{"id":"https://openalex.org/W4406023017","doi":"https://doi.org/10.1093/bib/bbae689","title":"BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data","display_name":"BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406023017","doi":"https://doi.org/10.1093/bib/bbae689","pmid":"https://pubmed.ncbi.nlm.nih.gov/39751646"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae689","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae689/61325133/bbae689.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae689/61325133/bbae689.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055503349","display_name":"Yinqiao Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I37796252","display_name":"Beijing University of Technology","ror":"https://ror.org/037b1pp87","country_code":"CN","type":"education","lineage":["https://openalex.org/I37796252"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yinqiao Yan","raw_affiliation_strings":["Beijing University of Technology , Statistics and Mechanics, , No. 100 Pingleyuan, 100124 Beijing,","School of Mathematics , Statistics and Mechanics, , No. 100 Pingleyuan, 100124 Beijing,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing University of Technology , Statistics and Mechanics, , No. 100 Pingleyuan, 100124 Beijing,","institution_ids":["https://openalex.org/I37796252"]},{"raw_affiliation_string":"School of Mathematics , Statistics and Mechanics, , No. 100 Pingleyuan, 100124 Beijing,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064436308","display_name":"Xiangyu Luo","orcid":"https://orcid.org/0000-0002-1062-7443"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangyu Luo","raw_affiliation_strings":["Institute of Statistics and Big Data, Renmin University of China , No. 59 Zhongguancun Street, 100872 Beijing,"],"raw_orcid":"https://orcid.org/0000-0002-1062-7443","affiliations":[{"raw_affiliation_string":"Institute of Statistics and Big Data, Renmin University of China , No. 59 Zhongguancun Street, 100872 Beijing,","institution_ids":["https://openalex.org/I78988378"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055503349"],"corresponding_institution_ids":["https://openalex.org/I37796252"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.6499,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.70587981,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"26","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":1.0,"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":1.0,"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":0.9753999710083008,"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/computer-science","display_name":"Computer science","score":0.7030340433120728},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5712361931800842},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5571239590644836},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5337240695953369},{"id":"https://openalex.org/keywords/nonparametric-statistics","display_name":"Nonparametric statistics","score":0.5279383063316345},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.5276048183441162},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46512719988822937},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4291319251060486},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36940062046051025},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34133845567703247},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21430963277816772},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17360597848892212},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17068150639533997},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10240361094474792},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09870877861976624},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09437897801399231}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7030340433120728},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5712361931800842},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5571239590644836},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5337240695953369},{"id":"https://openalex.org/C102366305","wikidata":"https://www.wikidata.org/wiki/Q1097688","display_name":"Nonparametric statistics","level":2,"score":0.5279383063316345},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.5276048183441162},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46512719988822937},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4291319251060486},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36940062046051025},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34133845567703247},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21430963277816772},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17360597848892212},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17068150639533997},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10240361094474792},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09870877861976624},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09437897801399231}],"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":"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","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},{"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/bib/bbae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae689","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae689/61325133/bbae689.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39751646","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39751646","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11697130","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11697130","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11697130/pdf/bbae689.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae689","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae689/61325133/bbae689.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322499","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406023017.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1974565082","https://openalex.org/W1984048068","https://openalex.org/W1989692914","https://openalex.org/W2042789810","https://openalex.org/W2063390378","https://openalex.org/W2151967501","https://openalex.org/W2225156818","https://openalex.org/W2804211145","https://openalex.org/W2809368942","https://openalex.org/W2915848182","https://openalex.org/W2954992101","https://openalex.org/W2962851448","https://openalex.org/W3004640473","https://openalex.org/W3108118546","https://openalex.org/W3120427588","https://openalex.org/W3120554937","https://openalex.org/W3126958162","https://openalex.org/W3204015056","https://openalex.org/W4226192560","https://openalex.org/W4235169531","https://openalex.org/W4289745500","https://openalex.org/W4290154117","https://openalex.org/W4309918428","https://openalex.org/W4391103396","https://openalex.org/W4392198237","https://openalex.org/W4392868645","https://openalex.org/W4401157960","https://openalex.org/W6682569104"],"related_works":["https://openalex.org/W4243114048","https://openalex.org/W2399513595","https://openalex.org/W2529605301","https://openalex.org/W4237896776","https://openalex.org/W4231665652","https://openalex.org/W1837630526","https://openalex.org/W2000242494","https://openalex.org/W2335589441","https://openalex.org/W4296826658","https://openalex.org/W1979697693"],"abstract_inverted_index":{"The":[0,155],"spatial":[1,18,26,45,58,103,117,140,151],"transcriptomics":[2],"is":[3,71],"a":[4,62,87,109],"rapidly":[5],"evolving":[6],"biological":[7],"technology":[8],"that":[9],"simultaneously":[10],"measures":[11],"the":[12,17,31,35,43,66,76,126,132,144,159],"gene":[13,99],"expression":[14,100],"profiles":[15],"and":[16,102,158],"locations":[19],"of":[20,47,65,105,147,162],"spots.":[21],"With":[22],"progressive":[23],"advances,":[24],"current":[25],"transcriptomic":[27,141],"techniques":[28],"can":[29,123],"achieve":[30],"cellular":[32],"or":[33],"even":[34],"subcellular":[36],"resolution,":[37],"making":[38],"it":[39,122],"possible":[40],"to":[41,73,92,113],"explore":[42],"fine-grained":[44],"pattern":[46],"cell":[48,57,67,127,152],"types":[49],"within":[50],"one":[51],"tissue":[52],"section.":[53],"However,":[54],"most":[55],"existing":[56],"clustering":[59],"methods":[60],"require":[61],"correct":[63],"specification":[64],"type":[68,128],"number,":[69],"which":[70],"hard":[72],"determine":[74],"in":[75],"practical":[77],"exploratory":[78],"data":[79,133],"analysis.":[80],"To":[81],"address":[82],"this":[83],"issue,":[84],"we":[85],"present":[86],"nonparametric":[88,110],"Bayesian":[89],"model":[90],"BACT":[91,107,148,163],"perform":[93],"BAyesian":[94],"Cell":[95],"Typing":[96],"by":[97],"utilizing":[98],"information":[101],"coordinates":[104],"cells.":[106],"incorporates":[108],"Potts":[111],"prior":[112],"induce":[114],"neighboring":[115],"cells'":[116],"dependency,":[118],"and,":[119],"more":[120],"importantly,":[121],"automatically":[124],"learn":[125],"number":[129],"directly":[130],"from":[131],"without":[134],"prespecification.":[135],"Evaluations":[136],"on":[137],"three":[138],"single-cell":[139],"datasets":[142],"demonstrate":[143],"better":[145],"performance":[146],"than":[149],"competing":[150],"typing":[153],"methods.":[154],"R":[156],"package":[157],"user":[160],"manual":[161],"are":[164],"publicly":[165],"available":[166],"at":[167],"https://github.com/yinqiaoyan/BACT.":[168]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-10T08:33:47.465468","created_date":"2025-10-10T00:00:00"}
