{"id":"https://openalex.org/W4411472180","doi":"https://doi.org/10.1109/mcg.2025.3581560","title":"AuraGenome: An LLM-Powered Framework for On-the-Fly Reusable and Scalable Circular Genome Visualizations","display_name":"AuraGenome: An LLM-Powered Framework for On-the-Fly Reusable and Scalable Circular Genome Visualizations","publication_year":2025,"publication_date":"2025-06-20","ids":{"openalex":"https://openalex.org/W4411472180","doi":"https://doi.org/10.1109/mcg.2025.3581560","pmid":"https://pubmed.ncbi.nlm.nih.gov/40540387"},"language":"en","primary_location":{"id":"doi:10.1109/mcg.2025.3581560","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcg.2025.3581560","pdf_url":null,"source":{"id":"https://openalex.org/S105380075","display_name":"IEEE Computer Graphics and Applications","issn_l":"0272-1716","issn":["0272-1716","1558-1756"],"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 Computer Graphics and Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Chi Zhang","orcid":"https://orcid.org/0009-0002-9926-3590"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chi Zhang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102817883","display_name":"Yu Dong","orcid":"https://orcid.org/0000-0002-2353-6567"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Dong","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114778054","display_name":"Yang Wang","orcid":"https://orcid.org/0009-0009-8628-5863"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Wang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuetong Han","orcid":"https://orcid.org/0009-0002-1254-4390"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuetong Han","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039874476","display_name":"Guihua Shan","orcid":"https://orcid.org/0000-0002-8283-2278"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guihua Shan","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037875779","display_name":"Bixia Tang","orcid":"https://orcid.org/0000-0002-9357-4411"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bixia Tang","raw_affiliation_strings":["National Genomics Data Center, China National Center for Bioinformation, Beijing, China"],"affiliations":[{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation, Beijing, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210108629"],"apc_list":null,"apc_paid":null,"fwci":1.5162,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82630486,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"45","issue":"5","first_page":"78","last_page":"92"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9629999995231628,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9629999995231628,"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/computer-science","display_name":"Computer science","score":0.8310617804527283},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7821352481842041},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.660962700843811},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6330636143684387},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6072627305984497},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.539142906665802},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4964445233345032},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.43350058794021606},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.32522517442703247},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.23253300786018372},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20312124490737915},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20030748844146729}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8310617804527283},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7821352481842041},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.660962700843811},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6330636143684387},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6072627305984497},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.539142906665802},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4964445233345032},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.43350058794021606},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.32522517442703247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.23253300786018372},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20312124490737915},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20030748844146729},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"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":"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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"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":2,"locations":[{"id":"doi:10.1109/mcg.2025.3581560","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcg.2025.3581560","pdf_url":null,"source":{"id":"https://openalex.org/S105380075","display_name":"IEEE Computer Graphics and Applications","issn_l":"0272-1716","issn":["0272-1716","1558-1756"],"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 Computer Graphics and Applications","raw_type":"journal-article"},{"id":"pmid:40540387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40540387","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 computer graphics and applications","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G621680304","display_name":null,"funder_award_id":"4254090","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"}],"funders":[{"id":"https://openalex.org/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W2091030812","https://openalex.org/W2150677022","https://openalex.org/W2153369847","https://openalex.org/W2157748357","https://openalex.org/W2158804744","https://openalex.org/W2268687088","https://openalex.org/W3044744861","https://openalex.org/W3125161619","https://openalex.org/W3135628515","https://openalex.org/W3203255635","https://openalex.org/W3203717592","https://openalex.org/W4214807811","https://openalex.org/W4379116803","https://openalex.org/W4382498938","https://openalex.org/W4385565383","https://openalex.org/W4389988607","https://openalex.org/W4392026410","https://openalex.org/W4399491739","https://openalex.org/W4402402204","https://openalex.org/W4410705969"],"related_works":["https://openalex.org/W4367333290","https://openalex.org/W2158984754","https://openalex.org/W3149127250","https://openalex.org/W2564956852","https://openalex.org/W4246764483","https://openalex.org/W4378086562","https://openalex.org/W3208630418","https://openalex.org/W2126824079","https://openalex.org/W2143428259","https://openalex.org/W4409660181"],"abstract_inverted_index":{"Circular":[0],"genome":[1,53,115],"visualizations":[2],"are":[3],"essential":[4],"for":[5,44,102],"exploring":[6],"structural":[7],"variants":[8],"and":[9,19,27,47,84,108,122,130,142],"gene":[10],"regulation.":[11],"However,":[12],"existing":[13],"tools":[14],"often":[15],"require":[16],"complex":[17],"scripting":[18],"manual":[20],"configuration,":[21],"making":[22],"the":[23,125],"process":[24],"time-consuming,":[25],"error-prone,":[26],"difficult":[28],"to":[29,87,111,119],"learn.":[30],"To":[31],"address":[32],"these":[33],"challenges,":[34],"we":[35],"introduce":[36],"AuraGenome,":[37],"a":[38,57,143],"large":[39],"language":[40],"model":[41],"(LLM)-powered":[42],"framework":[43],"rapid,":[45],"reusable,":[46],"scalable":[48],"generation":[49],"of":[50],"multilayered":[51,113],"circular":[52,114],"visualizations.":[54,94,116],"AuraGenome":[55,147],"combines":[56],"semantic-driven":[58],"multiagent":[59],"workflow":[60,68],"with":[61],"an":[62],"interactive":[63],"visual":[64],"analytics":[65],"system.":[66],"The":[67,95],"employs":[69],"seven":[70],"specialized":[71],"LLM-driven":[72],"agents,":[73],"each":[74],"assigned":[75],"distinct":[76],"roles,":[77],"such":[78],"as":[79],"intent":[80],"recognition,":[81],"layout":[82],"planning,":[83],"code":[85],"generation,":[86],"transform":[88],"raw":[89],"genomic":[90,103],"data":[91],"into":[92],"tailored":[93,101],"system":[96,126],"supports":[97,127],"multiple":[98],"coordinated":[99],"views":[100],"data,":[104],"offering":[105],"ring,":[106],"radial,":[107],"chord-based":[109],"layouts":[110],"represent":[112],"In":[117],"addition":[118],"enabling":[120],"interactions":[121],"configuration":[123],"reuse,":[124],"real-time":[128],"refinement":[129],"high-quality":[131],"report":[132],"export.":[133],"We":[134],"validate":[135],"its":[136],"effectiveness":[137],"through":[138],"two":[139],"case":[140],"studies":[141],"comprehensive":[144],"user":[145],"study.":[146],"is":[148],"available":[149],"at":[150],"https://github.com/Darius18/AuraGenome.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
