{"id":"https://openalex.org/W7148922654","doi":"https://doi.org/10.1038/s43588-026-00977-z","title":"Benchmarking alignment methods for spatial transcriptomics data","display_name":"Benchmarking alignment methods for spatial transcriptomics data","publication_year":2026,"publication_date":"2026-04-03","ids":{"openalex":"https://openalex.org/W7148922654","doi":"https://doi.org/10.1038/s43588-026-00977-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/41933187"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-026-00977-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-026-00977-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","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":"Yunzhi Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunzhi Yan","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tianyi Gu","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianyi Gu","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chengcheng Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengcheng Sun","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yinghao Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinghao Zhang","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yan Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Cui","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Senlin Lin","orcid":"https://orcid.org/0009-0001-6593-4088"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Senlin Lin","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0001-6593-4088","affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qi Zou","orcid":"https://orcid.org/0000-0002-8662-5874"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Zou","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University, Jinan, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0002-8662-5874","affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I34949971"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yixuan Du","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixuan Du","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chuangyi Han","orcid":"https://orcid.org/0009-0005-8075-261X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuangyi Han","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0005-8075-261X","affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kairan Kang","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kairan Kang","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sijie Li","orcid":"https://orcid.org/0009-0005-0521-0722"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sijie Li","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0005-0521-0722","affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yihan Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yihan Zhao","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhihong Lin","orcid":"https://orcid.org/0009-0001-8907-7797"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihong Lin","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0001-8907-7797","affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhiyuan Yuan","orcid":"https://orcid.org/0000-0002-9367-4236"},"institutions":[{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhiyuan Yuan","raw_affiliation_strings":["Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China. zhiyuan@fudan.edu.cn","Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China. zhiyuan@fudan.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-9367-4236","affiliations":[{"raw_affiliation_string":"Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China. zhiyuan@fudan.edu.cn","institution_ids":["https://openalex.org/I4210127380"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Center for Integrative Spatial-Omics Research, Fudan University, Shanghai, China. zhiyuan@fudan.edu.cn","institution_ids":["https://openalex.org/I4210164150"]}]},{"author_position":"last","author":{"id":null,"display_name":"Bin-Zhi Qian","orcid":"https://orcid.org/0000-0002-5796-1078"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin-Zhi Qian","raw_affiliation_strings":["Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China. qianbinzhi@fudan.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-5796-1078","affiliations":[{"raw_affiliation_string":"Fudan University Shanghai Cancer Center, Shanghai Medical College, Center for Integrative Spatial-Omics Research, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai, China. qianbinzhi@fudan.edu.cn","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210093194","https://openalex.org/I4210127380","https://openalex.org/I4210164150"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":null,"fwci":4.0547,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.92921003,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"6","issue":"5","first_page":"524","last_page":"541"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9431999921798706,"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":0.9431999921798706,"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":0.008500000461935997,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.007300000172108412,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6053000092506409},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.2854999899864197},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.2581999897956848},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.25369998812675476},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.25220000743865967}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6211000084877014},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6053000092506409},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46889999508857727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42329999804496765},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.2854999899864197},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.25369998812675476},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.25220000743865967},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.250900000333786},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.24210000038146973}],"mesh":[{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"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":"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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-026-00977-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-026-00977-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:41933187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41933187","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":"Nature computational science","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2115167851","https://openalex.org/W2151631165","https://openalex.org/W2167105834","https://openalex.org/W2471536144","https://openalex.org/W2809368942","https://openalex.org/W2899224111","https://openalex.org/W2915848182","https://openalex.org/W2949535577","https://openalex.org/W3003257820","https://openalex.org/W3036371598","https://openalex.org/W3037329734","https://openalex.org/W3112563877","https://openalex.org/W3126958162","https://openalex.org/W3203364159","https://openalex.org/W4229021644","https://openalex.org/W4229033508","https://openalex.org/W4280494993","https://openalex.org/W4280551568","https://openalex.org/W4281716652","https://openalex.org/W4283704002","https://openalex.org/W4286005528","https://openalex.org/W4289745500","https://openalex.org/W4297243391","https://openalex.org/W4302362633","https://openalex.org/W4303986417","https://openalex.org/W4322738920","https://openalex.org/W4385515928","https://openalex.org/W4385955242","https://openalex.org/W4387095485","https://openalex.org/W4387580076","https://openalex.org/W4387772836","https://openalex.org/W4388530027","https://openalex.org/W4388899046","https://openalex.org/W4389347083","https://openalex.org/W4389481214","https://openalex.org/W4389670373","https://openalex.org/W4389670555","https://openalex.org/W4389670703","https://openalex.org/W4389938094","https://openalex.org/W4390814844","https://openalex.org/W4391688273","https://openalex.org/W4392168151","https://openalex.org/W4392868645","https://openalex.org/W4399970333","https://openalex.org/W4400783289","https://openalex.org/W4401450053","https://openalex.org/W4402634766","https://openalex.org/W4404212754","https://openalex.org/W4404236873","https://openalex.org/W4406867208","https://openalex.org/W4407360292","https://openalex.org/W4410866390","https://openalex.org/W4415692570","https://openalex.org/W6929596235","https://openalex.org/W7128616442"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2026-02-13T00:00:00"}
