{"id":"https://openalex.org/W4417338041","doi":"https://doi.org/10.1109/tvcg.2025.3634654","title":"Design Space and Declarative Grammar for 3D Genomic Data Visualization","display_name":"Design Space and Declarative Grammar for 3D Genomic Data Visualization","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W4417338041","doi":"https://doi.org/10.1109/tvcg.2025.3634654","pmid":"https://pubmed.ncbi.nlm.nih.gov/41396765"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2025.3634654","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634654","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13006923/pdf/nihms-2146288.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120807611","display_name":"David Kou\u02c7ril","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":"David Kou\u0159il","raw_affiliation_strings":["Harvard Medical School, USA"],"affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","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":["Harvard Medical School, USA"],"affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060888358","display_name":"Sehi L\u2019Yi","orcid":"https://orcid.org/0000-0001-7720-2848"},"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":"Sehi L'Yi","raw_affiliation_strings":["Harvard Medical School, USA"],"affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066335313","display_name":"Nils Gehlenborg","orcid":"https://orcid.org/0000-0003-0327-8297"},"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":"Nils Gehlenborg","raw_affiliation_strings":["Harvard Medical School, USA"],"affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5120807611"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":null,"apc_paid":null,"fwci":0.7625,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.78457858,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"32","issue":"1","first_page":"890","last_page":"900"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.6478000283241272,"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":0.6478000283241272,"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/T10799","display_name":"Data Visualization and Analytics","score":0.18019999563694,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.05990000069141388,"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/visualization","display_name":"Visualization","score":0.7861999869346619},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.6003999710083008},{"id":"https://openalex.org/keywords/information-visualization","display_name":"Information visualization","score":0.5551999807357788},{"id":"https://openalex.org/keywords/grammar","display_name":"Grammar","score":0.4867999851703644},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.4392000138759613},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.40869998931884766},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3991999924182892},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.37139999866485596},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.3659000098705292}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8105999827384949},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7861999869346619},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.6003999710083008},{"id":"https://openalex.org/C185578843","wikidata":"https://www.wikidata.org/wiki/Q10609775","display_name":"Information visualization","level":3,"score":0.5551999807357788},{"id":"https://openalex.org/C26022165","wikidata":"https://www.wikidata.org/wiki/Q8091","display_name":"Grammar","level":2,"score":0.4867999851703644},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.4392000138759613},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.40869998931884766},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3991999924182892},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.397599995136261},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.37139999866485596},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.3659000098705292},{"id":"https://openalex.org/C99740376","wikidata":"https://www.wikidata.org/wiki/Q17092520","display_name":"Interactive visual analysis","level":4,"score":0.3582000136375427},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3564000129699707},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3481999933719635},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.3391999900341034},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.31630000472068787},{"id":"https://openalex.org/C2780878386","wikidata":"https://www.wikidata.org/wiki/Q1659648","display_name":"Visual language","level":2,"score":0.3012999892234802},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3012000024318695},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.29260000586509705},{"id":"https://openalex.org/C59740354","wikidata":"https://www.wikidata.org/wiki/Q2737866","display_name":"Scientific visualization","level":3,"score":0.2865000069141388},{"id":"https://openalex.org/C78780964","wikidata":"https://www.wikidata.org/wiki/Q7233193","display_name":"Position paper","level":2,"score":0.26739999651908875},{"id":"https://openalex.org/C207363949","wikidata":"https://www.wikidata.org/wiki/Q462915","display_name":"Visual space","level":3,"score":0.2667999863624573},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2621000111103058},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.25839999318122864},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25270000100135803},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.2500999867916107}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":3,"locations":[{"id":"doi:10.1109/tvcg.2025.3634654","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634654","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:41396765","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41396765","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":"IEEE transactions on visualization and computer graphics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13006923","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13006923/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13006923/pdf/nihms-2146288.