{"id":"https://openalex.org/W4225367171","doi":"https://doi.org/10.1093/bib/bbac116","title":"SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression","display_name":"SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression","publication_year":2022,"publication_date":"2022-03-10","ids":{"openalex":"https://openalex.org/W4225367171","doi":"https://doi.org/10.1093/bib/bbac116","pmid":"https://pubmed.ncbi.nlm.nih.gov/35380614"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac116","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac116/43744892/bbac116.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/23/3/bbac116/43744892/bbac116.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045253111","display_name":"Yusong Liu","orcid":"https://orcid.org/0000-0003-4950-6304"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yusong Liu","raw_affiliation_strings":["College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China"],"raw_orcid":"https://orcid.org/0000-0003-4950-6304","affiliations":[{"raw_affiliation_string":"College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I151727225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079050779","display_name":"Tongxin Wang","orcid":"https://orcid.org/0000-0001-5826-1842"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tongxin Wang","raw_affiliation_strings":["Department of Computer Science, Indiana University Bloomington, Bloomington, IN 47408, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Indiana University Bloomington, Bloomington, IN 47408, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033805241","display_name":"Ben Duggan","orcid":"https://orcid.org/0000-0002-1819-2130"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Duggan","raw_affiliation_strings":["Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039180089","display_name":"Michael F. Sharpnack","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Sharpnack","raw_affiliation_strings":["Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100683421","display_name":"Kun Huang","orcid":"https://orcid.org/0000-0003-0797-8338"},"institutions":[{"id":"https://openalex.org/I1324682000","display_name":"Regenstrief Institute","ror":"https://ror.org/05f2ywb48","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1324682000"]},{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kun Huang","raw_affiliation_strings":["Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA","Regenstrief Institute, Indianapolis, IN 46202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Regenstrief Institute, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I1324682000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436623","display_name":"Jie Zhang","orcid":"https://orcid.org/0000-0001-6939-7905"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jie Zhang","raw_affiliation_strings":["Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083889663","display_name":"Xiufen Ye","orcid":"https://orcid.org/0000-0001-9812-2679"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiufen Ye","raw_affiliation_strings":["College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I151727225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062080836","display_name":"Travis S. Johnson","orcid":"https://orcid.org/0000-0002-4628-2256"},"institutions":[{"id":"https://openalex.org/I2802732410","display_name":"Indiana Biosciences Research Institute","ror":"https://ror.org/04d52p729","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802732410"]},{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Travis S Johnson","raw_affiliation_strings":["Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA","Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA"],"raw_orcid":"https://orcid.org/0000-0002-4628-2256","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I2802732410"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5062080836","https://openalex.org/A5083889663","https://openalex.org/A5100436623"],"corresponding_institution_ids":["https://openalex.org/I151727225","https://openalex.org/I2802732410","https://openalex.org/I4394709130","https://openalex.org/I55769427"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.7236,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.84632316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"3","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":0.9990000128746033,"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":0.9990000128746033,"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/T10604","display_name":"RNA Research and Splicing","score":0.9907000064849854,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9884999990463257,"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/smoothing","display_name":"Smoothing","score":0.8085076212882996},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6706269979476929},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6643450856208801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5642844438552856},{"id":"https://openalex.org/keywords/common-spatial-pattern","display_name":"Common spatial pattern","score":0.4913000464439392},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44300758838653564},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4030027389526367},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3817245364189148},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3374421000480652},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.26533377170562744},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.25327837467193604},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23873230814933777},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.09312117099761963},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08259782195091248},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08257362246513367}],"concepts":[{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.8085076212882996},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6706269979476929},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6643450856208801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5642844438552856},{"id":"https://openalex.org/C173727882","wikidata":"https://www.wikidata.org/wiki/Q5153620","display_name":"Common spatial pattern","level":2,"score":0.4913000464439392},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44300758838653564},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4030027389526367},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3817245364189148},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3374421000480652},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26533377170562744},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.25327837467193604},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23873230814933777},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.09312117099761963},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08259782195091248},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08257362246513367},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbac116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac116","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac116/43744892/bbac116.