{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:18Z","timestamp":1772138058840,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T00:00:00Z","timestamp":1668038400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-18-CE12-0006-03"],"award-info":[{"award-number":["ANR-18-CE12-0006-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-18-CE45-0022-01"],"award-info":[{"award-number":["ANR-18-CE45-0022-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008367","name":"SNF","doi-asserted-by":"publisher","award":["31003A_176226"],"award-info":[{"award-number":["31003A_176226"]}],"id":[{"id":"10.13039\/100008367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009068","name":"University of Bern","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009068","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Here, we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Software available at https:\/\/gitlab.com\/togop\/3DPolyS-LE; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux and Mac OS).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary information are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac705","type":"journal-article","created":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T12:15:46Z","timestamp":1668082546000},"page":"5454-5456","source":"Crossref","is-referenced-by-count":8,"title":["3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7470-0646","authenticated-orcid":false,"given":"Todor","family":"Gitchev","sequence":"first","affiliation":[{"name":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"}]},{"given":"Gabriel","family":"Zala","sequence":"additional","affiliation":[{"name":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6230-4216","authenticated-orcid":false,"given":"Peter","family":"Meister","sequence":"additional","affiliation":[{"name":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9877-6864","authenticated-orcid":false,"given":"Daniel","family":"Jost","sequence":"additional","affiliation":[{"name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule, Ecole Normale Sup\u00e9rieure de Lyon, CNRS, UMR5239, Inserm U1293, Universit\u00e9 Claude Bernard Lyon 1 , Lyon 69007, France"}]}],"member":"286","published-online":{"date-parts":[[2022,11,10]]},"reference":[{"key":"2022121418412390100_btac705-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":"2020","journal-title":"Bioinformatics"},{"key":"2022121418412390100_btac705-B2","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/s41588-018-0161-5","article-title":"Enhancer hubs and loop collisions identified from Single-Allele topologies","volume":"50","author":"Allahyar","year":"2018","journal-title":"Nat. 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