{"id":"https://openalex.org/W4311404503","doi":"https://doi.org/10.1093/bioinformatics/btac805","title":"Benchmarking and integration of methods for deconvoluting spatial transcriptomic data","display_name":"Benchmarking and integration of methods for deconvoluting spatial transcriptomic data","publication_year":2022,"publication_date":"2022-12-13","ids":{"openalex":"https://openalex.org/W4311404503","doi":"https://doi.org/10.1093/bioinformatics/btac805","pmid":"https://pubmed.ncbi.nlm.nih.gov/36515467"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac805","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac805","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac805/48520680/btac805.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac805/48520680/btac805.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048901609","display_name":"Lulu Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lulu Yan","raw_affiliation_strings":["School of Mathematics, Sun Yat-sen University , Guangzhou 510275, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Sun Yat-sen University , Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047111777","display_name":"Xiaoqiang Sun","orcid":"https://orcid.org/0000-0002-3399-7260"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoqiang Sun","raw_affiliation_strings":["School of Mathematics, Sun Yat-sen University , Guangzhou 510275, China"],"raw_orcid":"https://orcid.org/0000-0002-3399-7260","affiliations":[{"raw_affiliation_string":"School of Mathematics, Sun Yat-sen University , Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5047111777"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.2632,"has_fulltext":true,"cited_by_count":101,"citation_normalized_percentile":{"value":0.98395152,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"39","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":0.9987999796867371,"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":0.9987999796867371,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.00019999999494757503,"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/benchmarking","display_name":"Benchmarking","score":0.9076952934265137},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5856059789657593},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41514289379119873},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36094361543655396},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12574002146720886},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.08620956540107727}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9076952934265137},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5856059789657593},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41514289379119873},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36094361543655396},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12574002146720886},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.08620956540107727},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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/btac805","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac805","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac805/48520680/btac805.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:36515467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36515467","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:9825747","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825747","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/btac805","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac805","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac805/48520680/btac805.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G1876640051","display_name":null,"funder_award_id":"11871070","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2415776301","display_name":null,"funder_award_id":"11931019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2563946583","display_name":null,"funder_award_id":"2020B151502120","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G6869372738","display_name":null,"funder_award_id":"62273364","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation 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/F4320321160","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71"},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311404503.pdf","grobid_xml":"https://content.openalex.org/works/W4311404503.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1979283544","https://openalex.org/W2102074241","https://openalex.org/W2231058499","https://openalex.org/W2471536144","https://openalex.org/W2899224111","https://openalex.org/W2942610007","https://openalex.org/W2949177718","https://openalex.org/W2953866345","https://openalex.org/W2965166405","https://openalex.org/W2996171578","https://openalex.org/W2999977864","https://openalex.org/W3092450854","https://openalex.org/W3112563877","https://openalex.org/W3120427588","https://openalex.org/W3124439729","https://openalex.org/W3127422037","https://openalex.org/W3129476455","https://openalex.org/W3134482219","https://openalex.org/W3145087249","https://openalex.org/W3161009639","https://openalex.org/W3171692328","https://openalex.org/W3176766013","https://openalex.org/W3190202966","https://openalex.org/W3208940117","https://openalex.org/W4205894915","https://openalex.org/W4206199829","https://openalex.org/W4221092226","https://openalex.org/W4224218779","https://openalex.org/W4225257442","https://openalex.org/W4280533477"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,120,234],"rapid":[2],"development":[3],"of":[4,37,62,65,76,88,99,142,159,167],"spatial":[5,54],"transcriptomics":[6],"(ST)":[7],"approaches":[8],"has":[9],"provided":[10],"new":[11,105,122,226],"insights":[12],"into":[13],"understanding":[14],"tissue":[15],"architecture":[16],"and":[17,96,128,147,151,199,216,224,227],"function.":[18],"However,":[19],"the":[20,35,56,63,86,97,140,157,165,168,175,192,201],"gene":[21],"expressions":[22],"measured":[23],"at":[24,239,248,256],"a":[25,59,73,104],"spot":[26,94,176],"may":[27],"contain":[28],"contributions":[29],"from":[30,53],"multiple":[31,113],"cells":[32],"due":[33],"to":[34,48,91,156,172],"low-resolution":[36],"current":[38],"ST":[39,135,189,209,221],"technologies.":[40],"Although":[41],"many":[42],"computational":[43],"methods":[44,79,90,115,170,183],"have":[45],"been":[46],"developed":[47],"disentangle":[49],"discrete":[50],"cell":[51],"types":[52],"mixtures,":[55],"community":[57],"lacks":[58],"thorough":[60],"evaluation":[61,141],"performance":[64],"those":[66],"deconvolution":[67,78,108,136,182,222],"methods.":[68,230],"RESULTS:":[69],"Here,":[70],"we":[71,84,102],"present":[72],"comprehensive":[74],"benchmarking":[75,235],"14":[77],"on":[80,139],"four":[81],"datasets.":[82],"Furthermore,":[83],"investigate":[85],"robustness":[87],"different":[89],"sequencing":[92,160],"depth,":[93],"size":[95,177],"choice":[98],"normalization.":[100],"Moreover,":[101],"propose":[103],"ensemble":[106],"learning-based":[107],"method":[109,193],"(EnDecon)":[110],"by":[111],"integrating":[112],"individual":[114],"for":[116,218,244],"more":[117,131,154,207,228],"accurate":[118,132,208],"deconvolution.":[119,210],"major":[121],"findings":[123],"include:":[124],"(i)":[125],"cell2loction,":[126],"RCTD":[127],"spatialDWLS":[129,152],"are":[130,153,254],"than":[133,162],"other":[134],"methods,":[137],"based":[138],"three":[143],"metrics:":[144],"RMSE,":[145],"PCC":[146],"JSD;":[148],"(ii)":[149],"cell2location":[150],"robust":[155],"variation":[158],"depth":[161],"RCTD;":[163],"(iii)":[164],"accuracy":[166],"existing":[169],"tends":[171],"decrease":[173],"as":[174],"becomes":[178],"smaller;":[179],"(iv)":[180],"most":[181],"perform":[184],"best":[185],"when":[186],"they":[187],"normalize":[188],"data":[190,253],"using":[191],"described":[194],"in":[195],"their":[196],"original":[197],"papers;":[198],"(v)":[200],"integrative":[202],"method,":[203],"EnDecon,":[204],"could":[205],"achieve":[206],"Our":[211],"study":[212],"provides":[213],"valuable":[214],"information":[215],"guideline":[217],"practically":[219],"applying":[220],"tools":[223],"developing":[225],"effective":[229],"AVAILABILITY":[231],"AND":[232],"IMPLEMENTATION:":[233],"pipeline":[236],"is":[237,246],"available":[238,247,255],"https://github.com/SunXQlab/ST-deconvoulution.":[240],"An":[241],"R":[242],"package":[243],"EnDecon":[245],"https://github.com/SunXQlab/EnDecon.":[249],"SUPPLEMENTARY":[250],"INFORMATION:":[251],"Supplementary":[252],"Bioinformatics":[257],"online.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":43},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-15T07:11:24.734988","created_date":"2025-10-10T00:00:00"}