{"id":"https://openalex.org/W4413323271","doi":"https://doi.org/10.1371/journal.pcbi.1013358","title":"The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon","display_name":"The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon","publication_year":2025,"publication_date":"2025-08-19","ids":{"openalex":"https://openalex.org/W4413323271","doi":"https://doi.org/10.1371/journal.pcbi.1013358","pmid":"https://pubmed.ncbi.nlm.nih.gov/40828848"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013358","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013358","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013358&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013358&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002442819","display_name":"J\u0119drzej Kubica","orcid":"https://orcid.org/0000-0001-7037-3900"},"institutions":[{"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/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR","PL"],"is_corresponding":true,"raw_author_name":"J\u0119drzej Kubica","raw_affiliation_strings":["Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland","Univ. Grenoble Alpes, CNRS, UMR, TIMC/ MAGe, Grenoble, France"],"affiliations":[{"raw_affiliation_string":"Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Univ. Grenoble Alpes, CNRS, UMR, TIMC/ MAGe, Grenoble, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I899635006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003072587","display_name":"Sevastianos Korsak","orcid":"https://orcid.org/0000-0002-7357-3315"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sevastianos Korsak","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]},{"raw_affiliation_string":"Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026645431","display_name":"Krzysztof Banecki","orcid":"https://orcid.org/0000-0001-9573-0804"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Krzysztof H. Banecki","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]},{"raw_affiliation_string":"Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080854195","display_name":"Dvir Schirman","orcid":"https://orcid.org/0000-0001-5175-0176"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Dvir Schirman","raw_affiliation_strings":["Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050907564","display_name":"Anurupa Devi Yadavalli","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anurupa Devi Yadavalli","raw_affiliation_strings":["Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003548772","display_name":"Ariana Brenner Clerkin","orcid":"https://orcid.org/0000-0003-0911-6619"},"institutions":[{"id":"https://openalex.org/I4210100942","display_name":"Tri-Institutional PhD Program in Chemical Biology","ror":"https://ror.org/016twdg30","country_code":"US","type":"education","lineage":["https://openalex.org/I4210100942"]},{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ariana Brenner Clerkin","raw_affiliation_strings":["Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, New York, United States of America","Tri-Institutional PhD Program in Computational Biology and Medicine, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, New York, United States of America","institution_ids":["https://openalex.org/I83399316"]},{"raw_affiliation_string":"Tri-Institutional PhD Program in Computational Biology and Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I4210100942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031138186","display_name":"David Kou\u0159il","orcid":"https://orcid.org/0000-0003-4043-3487"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Kou\u0159il","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, Maryland, United States of America","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056673563","display_name":"Micha\u0142 Kadlof","orcid":"https://orcid.org/0000-0002-4293-4456"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Micha\u0142 Kadlof","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070603357","display_name":"Ben Busby","orcid":"https://orcid.org/0000-0001-5267-4988"},"institutions":[{"id":"https://openalex.org/I4210130836","display_name":"DNAnexus (United States)","ror":"https://ror.org/043pjwk57","country_code":"US","type":"company","lineage":["https://openalex.org/I4210130836"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ben Busby","raw_affiliation_strings":["DNAnexus, Mountain View, California, United States of America"],"affiliations":[{"raw_affiliation_string":"DNAnexus, Mountain View, California, United States of America","institution_ids":["https://openalex.org/I4210130836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021916927","display_name":"Dariusz Plewczy\u0144ski","orcid":"https://orcid.org/0000-0002-3840-7610"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Dariusz Plewczynski","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]},{"raw_affiliation_string":"Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5002442819","https://openalex.org/A5003072587","https://openalex.org/A5003548772","https://openalex.org/A5021916927","https://openalex.org/A5026645431","https://openalex.org/A5031138186","https://openalex.org/A5050907564","https://openalex.org/A5056673563","https://openalex.org/A5070603357","https://openalex.org/A5080854195"],"corresponding_institution_ids":["https://openalex.org/I108403487","https://openalex.org/I123387679","https://openalex.org/I1294671590","https://openalex.org/I136199984","https://openalex.org/I32971472","https://openalex.org/I4210100942","https://openalex.org/I4210130836","https://openalex.org/I4654613","https://openalex.org/I83399316","https://openalex.org/I899635006"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18488095,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"8","first_page":"e1013358","last_page":"e1013358"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9854999780654907,"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/T11482","display_name":"RNA