{"id":"https://openalex.org/W7118419187","doi":"https://doi.org/10.1186/s12859-025-06361-4","title":"From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture","display_name":"From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture","publication_year":2026,"publication_date":"2026-01-08","ids":{"openalex":"https://openalex.org/W7118419187","doi":"https://doi.org/10.1186/s12859-025-06361-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/41507775"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06361-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06361-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06361-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122030586","display_name":"David H. Rogers","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David H. Rogers","raw_affiliation_strings":["Information Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, US. dhr@lanl.gov"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, US. dhr@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080946596","display_name":"Cullen Roth","orcid":"https://orcid.org/0000-0003-4934-6160"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cullen Roth","raw_affiliation_strings":["Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075879150","display_name":"Cameron Tauxe","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cameron Tauxe","raw_affiliation_strings":["Information Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, US","Neptune, Inc. & Vistar Media, New York City, NY, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, US","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Neptune, Inc. & Vistar Media, New York City, NY, US","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122069762","display_name":"Jeannie T. Lee","orcid":null},"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"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeannie T. Lee","raw_affiliation_strings":["Department of Genetics, Harvard Medical School, Boston, MA, US","Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Harvard Medical School, Boston, MA, US","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, US","institution_ids":["https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121542586","display_name":"Christina R. Steadman","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina R. Steadman","raw_affiliation_strings":["Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024203760","display_name":"Karissa Y. Sanbonmatsu","orcid":"https://orcid.org/0000-0002-7965-7392"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210110743","display_name":"New Mexico Consortium","ror":"https://ror.org/01qnpp968","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210110743"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karissa Y. Sanbonmatsu","raw_affiliation_strings":["New Mexico Consortium, Los Alamos, NM, US","Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Mexico Consortium, Los Alamos, NM, US","institution_ids":["https://openalex.org/I4210110743"]},{"raw_affiliation_string":"Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, US","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061744598","display_name":"Anna Lappala","orcid":"https://orcid.org/0000-0001-9926-2972"},"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"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Lappala","raw_affiliation_strings":["Department of Genetics, Harvard Medical School, Boston, MA, US","Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Harvard Medical School, Boston, MA, US","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, US","institution_ids":["https://openalex.org/I4210087915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005423301","display_name":"Shawn R. Starkenburg","orcid":"https://orcid.org/0000-0002-8564-1274"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shawn R. Starkenburg","raw_affiliation_strings":["Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US. shawns@lanl.gov"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US. shawns@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005423301","https://openalex.org/A5122030586"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02061807,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"37","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9948999881744385,"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":0.9948999881744385,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.0015999999595806003,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7508000135421753},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7069000005722046},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.6398000121116638},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.5917999744415283},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.5698000192642212},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5332000255584717},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4544999897480011},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.44839999079704285}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7508000135421753},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7069000005722046},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.6398000121116638},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5917999744415283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5855000019073486},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.5698000192642212},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5332000255584717},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.515500009059906},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4544999897480011},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.44839999079704285},{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.4131999909877777},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.39070001244544983},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33180001378059387},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.3021000027656555},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2994999885559082},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.27250000834465027},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2676999866962433},{"id":"https://openalex.org/C2776397876","wikidata":"https://www.wikidata.org/wiki/Q1450531","display_name":"Cyberinfrastructure","level":2,"score":0.2662000060081482},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.2621999979019165},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.26030001044273376}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06361-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06361-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41507775","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41507775","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:11678500","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12870729","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":"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:daeba4a33c9b42949ccec675362fbc50","is_oa":true,"landing_page_url":"https://doaj.org/article/daeba4a33c9b42949ccec675362fbc50","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-17 