{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T21:10:14Z","timestamp":1727212214287},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T00:00:00Z","timestamp":1727136000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018617","name":"Liaoning Revitalization Talents Program","doi-asserted-by":"publisher","award":["XLYC2002010"],"id":[{"id":"10.13039\/501100018617","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["DUT20RC(3)074"],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"Abstract<\/jats:title>\n Histone modifications (HMs) are pivotal in various biological processes, including transcription, replication, and DNA repair, significantly impacting chromatin structure. These modifications underpin the molecular mechanisms of cell-type-specific gene expression and complex diseases. However, annotating HMs across different cell types solely using experimental approaches is impractical due to cost and time constraints. Herein, we present dHICA (deep histone imputation using chromatin accessibility), a novel deep learning framework that integrates DNA sequences and chromatin accessibility data to predict multiple HM tracks. Employing the transformer architecture alongside dilated convolutions, dHICA boasts an extensive receptive field and captures more cell-type-specific information. dHICA outperforms state-of-the-art baselines and achieves superior performance in cell-type-specific loci and gene elements, aligning with biological expectations. Furthermore, dHICA\u2019s imputations hold significant potential for downstream applications, including chromatin state segmentation and elucidating the functional implications of SNPs (Single Nucleotide Polymorphisms). In conclusion, dHICA serves as a valuable tool for advancing the understanding of chromatin dynamics, offering enhanced predictive capabilities and interpretability.<\/jats:p>","DOI":"10.1093\/bib\/bbae459","type":"journal-article","created":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T04:32:56Z","timestamp":1725510776000},"source":"Crossref","is-referenced-by-count":0,"title":["dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility"],"prefix":"10.1093","volume":"25","author":[{"given":"Wen","family":"Wen","sequence":"first","affiliation":[{"name":"School of Software Technology, Dalian University of Technology , Linggong Rd, Liaoning 116024 ,","place":["China"]}]},{"given":"Jiaxin","family":"Zhong","sequence":"additional","affiliation":[{"name":"School of Software Technology, Dalian University of Technology , Linggong Rd, Liaoning 116024 ,","place":["China"]}]},{"given":"Zhaoxi","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Software Technology, Dalian University of Technology , Linggong Rd, Liaoning 116024 ,","place":["China"]}]},{"given":"Lijuan","family":"Jia","sequence":"additional","affiliation":[{"name":"School of Software Technology, Dalian University of Technology , Linggong Rd, Liaoning 116024 ,","place":["China"]}]},{"given":"Tinyi","family":"Chu","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University , Weill Hall, Ithaca, NY 14853 ,","place":["United States"]}]},{"given":"Nating","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Cornell University , Biotechnology Building, Ithaca, NY 14853 ,","place":["United States"]}]},{"given":"Charles G","family":"Danko","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, College of Veterinary 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