{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T11:34:37Z","timestamp":1772451277791,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,15]],"date-time":"2021-03-15T00:00:00Z","timestamp":1615766400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM133712"],"award-info":[{"award-number":["R35GM133712"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"crossref","award":["K22CA204439"],"award-info":[{"award-number":["K22CA204439"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Phi Beta Psi Sorority Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Identification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present BART3D, a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, leveraging public ChIP-seq data for human and mouse. We demonstrate that BART3D can detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation. BART3D can be a useful tool in 3D genome data analysis and functional genomics research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BART3D is implemented in Python and the source code is available at https:\/\/github.com\/zanglab\/bart3d.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab173","type":"journal-article","created":{"date-parts":[[2021,3,11]],"date-time":"2021-03-11T15:11:15Z","timestamp":1615475475000},"page":"3075-3078","source":"Crossref","is-referenced-by-count":16,"title":["BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data"],"prefix":"10.1093","volume":"37","author":[{"given":"Zhenjia","family":"Wang","sequence":"first","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, USA"}]},{"given":"Yifan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, USA"},{"name":"Department of Biomedical Engineering, University of Virginia , Charlottesville, VA 22908, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4812-3627","authenticated-orcid":false,"given":"Chongzhi","family":"Zang","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, USA"},{"name":"Department of Biomedical Engineering, University of Virginia , Charlottesville, VA 22908, USA"},{"name":"Department of Public Health Sciences, University of Virginia , Charlottesville, VA 22908, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,3,15]]},"reference":[{"key":"2023061310553676500_btab173-B1","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btz540","article-title":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","volume":"36","author":"Abdennur","year":"2020","journal-title":"Bioinformatics"},{"key":"2023061310553676500_btab173-B2","doi-asserted-by":"crossref","first-page":"i145","DOI":"10.1093\/bioinformatics\/btz362","article-title":"Selfish: discovery of differential chromatin interactions via a self-similarity measure","volume":"35","author":"Ardakany","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310553676500_btab173-B3","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nrg.2016.112","article-title":"Organization and function of the 3D genome","volume":"17","author":"Bonev","year":"2016","journal-title":"Nat. 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