{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T15:47:47Z","timestamp":1776008867622,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T00:00:00Z","timestamp":1606953600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01CA200059"],"award-info":[{"award-number":["U01CA200059"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["U01MH106883"],"award-info":[{"award-number":["U01MH106883"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>\u2002<\/jats:title>\n                    <jats:p>Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline Hi-C-based TE analyzer (HiTea) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole-genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE-insertion landscape. We employ the pipeline to identify TE-insertions from human cell-line Hi-C samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HiTea is available at https:\/\/github.com\/parklab\/HiTea and as a Docker image.<\/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\/btaa923","type":"journal-article","created":{"date-parts":[[2020,10,17]],"date-time":"2020-10-17T15:10:16Z","timestamp":1602947416000},"page":"1045-1051","source":"Crossref","is-referenced-by-count":5,"title":["HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data"],"prefix":"10.1093","volume":"37","author":[{"given":"Dhawal","family":"Jain","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chong","family":"Chu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5019-7652","authenticated-orcid":false,"given":"Burak Han","family":"Alver","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soohyun","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eunjung Alice","family":"Lee","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics, Boston Children\u2019s Hospital and Harvard Medical School , Boston, MA 02115, USA"},{"name":"Broad Institute of MIT and Harvard University , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9378-960X","authenticated-orcid":false,"given":"Peter J","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,3]]},"reference":[{"key":"2023051612081926000_btaa923-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2012\/947089","article-title":"Transposable elements are a significant contributor to tandem repeats in the human genome","volume":"2012","author":"Ahmed","year":"2012","journal-title":"Comp. 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