{"id":"https://openalex.org/W4408537402","doi":"https://doi.org/10.1093/bib/bbaf109","title":"Graph neural networks for single-cell omics data: a review of approaches and applications","display_name":"Graph neural networks for single-cell omics data: a review of approaches and applications","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408537402","doi":"https://doi.org/10.1093/bib/bbaf109","pmid":"https://pubmed.ncbi.nlm.nih.gov/40091193"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf109","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/bbaf109","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Sijie Li","orcid":"https://orcid.org/0009-0005-0521-0722"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sijie Li","raw_affiliation_strings":["School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,"],"raw_orcid":"https://orcid.org/0009-0005-0521-0722","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030551068","display_name":"Heyang Hua","orcid":"https://orcid.org/0009-0006-7754-7006"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Heyang Hua","raw_affiliation_strings":["School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,"],"raw_orcid":"https://orcid.org/0009-0006-7754-7006","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046058016","display_name":"Shengquan Chen","orcid":"https://orcid.org/0000-0002-3503-9306"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengquan Chen","raw_affiliation_strings":["School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,"],"raw_orcid":"https://orcid.org/0000-0002-3503-9306","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and The Key Laboratory of Pure Mathematics and Combinatorics, Ministry of Education (LPMC), Nankai University , No. 94 Weijin Road, Nankai District, Tianjin 300071 ,","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":14.1978,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.99377845,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9940999746322632,"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":0.993399977684021,"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":0.7062707543373108},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.568517804145813},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4498422145843506},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44672712683677673},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4246135354042053},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.4101925194263458},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40397435426712036},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39340439438819885},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35363876819610596},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.346744567155838},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.29644080996513367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18602418899536133},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.12721732258796692}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7062707543373108},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.568517804145813},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4498422145843506},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44672712683677673},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4246135354042053},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4101925194263458},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40397435426712036},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39340439438819885},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35363876819610596},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.346744567155838},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.29644080996513367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18602418899536133},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.12721732258796692}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf109","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40091193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40091193","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:10726890","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11911123","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"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf109","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G5364641554","display_name":null,"funder_award_id":"62203236","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6589146447","display_name":null,"funder_award_id":"62473212","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7755912295","display_name":null,"funder_award_id":"2023QNRC001","funder_id":"https://openalex.org/F4320311778","funder_display_name":"China Association for Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320311778","display_name":"China Association for Science and