{"id":"https://openalex.org/W4402661591","doi":"https://doi.org/10.1186/s12859-024-05926-z","title":"Leveraging gene correlations in single cell transcriptomic data","display_name":"Leveraging gene correlations in single cell transcriptomic data","publication_year":2024,"publication_date":"2024-09-18","ids":{"openalex":"https://openalex.org/W4402661591","doi":"https://doi.org/10.1186/s12859-024-05926-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/39294560"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05926-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05926-z","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05926-z.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05926-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035687299","display_name":"Kai Silkwood","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kai Silkwood","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031089317","display_name":"Emmanuel Dollinger","orcid":"https://orcid.org/0000-0002-2562-7980"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emmanuel Dollinger","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","Department of Mathematics, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Mathematics, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063354415","display_name":"Joshua Gervin","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Gervin","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091529238","display_name":"Scott X. Atwood","orcid":"https://orcid.org/0000-0001-7407-9792"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Atwood","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076311980","display_name":"Qing Nie","orcid":"https://orcid.org/0000-0002-8804-3368"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qing Nie","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","Department of Mathematics, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Mathematics, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030125759","display_name":"Arthur D. Lander","orcid":"https://orcid.org/0000-0002-4380-5525"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arthur D. Lander","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA. adlander@uci.edu","Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. adlander@uci.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA. adlander@uci.edu","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. adlander@uci.edu","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5030125759"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":2890,"currency":"USD","value_usd":2890},"apc_paid":{"value":2890,"currency":"USD","value_usd":2890},"fwci":1.0915,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.76306243,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"25","issue":"1","first_page":"305","last_page":"305"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9980999827384949,"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":0.9980999827384949,"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":0.0005000000237487257,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6604098081588745},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5336241126060486},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5024471282958984},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48309993743896484},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.459220826625824},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.45797109603881836},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.45774194598197937},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.35844892263412476},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35448306798934937},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24360397458076477},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22037750482559204},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12120813131332397}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6604098081588745},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5336241126060486},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5024471282958984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48309993743896484},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.459220826625824},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.45797109603881836},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.45774194598197937},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.35844892263412476},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35448306798934937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24360397458076477},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22037750482559204},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12120813131332397},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"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":"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":"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":"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":"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":"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":"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":"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":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-05926-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05926-z","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05926-z.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39294560","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39294560","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11411778","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11411778","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11411778/pdf/12859_2024_Article_5926.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:1c805c6f0a6e47c8a01756342320121c","is_oa":true,"landing_page_url":"https://doaj.org/article/1c805c6f0a6e47c8a01756342320121c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-43 (2024)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt15k712w5","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/15k712w5","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"BMC Bioinformatics, vol 25, iss 1","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05926-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05926-z","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05926-z.