{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T18:06:19Z","timestamp":1759773979700,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Science Foundation","award":["CRC992"],"award-info":[{"award-number":["CRC992"]}]},{"name":"German Federal Ministry of Education and Research","award":["031 A538A"],"award-info":[{"award-number":["031 A538A"]}]},{"name":"NBI"},{"DOI":"10.13039\/100012395","name":"RBC","doi-asserted-by":"publisher","award":["031 L0101C"],"award-info":[{"award-number":["031 L0101C"]}],"id":[{"id":"10.13039\/100012395","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NBI"},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Germany\u2019s Excellence Strategy"},{"name":"CIBSS-EXC-2189-Project","award":["390939984"],"award-info":[{"award-number":["390939984"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-cell Hi-C research currently lacks an efficient, easy to use and shareable data storage format. Recent studies have used a variety of sub-optimal solutions: publishing raw data only, text-based interaction matrices, or reusing established Hi-C storage formats for single interaction matrices. These approaches are storage and pre-processing intensive, require long labour time and are often error-prone.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The single-cell cooler file format (scool) provides an efficient, user-friendly and storage-saving approach for single-cell Hi-C data. It is a flavour of the established cooler format and guarantees stable API support.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The single-cell cooler format is part of the cooler file format as of API version 0.8.9. It is available via pip, conda and github: https:\/\/github.com\/mirnylab\/cooler.<\/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\/btaa924","type":"journal-article","created":{"date-parts":[[2020,10,20]],"date-time":"2020-10-20T19:13:55Z","timestamp":1603221235000},"page":"2053-2054","source":"Crossref","is-referenced-by-count":4,"title":["Scool: a new data storage format for single-cell Hi-C data"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9985-955X","authenticated-orcid":false,"given":"Joachim","family":"Wolff","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5814-0864","authenticated-orcid":false,"given":"Nezar","family":"Abdennur","sequence":"additional","affiliation":[{"name":"Institute for Medical Engineering and Science, Massachusetts Institute of Technology , Cambridge, MA 02139, USA"}]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg 79104, Germany"}]},{"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"2023061310291504100_btaa924-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":"2019","journal-title":"Bioinformatics"},{"key":"2023061310291504100_btaa924-B2","doi-asserted-by":"crossref","first-page":"3600","DOI":"10.15252\/embj.201798083","article-title":"A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture","volume":"36","author":"Gassler","year":"2017","journal-title":"EMBO J"},{"year":"2018","author":"Koziol","key":"2023061310291504100_btaa924-B3"},{"key":"2023061310291504100_btaa924-B4","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature12593","article-title":"Single-cell Hi-C reveals cell-to-cell variability in chromosome structure","volume":"502","author":"Nagano","year":"2013","journal-title":"Nature"},{"key":"2023061310291504100_btaa924-B5","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature23001","article-title":"Cell-cycle dynamics of chromosomal organization at single-cell resolution","volume":"547","author":"Nagano","year":"2017","journal-title":"Nature"},{"key":"2023061310291504100_btaa924-B6","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nmeth.4155","article-title":"Massively multiplex single-cell Hi-C","volume":"14","author":"Ramani","year":"2017","journal-title":"Nat. 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