{"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":true,"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"],"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,","Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, 100142, China","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China"],"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":"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"]},{"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"]}]},{"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"],"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"],"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"],"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"],"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,","Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China","Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China"],"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":"Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China","institution_ids":["https://openalex.org/I20231570"]},{"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"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021047181","display_name":"Xiaoqi Zheng","orcid":"https://orcid.org/0000-0002-1832-4404"},"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"],"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":["https://openalex.org/A5100632856"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8149,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.78628443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"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":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":"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":[],"funders":[],"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":{"All":[0],"codes,":[1],"simulated":[2],"ST":[3],"data":[4],"in":[5],"this":[6],"paper":[7],"are":[8],"publicly":[9],"available":[10],"at":[11],"https://github.com/YANG-ERA/Spider.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-11-14T00:00:00"}