{"id":"https://openalex.org/W4411222116","doi":"https://doi.org/10.3389/fbinf.2025.1562410","title":"Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics","display_name":"Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics","publication_year":2025,"publication_date":"2025-06-11","ids":{"openalex":"https://openalex.org/W4411222116","doi":"https://doi.org/10.3389/fbinf.2025.1562410","pmid":"https://pubmed.ncbi.nlm.nih.gov/40567596"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1562410","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1562410","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1562410/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1562410/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066478742","display_name":"Nicolina Sciaraffa","orcid":"https://orcid.org/0000-0002-3380-0181"},"institutions":[{"id":"https://openalex.org/I4210150906","display_name":"Ri.MED","ror":"https://ror.org/05qetrn02","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210150906"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Nicolina Sciaraffa","raw_affiliation_strings":["Advanced Data Analysis Group, Ri.MED Foundation, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"Advanced Data Analysis Group, Ri.MED Foundation, Palermo, Italy","institution_ids":["https://openalex.org/I4210150906"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Antonino Gagliano","orcid":null},"institutions":[{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonino Gagliano","raw_affiliation_strings":["Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084051300","display_name":"Luigi Augugliaro","orcid":"https://orcid.org/0000-0002-4603-7541"},"institutions":[{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luigi Augugliaro","raw_affiliation_strings":["Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026545305","display_name":"Claudia Coronnello","orcid":"https://orcid.org/0000-0001-5962-8642"},"institutions":[{"id":"https://openalex.org/I4210150906","display_name":"Ri.MED","ror":"https://ror.org/05qetrn02","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210150906"]},{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudia Coronnello","raw_affiliation_strings":["Advanced Data Analysis Group, Ri.MED Foundation, Palermo, Italy","National Center for Gene Therapy and Drugs based on RNA Technology, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"Advanced Data Analysis Group, Ri.MED Foundation, Palermo, Italy","institution_ids":["https://openalex.org/I4210150906"]},{"raw_affiliation_string":"National Center for Gene Therapy and Drugs based on RNA Technology, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5066478742"],"corresponding_institution_ids":["https://openalex.org/I4210150906"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1152476,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1562410","last_page":"1562410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9789999723434448,"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":0.9785000085830688,"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/goodness-of-fit","display_name":"Goodness of fit","score":0.7027320861816406},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5233299732208252},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4080834984779358},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3682417571544647},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3532114028930664},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3287767171859741}],"concepts":[{"id":"https://openalex.org/C132480984","wikidata":"https://www.wikidata.org/wiki/Q2034239","display_name":"Goodness of fit","level":2,"score":0.7027320861816406},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5233299732208252},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4080834984779358},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3682417571544647},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3532114028930664},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3287767171859741}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2025.1562410","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1562410","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1562410/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40567596","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40567596","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:435c1dba4a024aa0baa478f461b7aab7","is_oa":true,"landing_page_url":"https://doaj.org/article/435c1dba4a024aa0baa478f461b7aab7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:iris.unipa.it:10447/683971","is_oa":true,"landing_page_url":"https://hdl.handle.net/10447/683971","pdf_url":null,"source":{"id":"https://openalex.org/S4306401065","display_name":"Nova Science Publishers (Nova Science Publishers, Inc.)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12187673","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12187673","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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1562410","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1562410","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1562410/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411222116.pdf"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W974986761","https://openalex.org/W1498782169","https://openalex.org/W1813068103","https://openalex.org/W1963678392","https://openalex.org/W1983753875","https://openalex.org/W1987971958","https://openalex.org/W1996747841","https://openalex.org/W2029064186","https://openalex.org/W2049814849","https://openalex.org/W2053718475","https://openalex.org/W2061874589","https://openalex.org/W2082503527","https://openalex.org/W2120043163","https://openalex.org/W2122825543","https://openalex.org/W2127962710","https://openalex.org/W2128120736","https://openalex.org/W2129066856","https://openalex.org/W2519845840","https://openalex.org/W2560339715","https://openalex.org/W2598326928","https://openalex.org/W2800392236","https://openalex.org/W2896518632","https://openalex.org/W2897249806","https://openalex.org/W2900387735","https://openalex.org/W2907783748","https://openalex.org/W2949177718","https://openalex.org/W2949237386","https://openalex.org/W2950372712","https://openalex.org/W2952303649","https://openalex.org/W2973166438","https://openalex.org/W2977438002","https://openalex.org/W2997591727","https://openalex.org/W3021272327","https://openalex.org/W3037520141","https://openalex.org/W3039429923","https://openalex.org/W3106188259","https://openalex.org/W3118209272","https://openalex.org/W3128290568","https://openalex.org/W3163974418","https://openalex.org/W3194569097","https://openalex.org/W3203496375","https://openalex.org/W4206795115","https://openalex.org/W4210840193","https://openalex.org/W4220837089","https://openalex.org/W4235169531","https://openalex.org/W4238363316","https://openalex.org/W4280596398","https://openalex.org/W4311125341","https://openalex.org/W4319069334","https://openalex.org/W4390064086","https://openalex.org/W4390531707","https://openalex.org/W4392007235","https://openalex.org/W4393149489","https://openalex.org/W4402186921","https://openalex.org/W4403198130","https://openalex.org/W6611373715"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2935759653","https://openalex.org/W3105167352","https://openalex.org/W54078636","https://openalex.org/W2954470139","https://openalex.org/W1501425562","https://openalex.org/W1996146322","https://openalex.org/W162612539","https://openalex.org/W1605003866","https://openalex.org/W2042539525"],"abstract_inverted_index":{"The":[0,29,95],"first-order":[1],"interactions":[2],"demonstrated":[3,97],"that":[4,70,98],"the":[5,8,12,15,32,38,83,90,99,103],"use":[6],"of":[7,14,31,41,66,86,92,118],"UMAP":[9],"method":[10],"for":[11,112,114],"generation":[13],"neighborhood":[16],"graph":[17],"and":[18,47,102],"an":[19,115],"increase":[20],"in":[21,45],"resolution":[22,33],"has":[23,81],"a":[24],"beneficial":[25],"impact":[26,30],"on":[27],"accuracy.":[28],"parameter":[34,72,121],"is":[35,60,73],"accentuated":[36],"by":[37,76],"reduced":[39],"number":[40],"nearest":[42],"neighbors,":[43],"resulting":[44],"sparser":[46],"more":[48],"locally":[49],"sensitive":[50],"graphs,":[51],"which":[52],"better":[53],"preserve":[54],"fine-grained":[55],"cellular":[56],"relationships.":[57],"Furthermore,":[58],"it":[59],"advisable":[61],"to":[62],"test":[63],"different":[64,119],"numbers":[65],"principal":[67],"components,":[68],"given":[69],"this":[71],"highly":[74],"affected":[75],"data":[77],"complexity.":[78],"This":[79],"procedure":[80],"enabled":[82],"effective":[84],"prediction":[85],"clustering":[87,120],"accuracy":[88],"through":[89],"utilization":[91],"intrinsic":[93],"metrics.":[94],"findings":[96],"within-cluster":[100],"dispersion":[101],"Banfield-Raftery":[104],"index":[105],"could":[106],"be":[107],"effectively":[108],"used":[109],"as":[110],"proxies":[111],"accuracy,":[113],"immediate":[116],"comparison":[117],"configurations.":[122]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
