{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T01:27:20Z","timestamp":1778203640736,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,6,19]],"date-time":"2023-06-19T00:00:00Z","timestamp":1687132800000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM124820"],"award-info":[{"award-number":["R35GM124820"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG011207"],"award-info":[{"award-number":["R01HG011207"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG009906"],"award-info":[{"award-number":["R01HG009906"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>With the continuous effort to improve the quality of human reference genome and the generation of more and more personal genomes, the conversion of genomic coordinates between genome assemblies is critical in many integrative and comparative studies. While tools have been developed for such task for linear genome signals such as ChIP-Seq, no tool exists to convert genome assemblies for chromatin interaction data, despite the importance of three-dimensional genome organization in gene regulation and disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present HiCLift, a fast and efficient tool that can convert the genomic coordinates of chromatin contacts such as Hi-C and Micro-C from one assembly to another, including the latest T2T-CHM13 genome. Comparing with the strategy of directly remapping raw reads to a different genome, HiCLift runs on average 42 times faster (hours vs. days), while outputs nearly identical contact matrices. More importantly, as HiCLift does not need to remap the raw reads, it can directly convert human patient sample data, where the raw sequencing reads are sometimes hard to acquire or not available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HiCLift is publicly available at https:\/\/github.com\/XiaoTaoWang\/HiCLift.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad389","type":"journal-article","created":{"date-parts":[[2023,6,19]],"date-time":"2023-06-19T14:47:23Z","timestamp":1687186043000},"source":"Crossref","is-referenced-by-count":15,"title":["HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3531-2157","authenticated-orcid":false,"given":"Xiaotao","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , Chicago, IL 60611, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Yue","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , Chicago, IL 60611, United States"},{"name":"Robert H. Lurie Comprehensive Cancer Center of Northwestern University , Chicago, IL 60611, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,6,19]]},"reference":[{"key":"2023070312001785600_btad389-B1","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1038\/s41588-022-01188-8","article-title":"Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements","volume":"54","author":"Battaglia","year":"2022","journal-title":"Nat Genet"},{"key":"2023070312001785600_btad389-B2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-alpha-bound human chromatin interactome","volume":"462","author":"Fullwood","year":"2009","journal-title":"Nature"},{"key":"2023070312001785600_btad389-B3","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.cell.2015.05.048","article-title":"Mapping nucleosome resolution chromosome folding in yeast by Micro-C","volume":"162","author":"Hsieh","year":"2015","journal-title":"Cell"},{"key":"2023070312001785600_btad389-B4","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn","year":"2013","journal-title":"Brief Bioinform"},{"key":"2023070312001785600_btad389-B5","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2023070312001785600_btad389-B6","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/nmeth.3999","article-title":"HiChIP: efficient and sensitive analysis of protein-directed genome architecture","volume":"13","author":"Mumbach","year":"2016","journal-title":"Nat 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