{"id":"https://openalex.org/W4416222803","doi":"https://doi.org/10.1093/bioinformatics/btaf562","title":"Spider: a flexible and unified framework for simulating spatial transcriptomics data","display_name":"Spider: a flexible and unified framework for simulating spatial transcriptomics data","publication_year":2025,"publication_date":"2025-11-14","ids":{"openalex":"https://openalex.org/W4416222803","doi":"https://doi.org/10.1093/bioinformatics/btaf562","pmid":"https://pubmed.ncbi.nlm.nih.gov/41237053"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf562","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/btaf562","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100632856","display_name":"Jiyuan Yang","orcid":"https://orcid.org/0000-0001-7709-6088"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiyuan Yang","raw_affiliation_strings":["School of Mathematical Sciences, Shanghai Jiao Tong University , Shanghai, 200240,","School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Shanghai Jiao Tong University , Shanghai, 200240,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018437578","display_name":"Nana Wei","orcid":"https://orcid.org/0000-0002-8039-9626"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210147617","display_name":"Ministry of Education","ror":"https://ror.org/0429te836","country_code":"ET","type":"government","lineage":["https://openalex.org/I4210147617"]}],"countries":["CN","ET"],"is_corresponding":false,"raw_author_name":"Nana Wei","raw_affiliation_strings":["Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine , Shanghai, 200025,","Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute , Beijing, 100142,","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China","Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, 100142, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine , Shanghai, 200025,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute , Beijing, 100142,","institution_ids":["https://openalex.org/I4210147617"]},{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, 100142, China","institution_ids":["https://openalex.org/I4210147617"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104114124","display_name":"Yang Qu","orcid":"https://orcid.org/0009-0001-0963-6852"},"institutions":[{"id":"https://openalex.org/I4210112430","display_name":"Guangxi Zhuang Autonomous Region Health and Family Planning","ror":"https://ror.org/022z3g211","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210112430"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Qu","raw_affiliation_strings":["The Guangxi Key Laboratory of Intelligent Precision Medicine, Guangxi Zhuang Autonomous Region , Nanning, 530007,","The Guangxi Key Laboratory of Intelligent Precision Medicine, Guangxi Zhuang Autonomous Region, Nanning, 530007, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Guangxi Key Laboratory of Intelligent Precision Medicine, Guangxi Zhuang Autonomous Region , Nanning, 530007,","institution_ids":["https://openalex.org/I4210112430"]},{"raw_affiliation_string":"The Guangxi Key Laboratory of Intelligent Precision Medicine, Guangxi Zhuang Autonomous Region, Nanning, 530007, China","institution_ids":["https://openalex.org/I4210112430"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101941016","display_name":"Congcong Hu","orcid":"https://orcid.org/0000-0002-5438-7277"},"institutions":[{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Congcong Hu","raw_affiliation_strings":["School of Mathematical and Information Sciences, Shaoxing University , Shaoxing, Zhejiang 312000,","School of Mathematical and Information Sciences, Shaoxing University, Shaoxing, Zhejiang 312000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Information Sciences, Shaoxing University , Shaoxing, Zhejiang 312000,","institution_ids":["https://openalex.org/I192209268"]},{"raw_affiliation_string":"School of Mathematical and Information Sciences, Shaoxing University, Shaoxing, Zhejiang 312000, China","institution_ids":["https://openalex.org/I192209268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100446728","display_name":"Weiwei Zhang","orcid":"https://orcid.org/0000-0001-7836-8874"},"institutions":[{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwei Zhang","raw_affiliation_strings":["School of Mathematical and Information Sciences, Shaoxing University , Shaoxing, Zhejiang 312000,","School of Mathematical and Information Sciences, Shaoxing University, Shaoxing, Zhejiang 312000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Information Sciences, Shaoxing University , Shaoxing, Zhejiang 312000,","institution_ids":["https://openalex.org/I192209268"]},{"raw_affiliation_string":"School of Mathematical and Information Sciences, Shaoxing University, Shaoxing, Zhejiang 312000, China","institution_ids":["https://openalex.org/I192209268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091763718","display_name":"Lin Liu","orcid":"https://orcid.org/0000-0001-7982-6005"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210158445","display_name":"Institute of Natural Science","ror":"https://ror.org/004tze884","country_code":"KP","type":"education","lineage":["https://openalex.org/I4210158445"]}],"countries":["CN","KP"],"is_corresponding":false,"raw_author_name":"Lin Liu","raw_affiliation_strings":["Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University , Shanghai, 200240,","Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University , Shanghai, 