{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T02:41:01Z","timestamp":1774924861920,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T00:00:00Z","timestamp":1641168000000},"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":["U01 CA200059"],"award-info":[{"award-number":["U01 CA200059"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>As the amount of 3D chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The format specification and source code are available at https:\/\/github.com\/4dn-dcic\/pairix, https:\/\/github.com\/4dn-dcic\/Rpairix and https:\/\/github.com\/4dn-dcic\/pairsqc.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab870","type":"journal-article","created":{"date-parts":[[2021,12,28]],"date-time":"2021-12-28T15:28:16Z","timestamp":1640705296000},"page":"1729-1731","source":"Crossref","is-referenced-by-count":47,"title":["Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs"],"prefix":"10.1093","volume":"38","author":[{"given":"Soohyun","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"Clara R","family":"Bakker","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"Carl","family":"Vitzthum","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5019-7652","authenticated-orcid":false,"given":"Burak H","family":"Alver","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}]},{"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"}]}],"member":"286","published-online":{"date-parts":[[2022,1,3]]},"reference":[{"key":"2023033004320042800_","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":"2019","journal-title":"Bioinformatics"},{"key":"2023033004320042800_","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3 Data-Driven Documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. 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