{"id":"https://openalex.org/W4382632303","doi":"https://doi.org/10.1093/bioinformatics/btad242","title":"SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data","display_name":"SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data","publication_year":2023,"publication_date":"2023-05-24","ids":{"openalex":"https://openalex.org/W4382632303","doi":"https://doi.org/10.1093/bioinformatics/btad242","pmid":"https://pubmed.ncbi.nlm.nih.gov/37387130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad242","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i131/50741356/btad242.pdf","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://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i131/50741356/btad242.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008114519","display_name":"Eric Lee","orcid":"https://orcid.org/0000-0003-2114-3118"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eric Lee","raw_affiliation_strings":["Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","Graduate Bioinformatics Training Program, University of British Columbia , 100-570 West 7th Avenue , Vancouver, BC V5T4S6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Graduate Bioinformatics Training Program, University of British Columbia , 100-570 West 7th Avenue , Vancouver, BC V5T4S6, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016698633","display_name":"Kevin Chern","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kevin Chern","raw_affiliation_strings":["Department of Statistics, University of British Columbia , 2207 Main Mall , Vancouver, BC V6T1Z4, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of British Columbia , 2207 Main Mall , Vancouver, BC V6T1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103136122","display_name":"Michael Nissen","orcid":"https://orcid.org/0000-0001-5279-9174"},"institutions":[{"id":"https://openalex.org/I4210094500","display_name":"Terry Fox Research Institute","ror":"https://ror.org/00mtf6c40","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210094500"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michael Nissen","raw_affiliation_strings":["Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","institution_ids":["https://openalex.org/I4210094500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029271491","display_name":"Xuehai Wang","orcid":"https://orcid.org/0000-0002-1406-1846"},"institutions":[{"id":"https://openalex.org/I4210094500","display_name":"Terry Fox Research Institute","ror":"https://ror.org/00mtf6c40","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210094500"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Xuehai Wang","raw_affiliation_strings":["Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","institution_ids":["https://openalex.org/I4210094500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017812069","display_name":"C. Chris Huang","orcid":"https://orcid.org/0000-0002-1116-2756"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Huang","raw_affiliation_strings":["Translational Medicine Hematology, Bristol Myers Squibb , 86 Morris Ave , Summit, NJ 07901, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Medicine Hematology, Bristol Myers Squibb , 86 Morris Ave , Summit, NJ 07901, United States","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043395223","display_name":"Anita K. Gandhi","orcid":"https://orcid.org/0000-0001-5512-1625"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anita K Gandhi","raw_affiliation_strings":["Translational Medicine Hematology, Bristol Myers Squibb , 86 Morris Ave , Summit, NJ 07901, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Medicine Hematology, Bristol Myers Squibb , 86 Morris Ave , Summit, NJ 07901, United States","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003426513","display_name":"Alexandre Bouchard\u2010C\u00f4t\u00e9","orcid":"https://orcid.org/0000-0001-7402-8506"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alexandre Bouchard-C\u00f4t\u00e9","raw_affiliation_strings":["Department of Statistics, University of British Columbia , 2207 Main Mall , Vancouver, BC V6T1Z4, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of British Columbia , 2207 Main Mall , Vancouver, BC V6T1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069512440","display_name":"Andrew P. Weng","orcid":"https://orcid.org/0000-0001-7394-5425"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210094500","display_name":"Terry Fox Research Institute","ror":"https://ror.org/00mtf6c40","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210094500"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew P Weng","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, University of British Columbia , 2211 Wesbrook Mall , Vancouver, BC V6T1Z7, Canada","Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, University of British Columbia , 2211 Wesbrook Mall , Vancouver, BC V6T1Z7, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Terry Fox Laboratory, British Columbia Cancer Research Centre , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","institution_ids":["https://openalex.org/I4210094500"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066899464","display_name":"Andrew Roth","orcid":"https://orcid.org/0000-0003-3422-8823"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Andrew Roth","raw_affiliation_strings":["Department of Computer Science, University of British Columbia , 2366 Main Mall , Vancouver, BC V6T1Z4, Canada","Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","Department of Pathology and Laboratory Medicine, University of British Columbia , 2211 Wesbrook Mall , Vancouver, BC V6T1Z7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of British Columbia , 2366 Main Mall , Vancouver, BC V6T1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC V5Z1L3, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, University of British Columbia , 2211 Wesbrook Mall , Vancouver, BC V6T1Z7, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5066899464"],"corresponding_institution_ids":["https://openalex.org/I1289530486","https://openalex.org/I141945490"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6727,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.70617344,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"39","issue":"Supplement_1","first_page":"i131","last_page":"i139"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7736999988555908,"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":0.7736999988555908,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.04500000178813934,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.03759999945759773,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.767101526260376},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7585943937301636},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6194746494293213},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5576025247573853},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5195791721343994},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.5138635635375977},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48569831252098083},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.43886905908584595},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4362826347351074},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4164707660675049},{"id":"https://openalex.org/keywords/consensus-clustering","display_name":"Consensus clustering","score":0.41269218921661377},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3473246097564697},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3397619426250458},{"id":"https://openalex.org/keywords/fuzzy-clustering","display_name":"Fuzzy