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35380614","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35380614","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:scholarworks.iupui.edu:1805/33824","is_oa":true,"landing_page_url":"https://hdl.handle.net/1805/33824","pdf_url":"https://scholarworks.indianapolis.iu.edu/bitstreams/fd50f5c4-d436-4df1-9e7d-da105ddb4a83/download","source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"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":"PMC","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9116229","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9116229","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac116","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac116/43744892/bbac116.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G366217430","display_name":null,"funder_award_id":"61633004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5286470768","display_name":null,"funder_award_id":"41876100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8716505729","display_name":null,"funder_award_id":"P20 GM121176","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225367171.pdf"},"referenced_works_count":76,"referenced_works":["https://openalex.org/W1607313147","https://openalex.org/W1637526023","https://openalex.org/W1813388215","https://openalex.org/W1906211198","https://openalex.org/W1984689597","https://openalex.org/W1989277387","https://openalex.org/W2019552331","https://openalex.org/W2031215175","https://openalex.org/W2061674320","https://openalex.org/W2063042123","https://openalex.org/W2089468765","https://openalex.org/W2109890125","https://openalex.org/W2124954099","https://openalex.org/W2134179844","https://openalex.org/W2137084288","https://openalex.org/W2141012957","https://openalex.org/W2148043260","https://openalex.org/W2342688693","https://openalex.org/W2346302798","https://openalex.org/W2431298502","https://openalex.org/W2471536144","https://openalex.org/W2519132385","https://openalex.org/W2598344500","https://openalex.org/W2605054837","https://openalex.org/W2617939744","https://openalex.org/W2744335798","https://openalex.org/W2746479894","https://openalex.org/W2749679400","https://openalex.org/W2805619986","https://openalex.org/W2808465642","https://openalex.org/W2889990912","https://openalex.org/W2894765294","https://openalex.org/W2905444337","https://openalex.org/W2937443931","https://openalex.org/W2944545583","https://openalex.org/W2951217100","https://openalex.org/W2953049802","https://openalex.org/W2957190895","https://openalex.org/W2972661346","https://openalex.org/W2972983657","https://openalex.org/W2999977864","https://openalex.org/W3001478581","https://openalex.org/W3015184839","https://openalex.org/W3015897279","https://openalex.org/W3028391445","https://openalex.org/W3036882247","https://openalex.org/W3036895040","https://openalex.org/W3037329734","https://openalex.org/W3044030235","https://openalex.org/W3046064102","https://openalex.org/W3059664894","https://openalex.org/W3083945796","https://openalex.org/W3096660036","https://openalex.org/W3096828292","https://openalex.org/W3102147110","https://openalex.org/W3106811464","https://openalex.org/W3108118546","https://openalex.org/W3110435694","https://openalex.org/W3112600195","https://openalex.org/W3119379269","https://openalex.org/W3126958162","https://openalex.org/W3130329048","https://openalex.org/W3134482219","https://openalex.org/W3159020250","https://openalex.org/W3165120573","https://openalex.org/W3211402536","https://openalex.org/W4206174637","https://openalex.org/W4231254854","https://openalex.org/W4243979784","https://openalex.org/W6638266167","https://openalex.org/W6639979049","https://openalex.org/W6676268112","https://openalex.org/W6680447361","https://openalex.org/W6764456304","https://openalex.org/W6778465659","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W1978572805","https://openalex.org/W2399513595","https://openalex.org/W2383807498","https://openalex.org/W1997992934","https://openalex.org/W1987225439","https://openalex.org/W4238188170","https://openalex.org/W4388386498","https://openalex.org/W2125114371","https://openalex.org/W2019977573","https://openalex.org/W2149980199"],"abstract_inverted_index":{"High-dimensional,":[0],"localized":[1],"ribonucleic":[2],"acid":[3],"(RNA)":[4],"sequencing":[5,66],"is":[6,18,190],"now":[7],"possible":[8],"owing":[9],"to":[10,28,33,54,60,135],"recent":[11],"developments":[12],"in":[13,84,192],"spatial":[14,99,122,141],"transcriptomics":[15],"(ST).":[16],"ST":[17,38,110,148,168],"based":[19],"on":[20,146],"highly":[21],"multiplexed":[22],"sequence":[23],"analysis":[24],"and":[25,45,74,123,140,159,175],"uses":[26],"barcodes":[27],"match":[29],"the":[30,52,56,130,179],"sequenced":[31],"reads":[32],"their":[34],"respective":[35],"tissue":[36],"locations.":[37],"expression":[39],"data":[40,57,68],"suffer":[41,70],"from":[42,71,138,150],"high":[43],"noise":[44],"dropout":[46],"events;":[47],"however,":[48],"smoothing":[49,75,91,103,120,126],"techniques":[50],"have":[51,170],"promise":[53],"improve":[55],"interpretability":[58,177],"prior":[59],"performing":[61,144],"downstream":[62],"analyses.":[63],"Single-cell":[64],"RNA":[65],"(scRNA-seq)":[67],"similarly":[69],"these":[72,101],"limitations,":[73],"methods":[76,104],"developed":[77],"for":[78,98],"scRNA-seq":[79],"can":[80],"only":[81],"utilize":[82,136],"associations":[83],"transcriptome":[85,139],"space":[86],"(also":[87],"known":[88],"as":[89],"one-factor":[90,102,184],"methods).":[92],"Since":[93],"they":[94],"do":[95],"not":[96],"account":[97],"relationships,":[100],"cannot":[105],"take":[106],"full":[107],"advantage":[108],"of":[109,188],"data.":[111],"In":[112],"this":[113],"study,":[114],"we":[115],"present":[116],"a":[117],"novel":[118],"two-factor":[119],"technique,":[121],"pattern":[124],"combined":[125],"(SPCS),":[127],"that":[128],"employs":[129],"k-nearest":[131],"neighbor":[132],"(kNN)":[133],"technique":[134],"information":[137],"relationships.":[142],"By":[143],"SPCS":[145,189],"multiple":[147],"slides":[149,169],"pancreatic":[151],"ductal":[152],"adenocarcinoma":[153],"(PDAC),":[154],"dorsolateral":[155],"prefrontal":[156],"cortex":[157],"(DLPFC)":[158],"simulated":[160],"high-grade":[161],"serous":[162],"ovarian":[163],"cancer":[164],"(HGSOC)":[165],"datasets,":[166],"smoothed":[167,181],"better":[171],"separability,":[172],"partition":[173],"accuracy":[174],"biological":[176],"than":[178],"ones":[180],"by":[182],"preexisting":[183],"methods.":[185],"Source":[186],"code":[187],"provided":[191],"Github":[193],"(https://github.com/Usos/SPCS).":[194]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
