{"id":"https://openalex.org/W4399595336","doi":"https://doi.org/10.1093/bib/bbag214","title":"Cross-modality representation and multi-sample integration of spatially resolved omics data","display_name":"Cross-modality representation and multi-sample integration of spatially resolved omics data","publication_year":2026,"publication_date":"2026-04-25","ids":{"openalex":"https://openalex.org/W4399595336","doi":"https://doi.org/10.1093/bib/bbag214","pmid":"https://pubmed.ncbi.nlm.nih.gov/42114120"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag214","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":null,"license_id":null,"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/bbag214","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100332591","display_name":"Zhen Li","orcid":"https://orcid.org/0000-0002-3013-3416"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Li","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":"https://orcid.org/0000-0002-3013-3416","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031327612","display_name":"Xuejian Cui","orcid":"https://orcid.org/0009-0007-8145-212X"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuejian Cui","raw_affiliation_strings":["Faculty of Computing, Harbin Institute of Technology , Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing, Harbin Institute of Technology , Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001 ,","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100463021","display_name":"Xiaoyang Chen","orcid":"https://orcid.org/0000-0002-7356-8129"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyang Chen","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":"https://orcid.org/0000-0002-7356-8129","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080423090","display_name":"Zijing Gao","orcid":"https://orcid.org/0009-0005-7269-0244"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zijing Gao","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":"https://orcid.org/0009-0005-7269-0244","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073793409","display_name":"Yuyao Liu","orcid":"https://orcid.org/0009-0006-3695-3841"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuyao Liu","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087294951","display_name":"Yan Pan","orcid":"https://orcid.org/0000-0002-0466-3763"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Pan","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":"https://orcid.org/0009-0003-3422-4635","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","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 LPMC, Nankai University , Weijin Road, Nanjiao District, Tianjin 300071 ,","School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China"],"raw_orcid":"https://orcid.org/0000-0002-3503-9306","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University , Weijin Road, Nanjiao District, Tianjin 300071 ,","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hairong Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hairong Lv","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 00084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lei Zhai","orcid":null},"institutions":[{"id":"https://openalex.org/I2802459333","display_name":"China Rehabilitation Research Center","ror":"https://ror.org/02bpqmq41","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802459333"]},{"id":"https://openalex.org/I4210161138","display_name":"Beijing Fengtai Hospital","ror":"https://ror.org/0579e9266","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161138"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Zhai","raw_affiliation_strings":["Department of Critical Rehabilitation, Beijing Bo\u2019ai Hospital, China Rehabilitation Research Center , Jiangmen North Road, Fengtai District, Beijing 100068 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Critical Rehabilitation, Beijing Bo\u2019ai Hospital, China Rehabilitation Research Center , Jiangmen North Road, Fengtai District, Beijing 100068 ,","institution_ids":["https://openalex.org/I2802459333","https://openalex.org/I4210161138"]}]},{"author_position":"last","author":{"id":null,"display_name":"Rui Jiang","orcid":"https://orcid.org/0000-0002-7533-3753"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Jiang","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,"],"raw_orcid":"https://orcid.org/0000-0002-7533-3753","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Shuangqing Road, Haidian District, Beijing 100084 ,","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":12.8361,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.98332084,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9957000017166138,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9957000017166138,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9929999709129333,"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":0.9907000064849854,"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/representation","display_name":"Representation (politics)","score":0.6139336824417114},{"id":"https://openalex.org/keywords/modality","display_name":"Modality (human\u2013computer interaction)","score":0.6117086410522461},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.5999153256416321},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.5138723850250244},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4796352982521057},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37979546189308167},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3642871379852295},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3293757140636444},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2604016065597534},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20693865418434143},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20349538326263428},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.17082181572914124},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.1293524205684662}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6139336824417114},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.6117086410522461},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.5999153256416321},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5138723850250244},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4796352982521057},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37979546189308167},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3642871379852295},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3293757140636444},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2604016065597534},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20693865418434143},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20349538326263428},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.17082181572914124},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.1293524205684662},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":false},{"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":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":false},{"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":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":true},{"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":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/bib/bbag214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag214","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2024.06.10.598155","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.06.10.598155","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42114120","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42114120","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13160428","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13160428/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag214","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag214","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1135421935","display_name":null,"funder_award_id":"2025YFC3409300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G1800556644","display_name":null,"funder_award_id":"2023YFF1204802","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4089425664","display_name":null,"funder_award_id":"32550616, 62273194","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7517475385","display_name":null,"funder_award_id":"L242026","funder_id":"https://openalex.org/F4320334977","funder_display_name":"Beijing Municipal Natural Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320334977","display_name":"Beijing Municipal Natural Science Foundation","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":105,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1773194113","https://openalex.org/W1971063595","https://openalex.org/W1974565082","https://openalex.org/W1988344484","https://openalex.org/W2035618305","https://openalex.org/W2070454091","https://openalex.org/W2089689396","https://openalex.org/W2125596540","https://openalex.org/W2147142971","https://openalex.org/W2154598603","https://openalex.org/W2165247488","https://openalex.org/W2328543163","https://openalex.org/W2344649716","https://openalex.org/W2566234254","https://openalex.org/W2739492614","https://openalex.org/W2752426001","https://openalex.org/W2765284830","https://openalex.org/W2786672974","https://openalex.org/W2789419608","https://openalex.org/W2792647356","https://openalex.org/W2794521141","https://openalex.org/W2887910040","https://openalex.org/W2889326414","https://openalex.org/W2897249806","https://openalex.org/W2918621261","https://openalex.org/W2932322081","https://openalex.org/W2934716754","https://openalex.org/W2942880491","https://openalex.org/W2945827377","https://openalex.org/W2951381561","https://openalex.org/W2953176424","https://openalex.org/W2963083182","https://openalex.org/W2979464975","https://openalex.org/W2984472267","https://openalex.org/W2989830005","https://openalex.org/W3005680577","https://openalex.org/W3007172120","https://openalex.org/W3009609875","https://openalex.org/W3023456235","https://openalex.org/W3044618203","https://openalex.org/W3087547719","https://openalex.org/W3099810371","https://openalex.org/W3101553402","https://openalex.