200240,","institution_ids":["https://openalex.org/I4210158445"]},{"raw_affiliation_string":"Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001021363","display_name":"Hua\u2010Jun Wu","orcid":"https://orcid.org/0000-0003-3498-3095"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116328","display_name":"Precision for Medicine (United States)","ror":"https://ror.org/02eps3588","country_code":"US","type":"company","lineage":["https://openalex.org/I4210116328"]},{"id":"https://openalex.org/I4210147617","display_name":"Ministry of Education","ror":"https://ror.org/0429te836","country_code":"ET","type":"government","lineage":["https://openalex.org/I4210147617"]}],"countries":["CN","ET","US"],"is_corresponding":false,"raw_author_name":"Hua-Jun Wu","raw_affiliation_strings":["Center for Precision Medicine Multi-Omics Research, Institute of Advanced Clinical Medicine, Peking University , Beijing, 100191,","Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center , Beijing, 100191,","Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute , Beijing, 100142,","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China","Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Medicine Multi-Omics Research, Institute of Advanced Clinical Medicine, Peking University , Beijing, 100191,","institution_ids":["https://openalex.org/I4210116328"]},{"raw_affiliation_string":"Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center , Beijing, 100191,","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute , Beijing, 100142,","institution_ids":["https://openalex.org/I4210147617"]},{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":null,"display_name":"Xiaoqi Zheng","orcid":"https://orcid.org/0000-0002-5438-7277"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I79731167","display_name":"Hainan Medical University","ror":"https://ror.org/004eeze55","country_code":"CN","type":"education","lineage":["https://openalex.org/I79731167"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqi Zheng","raw_affiliation_strings":["Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine , Shanghai, 200025,","Hainan International Medical Center, Shanghai Jiao Tong University School of Medicine , Hainan, 571400,","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China"],"raw_orcid":"https://orcid.org/0000-0002-5438-7277","affiliations":[{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine , Shanghai, 200025,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Hainan International Medical Center, Shanghai Jiao Tong University School of Medicine , Hainan, 571400,","institution_ids":["https://openalex.org/I79731167"]},{"raw_affiliation_string":"Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9736,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.77851031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"42","issue":"1","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":0.9535999894142151,"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":0.9535999894142151,"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":0.010200000368058681,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.00930000003427267,"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/software","display_name":"Software","score":0.46950000524520874},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.32429999113082886},{"id":"https://openalex.org/keywords/noisy-data","display_name":"Noisy data","score":0.2922999858856201},{"id":"https://openalex.org/keywords/data-processing","display_name":"Data processing","score":0.2655999958515167},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.2549999952316284}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7675999999046326},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5810999870300293},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46950000524520874},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34389999508857727},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.32429999113082886},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.2922999858856201},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2549999952316284},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.25270000100135803},{"id":"https://openalex.org/C2983325608","wikidata":"https://www.wikidata.org/wiki/Q17084606","display_name":"Data association","level":3,"score":0.24819999933242798}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf562","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41237053","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41237053","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12790819","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12790819/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf562","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2536134956","display_name":null,"funder_award_id":"32270683","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2942662574","display_name":null,"funder_award_id":"12471274","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3484123739","display_name":null,"funder_award_id":"62372286","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G606079916","display_name":null,"funder_award_id":"12090024","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7205878350","display_name":null,"funder_award_id":"2021YFC1712805","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"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":100,"referenced_works":["https://openalex.org/W1531194977","https://openalex.org/W2002827932","https://openalex.org/W2024060531","https://openalex.org/W2042789810","https://