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Vis Comput Graph","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13006923","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13006923/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13006923/pdf/nihms-2146288.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Vis Comput Graph","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"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/G8385475556","display_name":null,"funder_award_id":"K99HG013348","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"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417338041.pdf","grobid_xml":"https://content.openalex.org/works/W4417338041.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W1481598211","https://openalex.org/W1701083935","https://openalex.org/W1896226795","https://openalex.org/W1970569592","https://openalex.org/W2011301426","https://openalex.org/W2020541351","https://openalex.org/W2050892199","https://openalex.org/W2073026107","https://openalex.org/W2090037139","https://openalex.org/W2098549100","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2145619687","https://openalex.org/W2201171270","https://openalex.org/W2402173511","https://openalex.org/W2472803348","https://openalex.org/W2516678343","https://openalex.org/W2531349095","https://openalex.org/W2549327495","https://openalex.org/W2564812046","https://openalex.org/W2569095710","https://openalex.org/W2580178967","https://openalex.org/W2597274540","https://openalex.org/W2738924259","https://openalex.org/W2772099288","https://openalex.org/W2774297138","https://openalex.org/W2782774915","https://openalex.org/W2799296221","https://openalex.org/W2888068719","https://openalex.org/W2888425844","https://openalex.org/W2888508568","https://openalex.org/W2888619565","https://openalex.org/W2889474202","https://openalex.org/W2891656888","https://openalex.org/W2900048067","https://openalex.org/W2903675476","https://openalex.org/W2913787191","https://openalex.org/W2944634251","https://openalex.org/W2969277937","https://openalex.org/W3000695681","https://openalex.org/W3047380455","https://openalex.org/W3080497669","https://openalex.org/W3133847258","https://openalex.org/W3164981937","https://openalex.org/W3203255635","https://openalex.org/W3212860783","https://openalex.org/W4200537317","https://openalex.org/W4237462920","https://openalex.org/W4286203308","https://openalex.org/W4286499647","https://openalex.org/W4296713628","https://openalex.org/W4297460104","https://openalex.org/W4317435353","https://openalex.org/W4317780717","https://openalex.org/W4366548422","https://openalex.org/W4379600412","https://openalex.org/W4383377610","https://openalex.org/W4388126361","https://openalex.org/W4388722442","https://openalex.org/W4389988693","https://openalex.org/W4394813096","https://openalex.org/W4394994940","https://openalex.org/W4401334619","https://openalex.org/W4402037672","https://openalex.org/W4402479884","https://openalex.org/W4402570602","https://openalex.org/W4407010921","https://openalex.org/W4407855361"],"related_works":[],"abstract_inverted_index":{"Various":[0],"computational":[1,76],"approaches":[2],"predict":[3],"chromatin":[4],"structure,":[5],"yielding":[6],"concrete":[7],"models":[8,70],"that":[9,85,160],"position":[10,124],"genomic":[11,57,88,151],"loci":[12],"in":[13,75],"physical":[14],"space":[15,37,104],"and":[16,21,30,73,90,113,121,134,196],"help":[17],"reveal":[18],"genome":[19,43,69,108,167],"organization":[20],"function.":[22],"While":[23],"prior":[24],"visualization":[25,55,131,144],"research":[26],"has":[27],"explored":[28],"data":[29,58,89],"task":[31],"abstractions":[32],"for":[33,38,94,105,146],"genomics,":[34,147],"the":[35,54,92],"design":[36,103],"depicting":[39],"these":[40,125],"three-dimensional":[41],"(3D)":[42],"models-and":[44],"associated":[45],"genome-mapped":[46,163],"data-remains":[47],"unclear.":[48],"In":[49],"this":[50,98],"paper,":[51],"we":[52,64,100,139,177],"investigate":[53],"of":[56,158],"with":[59,83,165],"a":[60,102,142],"spatial":[61,171],"component.":[62],"First,":[63],"systematically":[65],"survey":[66],"how":[67],"3D":[68,87,107,150,166],"are":[71,200],"used":[72],"depicted":[74],"biology.":[77],"We":[78,123],"analyze":[79],"over":[80],"300":[81],"papers":[82],"figures":[84],"visualize":[86],"categorize":[91],"methods":[93],"visual":[95,119,192],"representation.":[96],"From":[97],"survey,":[99],"derive":[101],"visualizing":[106],"data,":[109],"identifying":[110],"common":[111],"patterns":[112],"key":[114],"properties":[115],"such":[116],"as":[117],"representation,":[118],"channels,":[120],"composition.":[122],"findings":[126],"within":[127],"an":[128,197],"existing":[129,136],"genomics":[130],"taxonomy,":[132],"refining":[133],"extending":[135],"classifications.":[137],"Second,":[138],"augment":[140],"Gosling,":[141],"declarative":[143],"grammar":[145,181],"to":[148,182,189],"support":[149],"data.":[152],"Our":[153],"integration":[154],"enables":[155],"expressive":[156],"authoring":[157],"visualizations":[159],"connect":[161],"traditional":[162],"information":[164],"models,":[168],"emphasizing":[169],"their":[170],"characteristics.":[172],"To":[173],"demonstrate":[174],"its":[175,187],"utility,":[176],"employ":[178],"our":[179],"extended":[180],"recreate":[183],"interactive":[184,198],"examples,":[185],"showcasing":[186],"ability":[188],"represent":[190],"complex":[191],"designs.":[193],"Comprehensive":[194],"examples":[195],"editor":[199],"available":[201],"at":[202],"3d.gosling-lang.org.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-12-10T00:00:00"}
