{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:15Z","timestamp":1772138055850,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,10]],"date-time":"2022-09-10T00:00:00Z","timestamp":1662768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science KAKENHI","doi-asserted-by":"crossref","award":["18H05412"],"award-info":[{"award-number":["18H05412"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science KAKENHI","doi-asserted-by":"crossref","award":["20H05550"],"award-info":[{"award-number":["20H05550"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science KAKENHI","doi-asserted-by":"crossref","award":["21H05763"],"award-info":[{"award-number":["21H05763"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"name":"RIKEN BDR Structural Cell Biology Project"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into the polymer model\u2019s dynamics, structural conformations and rheological features. The updated optimization algorithm for regenerating a highly similar Hi-C matrix provides a fast and accurate optimal solution compared to the previous version by eliminating the factors underlying the inefficiency of the optimization algorithm in the iterative optimization process. In addition, we have enabled a Google Colab workflow to run the algorithm, wherein users can easily change the parameters and check the results in the notebook. Overall, PHi-C2 represents a valuable tool for mining the dynamic 3D genome state embedded in Hi-C data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PHi-C2 as the phic Python package is freely available under the GPL license and can be installed from the Python package index. The source code is available from GitHub at https:\/\/github.com\/soyashinkai\/PHi-C2. Moreover, users do not have to prepare a Python environment because PHi-C2 can run on Google Colab (https:\/\/bit.ly\/3rlptGI).<\/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\/btac613","type":"journal-article","created":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T21:14:20Z","timestamp":1662758060000},"page":"4984-4986","source":"Crossref","is-referenced-by-count":13,"title":["PHi-C2: interpreting Hi-C data as the dynamic 3D genome state"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6852-2751","authenticated-orcid":false,"given":"Soya","family":"Shinkai","sequence":"first","affiliation":[{"name":"Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research , Kobe 650-0047, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5224-3811","authenticated-orcid":false,"given":"Hiroya","family":"Itoga","sequence":"additional","affiliation":[{"name":"Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research , Kobe 650-0047, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9455-2153","authenticated-orcid":false,"given":"Koji","family":"Kyoda","sequence":"additional","affiliation":[{"name":"Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research , Kobe 650-0047, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8255-1724","authenticated-orcid":false,"given":"Shuichi","family":"Onami","sequence":"additional","affiliation":[{"name":"Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research , Kobe 650-0047, Japan"},{"name":"Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters , Kobe 650-0047, Japan"}]}],"member":"286","published-online":{"date-parts":[[2022,9,10]]},"reference":[{"key":"2022103112480353700_btac613-B1","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/s41588-018-0098-8","article-title":"Polymer physics predicts the effects of structural variants on chromatin architecture","volume":"50","author":"Bianco","year":"2018","journal-title":"Nat. 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