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06361-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06361-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1967086347","https://openalex.org/W1991149014","https://openalex.org/W2007479836","https://openalex.org/W2096403311","https://openalex.org/W2102368172","https://openalex.org/W2103441770","https://openalex.org/W2117131162","https://openalex.org/W2128016314","https://openalex.org/W2169047304","https://openalex.org/W2481029670","https://openalex.org/W2558135510","https://openalex.org/W2584394140","https://openalex.org/W2765865112","https://openalex.org/W2766856260","https://openalex.org/W2806359197","https://openalex.org/W2884100980","https://openalex.org/W2888425844","https://openalex.org/W2945135442","https://openalex.org/W2945475836","https://openalex.org/W2960230796","https://openalex.org/W2988126442","https://openalex.org/W3091034669","https://openalex.org/W3092515417","https://openalex.org/W3097933316","https://openalex.org/W3201073812","https://openalex.org/W3206400375","https://openalex.org/W4200537317","https://openalex.org/W4220999759","https://openalex.org/W4225279860","https://openalex.org/W4285097960","https://openalex.org/W4286499647","https://openalex.org/W4296488518","https://openalex.org/W4360612388","https://openalex.org/W4379792586","https://openalex.org/W4386471322","https://openalex.org/W4392757646","https://openalex.org/W4399532233","https://openalex.org/W4402983315","https://openalex.org/W4406692105","https://openalex.org/W4410249356","https://openalex.org/W4410953803","https://openalex.org/W4414792949","https://openalex.org/W4414796584"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Characterizing":[1],"the":[2,6,33,45,51,107,173,180,190,194,241,249,264,304],"physical":[3,115,140],"organization":[4],"of":[5,28,100,246,263,285,297,306],"genome":[7,54,67,101,310],"is":[8,62,93,187,197],"essential":[9],"for":[10,95,280],"understanding":[11,99],"long-range":[12],"gene":[13],"regulation,":[14],"chromatin":[15,29,167,210,290],"compartmentalization,":[16],"and":[17,69,83,123,161,179,193,205,209,222,259,273,283,292,315],"epigenetic":[18,60,255],"accessibility.":[19],"Hi-C":[20,137,153,238,298],"experiments":[21],"generate":[22],"two-dimensional":[23],"(2D)":[24],"genome-wide":[25],"contact":[26,154],"maps":[27],"interactions":[30],"by":[31,134,152],"capturing":[32],"spatial":[34,46],"proximity":[35],"between":[36],"genomic":[37],"loci,":[38],"which":[39],"reveal":[40,162],"interaction":[41],"frequencies":[42],"but":[43],"lack":[44],"resolution":[47],"needed":[48],"to":[49,65,142,214,219],"interpret":[50],"three-dimensional":[52,216],"(3D)":[53],"structure(s).":[55],"Emerging":[56],"evidence":[57],"suggests":[58],"that":[59,70,114,201],"regulation":[61],"closely":[63],"linked":[64],"3D":[66,88,244,309],"architecture,":[68],"structural":[71,159],"changes":[72,160],"over":[73],"time":[74,307],"(4D)":[75],"drive":[76],"key":[77],"biological":[78],"processes":[79],"in":[80,120,166,266],"development,":[81],"disease,":[82],"environmental":[84],"response.":[85],"Thus,":[86,147],"integrating":[87,135],"structure":[89],"with":[90,139,251,300],"functional":[91],"data":[92,138,253,299,316],"critical":[94],"a":[96,229,267],"more":[97],"complete":[98],"regulation.":[102],"Previous":[103],"work,":[104],"most":[105],"notably":[106],"4DHiC":[108,191],"chromosome":[109,145,287],"modeling":[110,117,217],"framework,":[111],"has":[112],"shown":[113],"multi-dimensional":[116],"approaches":[118],"rooted":[119],"polymer":[121],"physics":[122],"molecular":[124,148,301],"dynamics":[125,149,302],"can":[126,156,202],"resolve":[127,157],"these":[128],"structures":[129],"at":[130],"biologically":[131],"meaningful":[132],"resolutions":[133],"temporal":[136],"constraints":[141],"uncover":[143],"dynamic":[144],"reorganization.":[146],"simulations,":[150],"constrained":[151],"matrices,":[155],"fine-scale":[158],"functionally":[163],"significant":[164],"transitions":[165],"conformation.":[168],"RESULTS:":[169],"Herein,":[170],"we":[171],"present":[172],"4D":[174,181,207,274,286],"Genome":[175,182,275],"Browser":[176,183,276],"Workflow":[177],"(4DGBWorkflow)":[178],"(4DGB).":[184],"The":[185,225,271],"algorithm":[186],"based":[188],"on":[189,228],"method,":[192],"containerized":[195],"tool":[196],"an":[198],"end-to-end":[199],"workflow":[200],"transform,":[203],"filter,":[204],"view":[206],"epigenomics":[208],"datasets,":[211,288],"allowing":[212],"non-specialists":[213],"apply":[215],"principles":[218],"diverse":[220],"datasets":[221],"experimental":[223],"conditions.":[224],"software":[226],"executes":[227],"laptop":[230],"running":[231],"macOS,":[232],"Linux":[233],"or":[234],"Windows.":[235],"From":[236],"input":[237],"files":[239],"(.hic),":[240],"4DGBWorkflow":[242,272],"produces":[243],"reconstructions":[245],"chromosomes,":[247],"integrates":[248],"reconstruction":[250],"track":[252],"(e.g.,":[254],"marks,":[256],"transcriptome":[257],"profiles),":[258],"provides":[260],"comparative":[261,281],"visualization":[262,284],"results":[265],"single":[268],"workflow.":[269],"CONCLUSIONS:":[270],"are":[277],"open-source":[278],"tools":[279],"analysis":[282],"including":[289],"architecture":[291],"epigenomic":[293],"signals.":[294],"Automatic":[295],"integration":[296,317],"democratizes":[303],"construction":[305],"resolved":[308],"structures,":[311],"simplifying":[312],"complex":[313],"simulations":[314],"schemes.":[318]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-01-08T00:00:00"}