clustering","score":0.2356770634651184},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.12070518732070923},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.11855742335319519},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08564850687980652},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07960838079452515}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.767101526260376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7585943937301636},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6194746494293213},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5576025247573853},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5195791721343994},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.5138635635375977},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48569831252098083},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.43886905908584595},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4362826347351074},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4164707660675049},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.41269218921661377},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3473246097564697},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3397619426250458},{"id":"https://openalex.org/C17212007","wikidata":"https://www.wikidata.org/wiki/Q5511111","display_name":"Fuzzy clustering","level":3,"score":0.2356770634651184},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.12070518732070923},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.11855742335319519},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08564850687980652},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07960838079452515},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":false},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016403","descriptor_name":"Lymphoma, Large B-Cell, Diffuse","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016403","descriptor_name":"Lymphoma, Large B-Cell, Diffuse","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016403","descriptor_name":"Lymphoma, Large B-Cell, Diffuse","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016403","descriptor_name":"Lymphoma, Large B-Cell, Diffuse","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad242","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i131/50741356/btad242.pdf","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:37387130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37387130","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:10311307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10311307","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10311307/pdf/btad242.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad242","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i131/50741356/btad242.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1475195806","display_name":null,"funder_award_id":"V2021-033","funder_id":"https://openalex.org/F4320306536","funder_display_name":"V Foundation for Cancer Research"},{"id":"https://openalex.org/G2879747885","display_name":null,"funder_award_id":"C31893/A25050","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320306536","display_name":"V Foundation for Cancer Research","ror":"https://ror.org/00kbbk236"},{"id":"https://openalex.org/F4320319965","display_name":"Michael Smith Health Research BC","ror":"https://ror.org/020x39229"},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320322597","display_name":"Terry Fox Research Institute","ror":"https://ror.org/05vd00053"},{"id":"https://openalex.org/F4320329172","display_name":"BC Cancer Foundation","ror":"https://ror.org/03gqhbs95"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382632303.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W1567885833","https://openalex.org/W1631320694","https://openalex.org/W1829970718","https://openalex.org/W2024626836","https://openalex.org/W2041763398","https://openalex.org/W2043565262","https://openalex.org/W2051224630","https://openalex.org/W2053129129","https://openalex.org/W2064610182","https://openalex.org/W2101234009","https://openalex.org/W2179438025","https://openalex.org/W2594639291","https://openalex.org/W2800392236","https://openalex.org/W2810097927","https://openalex.org/W2890156321","https://openalex.org/W2899235059","https://openalex.org/W2949238013","https://openalex.org/W2973034691","https://openalex.org/W2999681746","https://openalex.org/W3005698181","https://openalex.org/W3047081808","https://openalex.org/W3124814274","https://openalex.org/W3134482219","https://openalex.org/W3145026833","https://openalex.org/W3165120573","https://openalex.org/W3214865687","https://openalex.org/W4383743072","https://openalex.org/W6675354045","https://openalex.org/W6792739027","https://openalex.org/W6797277546"],"related_works":["https://openalex.org/W4297904238","https://openalex.org/W2588165676","https://openalex.org/W2375454734","https://openalex.org/W210402007","https://openalex.org/W3197105638","https://openalex.org/W2378466817","https://openalex.org/W4287866654","https://openalex.org/W4386246753","https://openalex.org/W2289981285","https://openalex.org/W2168105568"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"advances":[2],"in":[3,15,20,36,82,124],"spatial":[4,42,66,159,177],"proteomics":[5],"technologies":[6],"have":[7],"enabled":[8],"the":[9,25,31,41,58,65,78,102,115,182],"profiling":[10],"of":[11,13,17,33,61,104,117,119,147,184],"dozens":[12],"proteins":[14],"thousands":[16],"single":[18],"cells":[19,62,118],"situ.":[21],"This":[22],"has":[23],"created":[24],"opportunity":[26],"to":[27,112,122,138],"move":[28],"beyond":[29],"quantifying":[30],"composition":[32],"cell":[34,80,133],"types":[35,121],"tissue,":[37],"and":[38,63,126,143,151,160,178],"instead":[39],"probe":[40],"relationships":[43],"between":[44,176],"cells.":[45],"However,":[46],"most":[47],"current":[48],"methods":[49],"for":[50,74,101,114],"clustering":[51,97,141,165],"data":[52],"from":[53],"these":[54,88],"assays":[55],"only":[56],"consider":[57],"expression":[59],"values":[60],"ignore":[64],"context.":[67],"Furthermore,":[68],"existing":[69],"approaches":[70],"do":[71],"not":[72],"account":[73,113],"prior":[75,105,129,161],"information":[76,130,162],"about":[77,131],"expected":[79,132],"populations":[81],"a":[83,93,185],"sample.":[84],"RESULTS:":[85],"To":[86],"address":[87],"shortcomings,":[89],"we":[90,154],"developed":[91],"SpatialSort,":[92],"spatially":[94],"aware":[95],"Bayesian":[96],"approach":[98],"that":[99,156],"allows":[100],"incorporation":[103],"biological":[106],"knowledge.":[107],"Our":[108],"method":[109],"is":[110,136,198],"able":[111,137],"affinities":[116],"different":[120],"neighbour":[123],"space,":[125],"by":[127,157],"incorporating":[128],"populations,":[134],"it":[135],"simultaneously":[139],"improve":[140],"accuracy":[142],"perform":[144,173],"automated":[145],"annotation":[146],"clusters.":[148],"Using":[149],"synthetic":[150],"real":[152,186],"data,":[153],"show":[155],"using":[158],"SpatialSort":[163,171],"improves":[164],"accuracy.":[166],"We":[167],"also":[168],"demonstrate":[169],"how":[170],"can":[172],"label":[174],"transfer":[175],"nonspatial":[179],"modalities":[180],"through":[181],"analysis":[183],"world":[187],"diffuse":[188],"large":[189],"B-cell":[190],"lymphoma":[191],"dataset.":[192],"AVAILABILITY":[193],"AND":[194],"IMPLEMENTATION:":[195],"Source":[196],"code":[197],"available":[199],"on":[200],"Github":[201],"at:":[202],"https://github.com/Roth-Lab/SpatialSort.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}