modifications and cancer","score":0.9846000075340271,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.785569429397583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5661436319351196},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.48347264528274536},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47099488973617554},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4632813334465027},{"id":"https://openalex.org/keywords/dynamism","display_name":"Dynamism","score":0.45861318707466125},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4172285795211792},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3700571060180664},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25209733843803406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14648598432540894},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11838960647583008}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.785569429397583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5661436319351196},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.48347264528274536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47099488973617554},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4632813334465027},{"id":"https://openalex.org/C2775836275","wikidata":"https://www.wikidata.org/wiki/Q3502310","display_name":"Dynamism","level":2,"score":0.45861318707466125},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4172285795211792},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3700571060180664},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25209733843803406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14648598432540894},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11838960647583008},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013358","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013358","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013358&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40828848","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40828848","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:DiVA.org:uu-566496","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-566496","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:77cbad5393214e96ae94df5a0f2428e6","is_oa":true,"landing_page_url":"https://doaj.org/article/77cbad5393214e96ae94df5a0f2428e6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 8, p e1013358 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11188622","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12380275","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013358","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013358","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013358&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2589273613","display_name":null,"funder_award_id":"1U54DK107967-01","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G5232606565","display_name":null,"funder_award_id":"1U54DK107967-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6988551844","display_name":null,"funder_award_id":"UM1HG011536","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7375032004","display_name":null,"funder_award_id":"R01HG011773","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8388340808","display_name":null,"funder_award_id":"HG011536","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8799024164","display_name":null,"funder_award_id":"2020/37/B/NZ2/03757","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320322637","display_name":"Politechnika Warszawska","ror":"https://ror.org/00y0xnp53"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413323271.pdf","grobid_xml":"https://content.openalex.org/works/W4413323271.grobid-xml"},"referenced_works_count":124,"referenced_works":["https://openalex.org/W1132040419","https://openalex.org/W1660678623","https://openalex.org/W1701083935","https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W1974342055","https://openalex.org/W1974463674","https://openalex.org/W1994556689","https://openalex.org/W2031057223","https://openalex.org/W2036108598","https://openalex.org/W2044606399","https://openalex.org/W2063124224","https://openalex.org/W2080479776","https://openalex.org/W2082852695","https://openalex.org/W2084133980","https://openalex.org/W2087588724","https://openalex.org/W2090037139","https://openalex.org/W2119267663","https://openalex.org/W2144792857","https://openalex.org/W2163535412","https://openalex.org/W2165780114","https://openalex.org/W2259938310","https://openalex.org/W2292234541","https://openalex.org/W2302999593","https://openalex.org/W2321233811","https://openalex.org/W2523898334","https://openalex.org/W2529955155","https://openalex.org/W2531252302","https://openalex.org/W2569095710","https://openalex.org/W2580178967","https://openalex.org/W2584394140","https://openalex.org/W2594764564","https://openalex.org/W2597274540","https://openalex.org/W2610883583","https://openalex.org/W2738924259","https://openalex.org/W2739969873","https://openalex.org/W2742892125","https://openalex.org/W2787198910","https://openalex.org/W2793253652","https://openalex.org/W2796319511","https://openalex.org/W2883604250","https://openalex.org/W2896477989","https://openalex.org/W2898514070","https://openalex.org/W2901071798","https://openalex.org/W2905598336","https://openalex.org/W2911835695","https://openalex.org/W2920923857","https://openalex.org/W2921773684","https://openalex.org/W2922283820","https://openalex.org/W2931039481","https://openalex.org/W2945135442","https://openalex.org/W2949391446","https://openalex.org/W2951074257","https://openalex.org/W2951559295","https://openalex.org/W2952117