openalex.org/W2112138633","https://openalex.org/W2146402105","https://openalex.org/W2342603028","https://openalex.org/W2401005551","https://openalex.org/W2471536144","https://openalex.org/W2515199119","https://openalex.org/W2554889266","https://openalex.org/W2617691667","https://openalex.org/W2619429253","https://openalex.org/W2743344672","https://openalex.org/W2790675139","https://openalex.org/W2801309958","https://openalex.org/W2804916645","https://openalex.org/W2809368942","https://openalex.org/W2890156321","https://openalex.org/W2899224111","https://openalex.org/W2909924790","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2948469692","https://openalex.org/W2949067670","https://openalex.org/W2949177718","https://openalex.org/W2952383043","https://openalex.org/W2953036966","https://openalex.org/W2978551960","https://openalex.org/W2992151131","https://openalex.org/W2999977864","https://openalex.org/W3001833132","https://openalex.org/W3004640473","https://openalex.org/W3012498554","https://openalex.org/W3022836409","https://openalex.org/W3033415403","https://openalex.org/W3087138957","https://openalex.org/W3092450854","https://openalex.org/W3092493138","https://openalex.org/W3108118546","https://openalex.org/W3111521801","https://openalex.org/W3112563877","https://openalex.org/W3124439729","https://openalex.org/W3126958162","https://openalex.org/W3127422037","https://openalex.org/W3129476455","https://openalex.org/W3132661792","https://openalex.org/W3134482219","https://openalex.org/W3137392859","https://openalex.org/W3147595666","https://openalex.org/W3161009639","https://openalex.org/W3165120573","https://openalex.org/W3165591717","https://openalex.org/W3173767537","https://openalex.org/W3173882906","https://openalex.org/W3177020879","https://openalex.org/W3182503854","https://openalex.org/W3190202966","https://openalex.org/W3191029526","https://openalex.org/W3192380610","https://openalex.org/W3204015056","https://openalex.org/W3205475594","https://openalex.org/W3208940117","https://openalex.org/W3214865687","https://openalex.org/W3215069361","https://openalex.org/W4205817967","https://openalex.org/W4210309458","https://openalex.org/W4210583065","https://openalex.org/W4210853280","https://openalex.org/W4213238696","https://openalex.org/W4220765701","https://openalex.org/W4221095552","https://openalex.org/W4221114856","https://openalex.org/W4224059281","https://openalex.org/W4224218779","https://openalex.org/W4225257442","https://openalex.org/W4225272983","https://openalex.org/W4225367171","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4235169531","https://openalex.org/W4280533477","https://openalex.org/W4283704002","https://openalex.org/W4288758477","https://openalex.org/W4289745500","https://openalex.org/W4289956737","https://openalex.org/W4296371910","https://openalex.org/W4300862018","https://openalex.org/W4309918428","https://openalex.org/W4317757307","https://openalex.org/W4321112079","https://openalex.org/W4323044112","https://openalex.org/W4376134478","https://openalex.org/W4378212544","https://openalex.org/W4387440956","https://openalex.org/W4387570050","https://openalex.org/W4387580076","https://openalex.org/W4388997570","https://openalex.org/W4390814844","https://openalex.org/W4399570238"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"transcriptomics":[2],"(ST)":[3],"technologies":[4],"provide":[5],"valuable":[6],"insights":[7],"into":[8],"cellular":[9,19],"heterogeneity":[10],"by":[11],"simultaneously":[12],"acquiring":[13],"both":[14],"gene":[15],"expression":[16],"profiles":[17],"and":[18,26,35,54,78,89,93,117,141,154],"location":[20],"information.":[21],"However,":[22],"the":[23,33,71,110,134,143],"limited":[24],"diversity":[25],"accuracy":[27],"of":[28,37,119,137,145],"\"gold":[29],"standard\"":[30],"datasets":[31],"hindered":[32],"effectiveness":[34],"fairness":[36],"benchmarking":[38],"rapidly":[39],"growing":[40],"ST":[41,59,64,139,164],"analysis":[42,147],"tools.":[43],"RESULTS:":[44],"To":[45],"address":[46],"this":[47,167],"issue,":[48],"we":[49],"proposed":[50],"Spider,":[51],"a":[52,67],"flexible":[53],"comprehensive":[55],"framework":[56],"for":[57,108],"simulating":[58],"data":[60,65,92,140,165],"without":[61],"requiring":[62],"real":[63,138],"as":[66,114],"reference.":[68],"By":[69],"characterizing":[70],"spatial":[72,111,135],"patterns":[73],"using":[74],"cell":[75],"type":[76],"proportions":[77],"transition":[79],"matrix":[80],"between":[81],"adjacent":[82],"cells,":[83],"Spider":[84,104,127,149],"can":[85],"produce":[86],"more":[87],"realistic":[88],"diverse":[90],"simulated":[91,163],"offer":[94],"enhanced":[95],"modeling":[96],"flexibility":[97],"compared":[98],"to":[99],"existing":[100],"simulation":[101,130],"methods.":[102,148],"Additionally,":[103],"provides":[105],"interactive":[106],"features":[107],"customizing":[109],"domain,":[112],"such":[113],"zone":[115],"segmentation":[116],"integration":[118],"histology":[120],"imaging":[121],"data.":[122],"Benchmark":[123],"analyses":[124],"demonstrate":[125],"that":[126],"outperforms":[128],"other":[129],"tools":[131],"in":[132,152,166],"preserving":[133],"characteristics":[136],"facilitating":[142],"evaluation":[144],"downstream":[146],"is":[150],"implemented":[151],"Python":[153],"available":[155,171],"at":[156,172],"https://github.com/YANG-ERA/Spider.":[157,173],"AVAILABILITY":[158],"AND":[159],"IMPLEMENTATION:":[160],"All":[161],"codes,":[162],"paper":[168],"are":[169],"publicly":[170]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-11-14T00:00:00"}
