{"id":"https://openalex.org/W4304891399","doi":"https://doi.org/10.1093/bioinformatics/btac705","title":"3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion","display_name":"3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion","publication_year":2022,"publication_date":"2022-11-10","ids":{"openalex":"https://openalex.org/W4304891399","doi":"https://doi.org/10.1093/bioinformatics/btac705","pmid":"https://pubmed.ncbi.nlm.nih.gov/36355469"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5454/47887017/btac705.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5454/47887017/btac705.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038271387","display_name":"Todor Gitchev","orcid":"https://orcid.org/0000-0002-7470-0646"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Todor Gitchev","raw_affiliation_strings":["Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"],"affiliations":[{"raw_affiliation_string":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073571799","display_name":"Gabriel Zala","orcid":null},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gabriel Zala","raw_affiliation_strings":["Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"],"affiliations":[{"raw_affiliation_string":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Peter Meister","orcid":"https://orcid.org/0000-0002-6230-4216"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Peter Meister","raw_affiliation_strings":["Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland"],"affiliations":[{"raw_affiliation_string":"Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern , Bern 3012, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090174880","display_name":"Daniel Jost","orcid":"https://orcid.org/0000-0002-9877-6864"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Daniel Jost","raw_affiliation_strings":["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"],"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I113428412","https://openalex.org/I100532134","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5090174880"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I118564535","https://openalex.org/I1294671590","https://openalex.org/I154526488"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6076,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64851999,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"38","issue":"24","first_page":"5454","last_page":"5456"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9625999927520752,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9625999927520752,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.023399999365210533,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/extrusion","display_name":"Extrusion","score":0.6512422561645508},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6436976790428162},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.6394907236099243},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4239719808101654},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.24975770711898804},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16937795281410217},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14313051104545593},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13585853576660156},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.09691646695137024},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.07457268238067627}],"concepts":[{"id":"https://openalex.org/C2778958987","wikidata":"https://www.wikidata.org/wiki/Q139143","display_name":"Extrusion","level":2,"score":0.6512422561645508},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6436976790428162},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.6394907236099243},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4239719808101654},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.24975770711898804},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16937795281410217},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14313051104545593},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13585853576660156},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.09691646695137024},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.07457268238067627},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btac705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5454/47887017/btac705.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36355469","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36355469","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-03797993v1","is_oa":false,"landing_page_url":"https://cnrs.hal.science/hal-03797993","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, In press","raw_type":"Journal articles"},{"id":"pmh:oai:boris.unibe.ch:174725","is_oa":true,"landing_page_url":"https://boris.unibe.ch/174725/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401086","display_name":"Bern Open Repository and Information System (University of Bern)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118564535","host_organization_name":"University of Bern","host_organization_lineage":["https://openalex.org/I118564535"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Gitchev, Todor; Zala, Gabriel; Meister, Peter; Jost, Daniel (2022). 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. Bioinformatics, 38(24), pp. 5454-5456. Oxford University Press 10.1093/bioinformatics/btac705 &lt;http://dx.doi.org/10.1093/bioinformatics/btac705&gt;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9750120","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9750120","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"doi:10.48350/174725","is_oa":true,"landing_page_url":"https://doi.org/10.48350/174725","pdf_url":null,"source":{"id":"https://openalex.org/S7407053152","display_name":"Open Access CRIS of the University of Bern","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5454/47887017/btac705.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1752262343","display_name":null,"funder_award_id":"31003A_176226","funder_id":"https://openalex.org/F4320310459","funder_display_name":"Statens Naturvidenskabelige Forskningsrad"},{"id":"https://openalex.org/G2230233169","display_name":null,"funder_award_id":"ANR-18-CE12-0006-03","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G246426947","display_name":null,"funder_award_id":"ANR-18-CE45-0022-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2659166393","display_name":null,"funder_award_id":"ANR-18-CE12-00","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G544591541","display_name":null,"funder_award_id":"31003A","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G6876561401","display_name":null,"funder_award_id":"ANR-18","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7091979907","display_name":null,"funder_award_id":"ANR-18-CE45-0022","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7457348722","display_name":null,"funder_award_id":"ANR-18-CE12-0006","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8328324002","display_name":"Mechanisms of gene regulation by chromatin compaction","funder_award_id":"176226","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G971298448","display_name":null,"funder_award_id":"31003","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320310459","display_name":"Statens Naturvidenskabelige Forskningsrad","ror":"https://ror.org/00znyv691"},{"id":"https://openalex.org/F4320310992","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4304891399.pdf","grobid_xml":"https://content.openalex.org/works/W4304891399.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W2070021921","https://openalex.org/W2161212572","https://openalex.org/W2291910142","https://openalex.org/W2401568148","https://openalex.org/W2567008309","https://openalex.org/W2594764564","https://openalex.org/W2757387674","https://openalex.org/W2761461280","https://openalex.org/W2788376770","https://openalex.org/W2810076504","https://openalex.org/W2812344549","https://openalex.org/W2950728164","https://openalex.org/W2951871954","https://openalex.org/W2960979937","https://openalex.org/W2989713781","https://openalex.org/W2991248607","https://openalex.org/W3009665504","https://openalex.org/W3024121050","https://openalex.org/W3026388278","https://openalex.org/W3184944554","https://openalex.org/W3200376887","https://openalex.org/W4225320261","https://openalex.org/W6838897700"],"related_works":["https://openalex.org/W2199098843","https://openalex.org/W1944488069","https://openalex.org/W2946328221","https://openalex.org/W3196534259","https://openalex.org/W4205107526","https://openalex.org/W1562819778","https://openalex.org/W2954952850","https://openalex.org/W3209707857","https://openalex.org/W2328519397","https://openalex.org/W2982087732"],"abstract_inverted_index":{"Supplementary":[0],"information":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