org/W3106188259","https://openalex.org/W3108118546","https://openalex.org/W3111725549","https://openalex.org/W3119836781","https://openalex.org/W3129866267","https://openalex.org/W3129982058","https://openalex.org/W3159800610","https://openalex.org/W3164692211","https://openalex.org/W3198658154","https://openalex.org/W3201125152","https://openalex.org/W3210860076","https://openalex.org/W4206092375","https://openalex.org/W4211255280","https://openalex.org/W4220765701","https://openalex.org/W4220802920","https://openalex.org/W4225278475","https://openalex.org/W4225598893","https://openalex.org/W4225731526","https://openalex.org/W4225919781","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4229083873","https://openalex.org/W4280494993","https://openalex.org/W4288758477","https://openalex.org/W4290672942","https://openalex.org/W4292121951","https://openalex.org/W4293569951","https://openalex.org/W4294042823","https://openalex.org/W4294753094","https://openalex.org/W4297733535","https://openalex.org/W4306391398","https://openalex.org/W4309667063","https://openalex.org/W4309918428","https://openalex.org/W4311232381","https://openalex.org/W4312128822","https://openalex.org/W4313454424","https://openalex.org/W4313561175","https://openalex.org/W4317757307","https://openalex.org/W4320491791","https://openalex.org/W4321112079","https://openalex.org/W4321611267","https://openalex.org/W4322738920","https://openalex.org/W4322768301","https://openalex.org/W4324344255","https://openalex.org/W4362521490","https://openalex.org/W4367395068","https://openalex.org/W4376602187","https://openalex.org/W4378212119","https://openalex.org/W4379521442","https://openalex.org/W4387580076","https://openalex.org/W4387639594","https://openalex.org/W4387772836","https://openalex.org/W4387808846","https://openalex.org/W4388017732","https://openalex.org/W4388615936","https://openalex.org/W4390669311","https://openalex.org/W4390795542","https://openalex.org/W4393515961","https://openalex.org/W4398240043","https://openalex.org/W6684488266","https://openalex.org/W6745537798"],"related_works":["https://openalex.org/W2385859805","https://openalex.org/W2530972254","https://openalex.org/W2374013449","https://openalex.org/W73545470","https://openalex.org/W2364381299","https://openalex.org/W2374430585","https://openalex.org/W3144423903","https://openalex.org/W2377397762","https://openalex.org/W2793967660","https://openalex.org/W2361654993"],"abstract_inverted_index":{"Spatially":[0],"resolved":[1],"sequencing":[2],"technologies":[3],"have":[4],"revolutionized":[5],"our":[6],"understanding":[7],"of":[8,20,30,46,72,81,123,129,187],"biological":[9,167],"regulatory":[10,131],"processes":[11],"within":[12],"tissue":[13,172,189],"microenvironments":[14],"by":[15],"simultaneously":[16],"capturing":[17],"the":[18,27,43,51,120,127,185],"states":[19],"genomic":[21],"regions,":[22],"genes,":[23],"and":[24,37,85,97,116,126,156,178],"proteins":[25],"alongside":[26],"spatial":[28,47,73,108,124],"organization":[29],"cells.":[31],"However,":[32],"inherent":[33],"heterogeneity":[34],"across":[35,113,174],"modalities":[36],"samples":[38,173],"poses":[39],"substantial":[40],"challenges":[41],"for":[42,54,69,102],"integrative":[44,67],"analysis":[45],"omics":[48],"data,":[49],"underscoring":[50],"urgent":[52],"need":[53],"advanced":[55],"computational":[56],"methods.":[57],"In":[58],"this":[59],"study,":[60],"we":[61],"propose":[62],"PRESENT,":[63],"a":[64,142,192],"contrastive":[65],"learning-based":[66],"framework":[68],"cross-modality":[70],"representation":[71],"multi-omics":[74,103,111],"data.":[75],"PRESENT":[76,118,134,183],"employs":[77],"omics-specific":[78],"encoders":[79],"consisting":[80],"graph":[82,158],"attention":[83],"networks":[84,88],"Bayesian":[86],"neural":[87],"coupled":[89],"with":[90,110],"distribution-aware":[91],"decoders":[92],"to":[93,138,161],"model":[94],"distinct":[95],"modalities,":[96],"an":[98],"inter-omics":[99],"alignment":[100,149],"module":[101],"integration.":[104],"By":[105],"effectively":[106],"incorporating":[107],"dependencies":[109],"information":[112],"diverse":[114],"species":[115],"technologies,":[117],"facilitates":[119],"accurate":[121],"identification":[122],"domains":[125],"elucidation":[128],"underlying":[130],"mechanisms.":[132],"Furthermore,":[133],"can":[135],"be":[136],"extended":[137],"multi-sample":[139],"integration":[140],"via":[141],"two-stage":[143],"training":[144],"workflow,":[145],"which":[146],"incorporates":[147],"inter-batch":[148],"loss,":[150,153],"intra-batch":[151],"preserving":[152],"batch-adversarial":[154],"learning,":[155],"cyclic":[157],"refinement":[159],"strategies":[160],"eliminate":[162],"batch":[163],"effects":[164],"while":[165],"retaining":[166],"signals.":[168],"Extensive":[169],"experiments":[170],"on":[171],"different":[175],"anatomical":[176],"regions":[177],"developmental":[179],"stages":[180],"demonstrate":[181],"that":[182],"enables":[184],"characterization":[186],"hierarchical":[188],"structures":[190],"from":[191],"spatiotemporal":[193],"perspective.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