Technology","ror":"https://ror.org/035vmht26"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":196,"referenced_works":["https://openalex.org/W1501856433","https://openalex.org/W1531821806","https://openalex.org/W1946550961","https://openalex.org/W1965863160","https://openalex.org/W1968263601","https://openalex.org/W1979273476","https://openalex.org/W1984708728","https://openalex.org/W2042789810","https://openalex.org/W2068767807","https://openalex.org/W2116341502","https://openalex.org/W2117757143","https://openalex.org/W2154431984","https://openalex.org/W2158787690","https://openalex.org/W2205615102","https://openalex.org/W2222000795","https://openalex.org/W2305364952","https://openalex.org/W2330978860","https://openalex.org/W2514448720","https://openalex.org/W2558748708","https://openalex.org/W2586644020","https://openalex.org/W2609731728","https://openalex.org/W2612758576","https://openalex.org/W2616922646","https://openalex.org/W2739492614","https://openalex.org/W2763574125","https://openalex.org/W2793370606","https://openalex.org/W2793965282","https://openalex.org/W2809368942","https://openalex.org/W2889236955","https://openalex.org/W2904174831","https://openalex.org/W2907492528","https://openalex.org/W2960029024","https://openalex.org/W2962756421","https://openalex.org/W2963367647","https://openalex.org/W2965985232","https://openalex.org/W2972334216","https://openalex.org/W2990138404","https://openalex.org/W3010683590","https://openalex.org/W3015416694","https://openalex.org/W3036159223","https://openalex.org/W3065829709","https://openalex.org/W3087998689","https://openalex.org/W3093858607","https://openalex.org/W3099179344","https://openalex.org/W3108118546","https://openalex.org/W3113349968","https://openalex.org/W3124439729","https://openalex.org/W3133653953","https://openalex.org/W3134897856","https://openalex.org/W3138479716","https://openalex.org/W3140605903","https://openalex.org/W3149361930","https://openalex.org/W3152893301","https://openalex.org/W3164112499","https://openalex.org/W3176693948","https://openalex.org/W3180540559","https://openalex.org/W3184580818","https://openalex.org/W3188579603","https://openalex.org/W3196630240","https://openalex.org/W3198628780","https://openalex.org/W3201933794","https://openalex.org/W3202332579","https://openalex.org/W3202393418","https://openalex.org/W3206783061","https://openalex.org/W3207419498","https://openalex.org/W3209470205","https://openalex.org/W3212776961","https://openalex.org/W3214158901","https://openalex.org/W3214280461","https://openalex.org/W3216323060","https://openalex.org/W4200119252","https://openalex.org/W4205126801","https://openalex.org/W4205281625","https://openalex.org/W4206078729","https://openalex.org/W4206826076","https://openalex.org/W4211255280","https://openalex.org/W4213136259","https://openalex.org/W4223557148","https://openalex.org/W4225278475","https://openalex.org/W4225287808","https://openalex.org/W4226192560","https://openalex.org/W4226218349","https://openalex.org/W4226296494","https://openalex.org/W4233182706","https://openalex.org/W4281776605","https://openalex.org/W4285388882","https://openalex.org/W4285803722","https://openalex.org/W4288384137","https://openalex.org/W4290154117","https://openalex.org/W4290852275","https://openalex.org/W4290930137","https://openalex.org/W4294631386","https://openalex.org/W4294990955","https://openalex.org/W4295064314","https://openalex.org/W4297733535","https://openalex.org/W4303986417","https://openalex.org/W4306406844","https://openalex.org/W4306639438","https://openalex.org/W4307006195","https://openalex.org/W4307497973","https://openalex.org/W4309185675","https://openalex.org/W4310155347","https://openalex.org/W4310937776","https://openalex.org/W4311823874","https://openalex.org/W4311946529","https://openalex.org/W4312094047","https://openalex.org/W4312210661","https://openalex.org/W4317568173","https://openalex.org/W4317888741","https://openalex.org/W4320491791","https://openalex.org/W4320883632","https://openalex.org/W4321112079","https://openalex.org/W4321234725","https://openalex.org/W4321452549","https://openalex.org/W4321748573","https://openalex.org/W4322614756","https://openalex.org/W4322738920","https://openalex.org/W4322766901","https://openalex.org/W4322768301","https://openalex.org/W4322832102","https://openalex.org/W4327675690","https://openalex.org/W4362521490","https://openalex.org/W4365482998","https://openalex.org/W4366465280","https://openalex.org/W4367187108","https://openalex.org/W4367627969","https://openalex.org/W4377287490","https://openalex.org/W4378348563","https://openalex.org/W4378640029","https://openalex.org/W4378806473","https://openalex.org/W4378838672","https://openalex.org/W4379599075","https://openalex.org/W4380272541","https://openalex.org/W4380368554","https://openalex.org/W4382630883","https://openalex.org/W4384562920","https://openalex.org/W4385955324","https://openalex.org/W4386306185","https://openalex.org/W4386575275","https://openalex.org/W4386692444","https://openalex.org/W4386699707","https://openalex.org/W4387035512","https://openalex.org/W4387068120","https://openalex.org/W4387499879","https