{"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"],"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"],"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"],"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"],"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"],"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"],"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"],"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":false,"raw_author_name":"Shawn R. Starkenburg","raw_affiliation_strings":["Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, US. shawns@lanl.gov"],"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":8,"corresponding_author_ids":["https://openalex.org/A5122030586"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04482559,"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":[],"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":null},{"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/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":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-17 (2026)","raw_type":"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"}],"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":{"Characterizing":[0],"the":[1,5,32,44,50,106,171,178,188,192,239,247,262,301],"physical":[2,114,139],"organization":[3],"of":[4,27,99,244,261,282,294,303],"genome":[6,53,66,100,307],"is":[7,61,92,185,195],"essential":[8],"for":[9,94,277],"understanding":[10,98],"long-range":[11],"gene":[12],"regulation,":[13],"chromatin":[14,28,166,208,287],"compartmentalization,":[15],"and":[16,68,82,122,160,177,191,203,207,220,257,270,280,289,312],"epigenetic":[17,59,253],"accessibility.":[18],"Hi-C":[19,136,152,236,295],"experiments":[20],"generate":[21],"two-dimensional":[22],"(2D)":[23],"genome-wide":[24],"contact":[25,153],"maps":[26],"interactions":[29],"by":[30,133,151],"capturing":[31],"spatial":[33,45],"proximity":[34],"between":[35],"genomic":[36],"loci,":[37],"which":[38],"reveal":[39,161],"interaction":[40],"frequencies":[41],"but":[42],"lack":[43],"resolution":[46],"needed":[47],"to":[48,64,141,212,217],"interpret":[49],"three-dimensional":[51,214],"(3D)":[52],"structure(s).":[54],"Emerging":[55],"evidence":[56],"suggests":[57],"that":[58,69,113,199],"regulation":[60],"closely":[62],"linked":[63],"3D":[65,87,242,306],"architecture,":[67],"structural":[70,158],"changes":[71,159],"over":[72],"time":[73,304],"(4D)":[74],"drive":[75],"key":[76],"biological":[77],"processes":[78],"in":[79,119,165,264],"development,":[80],"disease,":[81],"environmental":[83],"response.":[84],"Thus,":[85,146],"integrating":[86,134],"structure":[88],"with":[89,138,249,297],"functional":[90],"data":[91,137,251,296,313],"critical":[93],"a":[95,227,265],"more":[96],"complete":[97],"regulation.":[101],"Previous":[102],"work,":[103],"most":[104],"notably":[105],"4DHiC":[107,189],"chromosome":[108,144,284],"modeling":[109,116,215],"framework,":[110],"has":[111],"shown":[112],"multi-dimensional":[115],"approaches":[117],"rooted":[118],"polymer":[120],"physics":[121],"molecular":[123,147,298],"dynamics":[124,148,299],"can":[125,155,200],"resolve":[126,156],"these":[127],"structures":[128],"at":[129],"biologically":[130],"meaningful":[131],"resolutions":[132],"temporal":[135],"constraints":[140],"uncover":[142],"dynamic":[143],"reorganization.":[145],"simulations,":[149],"constrained":[150],"matrices,":[154],"fine-scale":[157],"functionally":[162],"significant":[163],"transitions":[164],"conformation.":[167],"Herein,":[168],"we":[169],"present":[170],"4D":[172,179,205,271,283],"Genome":[173,180,272],"Browser":[174,181,273],"Workflow":[175],"(4DGBWorkflow)":[176],"(4DGB).":[182],"The":[183,223,268],"algorithm":[184],"based":[186],"on":[187,226],"method,":[190],"containerized":[193],"tool":[194],"an":[196],"end-to-end":[197],"workflow":[198],"transform,":[201],"filter,":[202],"view":[204],"epigenomics":[206],"datasets,":[209,285],"allowing":[210],"non-specialists":[211],"apply":[213],"principles":[216],"diverse":[218],"datasets":[219],"experimental":[221],"conditions.":[222],"software":[224],"executes":[225],"laptop":[228],"running":[229],"macOS,":[230],"Linux":[231],"or":[232],"Windows.":[233],"From":[234],"input":[235],"files":[237],"(.hic),":[238],"4DGBWorkflow":[240,269],"produces":[241],"reconstructions":[243],"chromosomes,":[245],"integrates":[246],"reconstruction":[248],"track":[250],"(e.g.,":[252],"marks,":[254],"transcriptome":[255],"profiles),":[256],"provides":[258],"comparative":[259,278],"visualization":[260,281],"results":[263],"single":[266],"workflow.":[267],"are":[274],"open-source":[275],"tools":[276],"analysis":[279],"including":[286],"architecture":[288],"epigenomic":[290],"signals.":[291],"Automatic":[292],"integration":[293,314],"democratizes":[300],"construction":[302],"resolved":[305],"structures,":[308],"simplifying":[309],"complex":[310],"simulations":[311],"schemes.":[315]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-01-08T00:00:00"}