848","https://openalex.org/W2952699651","https://openalex.org/W2952940726","https://openalex.org/W2965970564","https://openalex.org/W2967111145","https://openalex.org/W2972380686","https://openalex.org/W2972564110","https://openalex.org/W2988126442","https://openalex.org/W2991086992","https://openalex.org/W3014345894","https://openalex.org/W3021581669","https://openalex.org/W3030245050","https://openalex.org/W3039452253","https://openalex.org/W3047025505","https://openalex.org/W3091921516","https://openalex.org/W3092624702","https://openalex.org/W3105698558","https://openalex.org/W3106609240","https://openalex.org/W3107536938","https://openalex.org/W3124332276","https://openalex.org/W3124946892","https://openalex.org/W3125103290","https://openalex.org/W3136776248","https://openalex.org/W3155536267","https://openalex.org/W3158393751","https://openalex.org/W3165454401","https://openalex.org/W3171639536","https://openalex.org/W3177624796","https://openalex.org/W3193986928","https://openalex.org/W3212860783","https://openalex.org/W3213694110","https://openalex.org/W4200134543","https://openalex.org/W4205374539","https://openalex.org/W4210417808","https://openalex.org/W4225108987","https://openalex.org/W4225279860","https://openalex.org/W4255154157","https://openalex.org/W4280554122","https://openalex.org/W4282946267","https://openalex.org/W4286874786","https://openalex.org/W4296129874","https://openalex.org/W4309218861","https://openalex.org/W4310598476","https://openalex.org/W4312995596","https://openalex.org/W4313893501","https://openalex.org/W4321366633","https://openalex.org/W4322719757","https://openalex.org/W4367692216","https://openalex.org/W4375954797","https://openalex.org/W4378782463","https://openalex.org/W4379792586","https://openalex.org/W4383377610","https://openalex.org/W4385812298","https://openalex.org/W4386019761","https://openalex.org/W4386471322","https://openalex.org/W4388036487","https://openalex.org/W4389073932","https://openalex.org/W4389565117","https://openalex.org/W4389871262","https://openalex.org/W4391101732","https://openalex.org/W4391309357","https://openalex.org/W4394813096","https://openalex.org/W4394841535","https://openalex.org/W4396672510","https://openalex.org/W4396894869","https://openalex.org/W4400537635","https://openalex.org/W4401011315","https://openalex.org/W4402727293","https://openalex.org/W4403097720","https://openalex.org/W4403478939"],"related_works":["https://openalex.org/W2000438032","https://openalex.org/W2775384662","https://openalex.org/W2385556862","https://openalex.org/W4297288183","https://openalex.org/W4297802007","https://openalex.org/W2117883229","https://openalex.org/W2367908682","https://openalex.org/W2586399084","https://openalex.org/W3122659832","https://openalex.org/W2045813810"],"abstract_inverted_index":{"The":[0,69,76],"computational":[1],"modeling":[2,33,52,164],"of":[3,14,71,90,99,110,114,170,181,239],"chromatin":[4,100,117,135,162,171,215],"structure":[5,32,163],"is":[6,208,221,227],"highly":[7],"complex":[8],"due":[9],"to":[10,45,82,92,123,133,143,210],"the":[11,51,59,97,111,115,127,237],"hierarchical":[12],"organization":[13],"chromatin,":[15],"which":[16,27,220],"reflects":[17],"its":[18,29],"diverse":[19,38],"biophysical":[20],"principles,":[21],"as":[22,24,148,150],"well":[23,149],"inherent":[25],"dynamism,":[26],"underlies":[28],"complexity.":[30],"Chromatin":[31],"can":[34],"be":[35],"based":[36],"on":[37,64,214],"approaches":[39],"and":[40,87,95,103,119,125,137,153,173,196,206,232,245],"assumptions,":[41],"making":[42],"it":[43],"essential":[44],"determine":[46],"how":[47],"different":[48,168],"methods":[49],"influence":[50],"outcomes.":[53],"We":[54,129,234],"conducted":[55],"a":[56],"project":[57],"at":[58,68],"NIH-funded":[60],"4D":[61],"Nucleome":[62],"Hackathon":[63],"March":[65],"18-21,":[66],"2024,":[67],"University":[70],"Washington":[72],"in":[73,161,190,203,224],"Seattle,":[74],"USA.":[75],"hackathon":[77],"provided":[78],"an":[79,84,108],"amazing":[80],"opportunity":[81],"gather":[83],"international,":[85],"multi-institutional":[86],"unbiased":[88],"group":[89],"experts":[91],"discuss,":[93],"understand":[94],"undertake":[96],"challenges":[98,160],"model":[101,176,199],"comparison":[102],"validation.":[104],"Here":[105],"we":[106,138,158],"give":[107],"overview":[109],"current":[112],"state":[113],"3D":[116],"field":[118],"discuss":[120,159],"our":[121],"efforts":[122],"run":[124],"validate":[126],"models.":[128],"used":[130],"distance":[131],"matrices":[132],"represent":[134],"models":[136,152],"calculated":[139],"Spearman":[140],"correlation":[141],"coefficients":[142],"estimate":[144],"differences":[145],"between":[146,151],"models,":[147],"experimental":[154,182],"data.":[155],"In":[156],"addition,":[157],"that":[165,188],"include:":[166],"1)":[167],"aspects":[169],"biophysics":[172],"scales":[174],"complicate":[175],"comparisons,":[177],"2)":[178],"large":[179],"diversity":[180],"data":[183],"(e.g.,":[184],"population-based,":[185],"single-cell,":[186],"protein-specific)":[187],"differ":[189],"mathematical":[191],"properties,":[192],"heatmap":[193],"smoothness,":[194],"noise":[195],"resolutions":[197],"complicates":[198],"validation,":[200],"3)":[201],"expertise":[202],"biology,":[204],"bioinformatics,":[205],"physics":[207],"necessary":[209],"conduct":[211],"comprehensive":[212],"research":[213],"structure,":[216],"4)":[217],"bioinformatic":[218],"software,":[219],"often":[222],"developed":[223],"academic":[225],"settings,":[226],"characterized":[228],"by":[229],"insufficient":[230],"support":[231],"documentation.":[233],"also":[235],"emphasize":[236],"importance":[238],"establishing":[240],"guidelines":[241],"for":[242],"software":[243],"development":[244],"standardization.":[246]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