://openalex.org/W4387583204","https://openalex.org/W4387772836","https://openalex.org/W4387986997","https://openalex.org/W4388017732","https://openalex.org/W4388562978","https://openalex.org/W4388624241","https://openalex.org/W4388684677","https://openalex.org/W4388694213","https://openalex.org/W4388870182","https://openalex.org/W4388891955","https://openalex.org/W4388899046","https://openalex.org/W4389262336","https://openalex.org/W4389982793","https://openalex.org/W4390011121","https://openalex.org/W4390563863","https://openalex.org/W4390615005","https://openalex.org/W4390636271","https://openalex.org/W4390658802","https://openalex.org/W4390678091","https://openalex.org/W4390814844","https://openalex.org/W4390863028","https://openalex.org/W4391642654","https://openalex.org/W4392044395","https://openalex.org/W4392449793","https://openalex.org/W4392956052","https://openalex.org/W4394011009","https://openalex.org/W4394014840","https://openalex.org/W4394564180","https://openalex.org/W4394674840","https://openalex.org/W4394691516","https://openalex.org/W4394763083","https://openalex.org/W4394881579","https://openalex.org/W4396812985","https://openalex.org/W4398236441","https://openalex.org/W4401057296","https://openalex.org/W4401332722","https://openalex.org/W4401459241","https://openalex.org/W4402654534","https://openalex.org/W4402986054","https://openalex.org/W4403007541","https://openalex.org/W4404122384","https://openalex.org/W4404874047","https://openalex.org/W6730084236","https://openalex.org/W6745537798","https://openalex.org/W6807327410","https://openalex.org/W6845966621","https://openalex.org/W6851837700","https://openalex.org/W6853808549","https://openalex.org/W6857344860","https://openalex.org/W6858377393","https://openalex.org/W6859826115","https://openalex.org/W6860709874"],"related_works":["https://openalex.org/W4296209631","https://openalex.org/W2561617217","https://openalex.org/W2025378473","https://openalex.org/W177137871","https://openalex.org/W4292302930","https://openalex.org/W2355801475","https://openalex.org/W4386960635","https://openalex.org/W4206659427","https://openalex.org/W2170062176","https://openalex.org/W2148135840"],"abstract_inverted_index":{"Rapid":[0],"advancement":[1],"of":[2,10,30,45,114,129,147,158,206,232],"sequencing":[3],"technologies":[4],"now":[5],"allows":[6],"for":[7,212,226],"the":[8,21,56,144,183,191,203,230],"utilization":[9],"precise":[11],"signals":[12],"at":[13],"single-cell":[14,31,52,94,117,137,163,186,235],"resolution":[15],"in":[16,93,116,135,162,190,194,234],"various":[17,136],"omics":[18,138,178],"studies.":[19,214],"However,":[20],"massive":[22],"volume,":[23],"ultra-high":[24],"dimensionality,":[25],"and":[26,47,90,131,149,169,209],"high":[27],"sparsity":[28],"nature":[29],"data":[32,118],"have":[33,81,106,181],"introduced":[34],"substantial":[35],"difficulties":[36],"to":[37,68,85,96,175,228],"traditional":[38],"computational":[39],"methods.":[40],"The":[41],"intricate":[42],"non-Euclidean":[43,86],"networks":[44,79],"intracellular":[46],"intercellular":[48],"signaling":[49],"molecules":[50],"within":[51,101],"datasets,":[53],"coupled":[54],"with":[55],"complex,":[57],"multimodal":[58],"structures":[59],"arising":[60],"from":[61],"multi-omics":[62],"joint":[63],"analysis,":[64],"pose":[65],"significant":[66],"challenges":[67],"conventional":[69],"deep":[70,83],"learning":[71,84],"operations":[72],"reliant":[73],"on":[74],"Euclidean":[75],"geometries.":[76],"Graph":[77],"neural":[78],"(GNNs)":[80],"extended":[82],"data,":[87],"allowing":[88],"cells":[89],"their":[91,132,150],"features":[92],"datasets":[95,187],"be":[97],"modeled":[98],"as":[99,222],"nodes":[100],"a":[102,111,155,176,223],"graph":[103],"structure.":[104],"GNNs":[105,130,148,233],"been":[107],"successfully":[108],"applied":[109,161],"across":[110],"broad":[112],"range":[113],"tasks":[115],"analysis.":[119],"In":[120,171],"this":[121,218],"survey,":[122],"we":[123,180,201],"systematically":[124],"review":[125,157,219],"107":[126],"successful":[127],"applications":[128],"six":[133,151],"variants":[134],"tasks.":[139],"We":[140,215],"begin":[141],"by":[142,154],"outlining":[143],"fundamental":[145],"principles":[146],"variants,":[152],"followed":[153],"systematic":[156],"GNN-based":[159],"models":[160],"epigenomics,":[164],"transcriptomics,":[165,167],"spatial":[166],"proteomics,":[168],"multi-omics.":[170],"each":[172],"section":[173],"dedicated":[174],"specific":[177],"type,":[179],"summarized":[182],"publicly":[184],"available":[185],"commonly":[188],"utilized":[189],"articles":[192],"reviewed":[193],"that":[195,217],"section,":[196],"totaling":[197],"77":[198],"datasets.":[199],"Finally,":[200],"summarize":[202],"potential":[204],"shortcomings":[205],"current":[207],"research":[208],"explore":[210],"directions":[211],"future":[213],"anticipate":[216],"will":[220],"serve":[221],"guiding":[224],"resource":[225],"researchers":[227],"deepen":[229],"application":[231],"omics.":[236]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}
