110 hasConceptScore W4386462110C81363708 @default.
- W4386462110 hasConceptScore W4386462110C83640560 @default.
- W4386462110 hasConceptScore W4386462110C86803240 @default.
- W4386462110 hasFunder F4320337354 @default.
- W4386462110 hasIssue "9" @default.
- W4386462110 hasLocation W43864621101 @default.
- W4386462110 hasLocation W43864621102 @default.
- W4386462110 hasOpenAccess W4386462110 @default.
- W4386462110 hasPrimaryLocation W43864621101 @default.
- W4386462110 hasRelatedWork W2731899572 @default.
- W4386462110 hasRelatedWork W2999805992 @default.
- W4386462110 hasRelatedWork W3011074480 @default.
- W4386462110 hasRelatedWork W3116150086 @default.
- W4386462110 hasRelatedWork W3133861977 @default.
- W4386462110 hasRelatedWork W3192840557 @default.
- W4386462110 hasRelatedWork W4200173597 @default.
- W4386462110 hasRelatedWork W4291897433 @default.
- W4386462110 hasRelatedWork W4312417841 @default.
- W4386462110 hasRelatedWork W4321369474 @default.
- W4386462110 hasVolume "39" @default.
- W4386462110 isParatext "false" @default.
- W4386462110 isRetracted "false" @default.
- W4386462110 workType "article" @default.