{"id":"https://openalex.org/W7125418904","doi":"https://doi.org/10.1093/bioinformatics/btag035","title":"Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks","display_name":"Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks","publication_year":2026,"publication_date":"2026-01-20","ids":{"openalex":"https://openalex.org/W7125418904","doi":"https://doi.org/10.1093/bioinformatics/btag035","pmid":"https://pubmed.ncbi.nlm.nih.gov/41566771"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag035","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag035","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090508229","display_name":"David Kou","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Kou\u0159il","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,"],"raw_orcid":"https://orcid.org/0000-0003-4043-3487","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057253726","display_name":"Trevor Manz","orcid":"https://orcid.org/0000-0001-7694-5164"},"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":false,"raw_author_name":"Trevor Manz","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,"],"raw_orcid":"https://orcid.org/0000-0001-7694-5164","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027768713","display_name":"Tereza Clarence","orcid":"https://orcid.org/0000-0002-0099-2797"},"institutions":[{"id":"https://openalex.org/I1314596251","display_name":"Allen Institute for Brain Science","ror":"https://ror.org/00dcv1019","country_code":"US","type":"facility","lineage":["https://openalex.org/I1314596251","https://openalex.org/I4210140341"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tereza Clarence","raw_affiliation_strings":["Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, NY 10029,"],"raw_orcid":"https://orcid.org/0000-0002-0099-2797","affiliations":[{"raw_affiliation_string":"Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, NY 10029,","institution_ids":["https://openalex.org/I1314596251"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123604098","display_name":"Nils Gehlenborg","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nils Gehlenborg","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,"],"raw_orcid":"https://orcid.org/0000-0003-0327-8297","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5123604098"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06867469,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.6096000075340271,"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":0.6096000075340271,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.25839999318122864,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.022600000724196434,"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/python","display_name":"Python (programming language)","score":0.8741999864578247},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.792900025844574},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.781499981880188},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7361000180244446},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.64410001039505},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.44839999079704285},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44440001249313354}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8741999864578247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8039000034332275},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.792900025844574},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.781499981880188},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7361000180244446},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.64410001039505},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6062999963760376},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.531000018119812},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.44839999079704285},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44440001249313354},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.38269999623298645},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.37599998712539673},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.36980000138282776},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.3677999973297119},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.36480000615119934},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.33329999446868896},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3197000026702881},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.29100000858306885},{"id":"https://openalex.org/C2988963302","wikidata":"https://www.wikidata.org/wiki/Q629206","display_name":"Program code","level":2,"score":0.26460000872612}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btag035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag035","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:41566771","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41566771","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:europepmc.org:11711533","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12904833","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:12904833","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12904833/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag035","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G578864555","display_name":null,"funder_award_id":"UM1 HG011536","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8986424483","display_name":null,"funder_award_id":"R01 HG011773","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1481598211","https://openalex.org/W1701083935","https://openalex.org/W2011301426","https://openalex.org/W2050892199","https://openalex.org/W2090037139","https://openalex.org/W2130479394","https://openalex.org/W2145619687","https://openalex.org/W2201171270","https://openalex.org/W2564812046","https://openalex.org/W2597274540","https://openalex.org/W2772099288","https://openalex.org/W2889474202","https://openalex.org/W2944634251","https://openalex.org/W2945135442","https://openalex.org/W3035965352","https://openalex.org/W3047380455","https://openalex.org/W3080497669","https://openalex.org/W3159719254","https://openalex.org/W3203255635","https://openalex.org/W4312220406","https://openalex.org/W4385289287","https://openalex.org/W4392173297","https://openalex.org/W4402570602","https://openalex.org/W4403665808","https://openalex.org/W4407010921","https://openalex.org/W4417338041"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Uchimata":[1,60,76],"is":[2,61,77,86,93,107,124],"a":[3,17,29,96],"toolkit":[4],"for":[5,32,105],"visualization":[6,33],"of":[7,10,14,23,26,49],"3D":[8,24,50],"structures":[9,52],"genomes.":[11],"It":[12],"consists":[13],"two":[15],"packages:":[16],"Javascript":[18,84],"library":[19,85],"facilitating":[20],"the":[21,80,91],"rendering":[22],"models":[25],"genomes,":[27],"and":[28,47,57,113,115,118],"Python":[30,97],"widget":[31,92],"in":[34,71],"Jupyter":[35],"Notebooks.":[36],"Main":[37],"features":[38],"include":[39],"an":[40],"expressive":[41],"way":[42],"to":[43,63],"specify":[44],"visual":[45],"encodings,":[46],"filtering":[48],"genome":[51],"based":[53],"on":[54,88,100,110],"genomic":[55],"semantics":[56],"spatial":[58],"aspects.":[59],"designed":[62],"be":[64],"highly":[65],"integratable":[66],"with":[67,122],"biological":[68],"tooling":[69],"available":[70,87,94,108],"Python.":[72],"AVAILABILITY":[73],"AND":[74],"IMPLEMENTATION:":[75],"released":[78],"under":[79],"MIT":[81],"License.":[82],"The":[83,102,120],"NPM,":[89],"while":[90],"as":[95],"package":[98],"hosted":[99,125],"PyPI.":[101],"source":[103],"code":[104],"both":[106],"publicly":[109],"Github":[111],"(https://github.com/hms-dbmi/uchimata":[112],"https://github.com/hms-dbmi/uchimata-py)":[114],"Zenodo":[116],"(https://doi.org/10.5281/zenodo.17831959":[117],"https://doi.org/10.5281/zenodo.17832045).":[119],"documentation":[121],"examples":[123],"at":[126],"https://hms-dbmi.github.io/uchimata/.":[127]},"counts_by_year":[],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