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1457823048","display_name":"Mathematical, Computational and Systems Biology","funder_award_id":"5t32gm136624-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4029146187","display_name":null,"funder_award_id":"T32GM136624","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G551278461","display_name":null,"funder_award_id":"U54 CA217378","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5805402537","display_name":null,"funder_award_id":"P30 AR075047","funder_id":"https://openalex.org/F4320337362","funder_display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases"},{"id":"https://openalex.org/G6840471226","display_name":"NSF-Simons Center for Multiscale Cell Fate Research","funder_award_id":"1763272","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7049559338","display_name":"Skin Biology Resource-Based Center at UCI","funder_award_id":"2p30ar075047-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7296013183","display_name":"Project 2: Understanding the Cellular Origins of Melanoma","funder_award_id":"5u54ca217378-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337362","display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","ror":"https://ror.org/006zn3t30"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402661591.pdf","grobid_xml":"https://content.openalex.org/works/W4402661591.grobid-xml"},"referenced_works_count":97,"referenced_works":["https://openalex.org/W276006551","https://openalex.org/W1813068103","https://openalex.org/W1951808778","https://openalex.org/W1976714996","https://openalex.org/W1981095308","https://openalex.org/W1984429906","https://openalex.org/W1984689597","https://openalex.org/W2002065472","https://openalex.org/W2003499939","https://openalex.org/W2006489188","https://openalex.org/W2018433132","https://openalex.org/W2018435536","https://openalex.org/W2018864252","https://openalex.org/W2020232110","https://openalex.org/W2023444927","https://openalex.org/W2097242011","https://openalex.org/W2098509290","https://openalex.org/W2102289460","https://openalex.org/W2107342968","https://openalex.org/W2108208689","https://openalex.org/W2110065044","https://openalex.org/W2111882541","https://openalex.org/W2116470416","https://openalex.org/W2123106337","https://openalex.org/W2130410032","https://openalex.org/W2140071472","https://openalex.org/W2158217645","https://openalex.org/W2181255501","https://openalex.org/W2278675766","https://openalex.org/W2286142055","https://openalex.org/W2297912038","https://openalex.org/W2471523968","https://openalex.org/W2473258837","https://openalex.org/W2519117646","https://openalex.org/W2559516379","https://openalex.org/W2589000475","https://openalex.org/W2626149768","https://openalex.org/W2734442787","https://openalex.org/W2767394894","https://openalex.org/W2771918070","https://openalex.org/W2775435647","https://openalex.org/W2788837643","https://openalex.org/W2793370606","https://openalex.org/W2794480084","https://openalex.org/W2797906965","https://openalex.org/W2900387735","https://openalex.org/W2904997010","https://openalex.org/W2925075625","https://openalex.org/W2949275240","https://openalex.org/W2952027905","https://openalex.org/W2953405766","https://openalex.org/W2956840440","https://openalex.org/W2965087092","https://openalex.org/W2979981308","https://openalex.org/W2996988556","https://openalex.org/W2997280954","https://openalex.org/W3001905890","https://openalex.org/W3017924613","https://openalex.org/W3041479271","https://openalex.org/W3041832488","https://openalex.org/W3045439564","https://openalex.org/W3046906716","https://openalex.org/W3093153369","https://openalex.org/W3104081055","https://openalex.org/W3119507732","https://openalex.org/W3120767723","https://openalex.org/W3126694418","https://openalex.org/W3128610319","https://openalex.org/W3132661792","https://openalex.org/W3142508408","https://openalex.org/W3164156820","https://openalex.org/W3196992636","https://openalex.org/W3202649987","https://openalex.org/W3203496375","https://openalex.org/W3208953781","https://openalex.org/W3213087815","https://openalex.org/W4205496949","https://openalex.org/W4206384630","https://openalex.org/W4206920504","https://openalex.org/W4210830253","https://openalex.org/W4224290465","https://openalex.org/W4225343266","https://openalex.org/W4281663889","https://openalex.org/W4285728106","https://openalex.org/W4288042632","https://openalex.org/W4289335819","https://openalex.org/W4291201938","https://openalex.org/W4291804529","https://openalex.org/W4301730562","https://openalex.org/W4303521024","https://openalex.org/W4308132330","https://openalex.org/W4310073528","https://openalex.org/W4360999291","https://openalex.org/W4380370818","https://openalex.org/W4391168988","https://openalex.org/W4403422749","https://openalex.org/W6767675789"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2132561013","https://openalex.org/W2144348650","https://openalex.org/W1994852842","https://openalex.org/W4246178523"],"abstract_inverted_index":{"BACKGROUND:":[0],"Many":[1],"approaches":[2],"have":[3],"been":[4],"developed":[5],"to":[6,98,186,240],"overcome":[7],"technical":[8],"noise":[9,101],"in":[10,70,181],"single":[11],"cell":[12,23,27,93,144,193,220],"RNA-sequencing":[13],"(scRNAseq).":[14],"As":[15],"researchers":[16],"dig":[17],"deeper":[18],"into":[19,205,226],"data-looking":[20],"for":[21,39,62,125,140,143],"rare":[22],"types,":[24],"subtleties":[25],"of":[26,31,198,243],"states,":[28],"and":[29,44,49,108,146,152,168,213,216],"details":[30],"gene":[32,206,229],"regulatory":[33,230],"networks-there":[34],"is":[35,54,77],"a":[36,189,236],"growing":[37],"need":[38],"algorithms":[40],"with":[41,132,209],"controllable":[42],"accuracy":[43],"fewer":[45],"ad":[46],"hoc":[47],"parameters":[48],"thresholds.":[50],"Impeding":[51],"this":[52,84,160],"goal":[53],"the":[55,241],"fact":[56],"that":[57,88,121,159],"an":[58,137],"appropriate":[59],"null":[60],"distribution":[61],"scRNAseq":[63,89,116,182],"cannot":[64],"simply":[65],"be":[66,233],"extracted":[67],"from":[68,171,188],"data":[69,90,117,187],"which":[71,162],"ground":[72],"truth":[73],"about":[74],"biological":[75,214,221],"variation":[76],"unknown":[78],"(i.e.,":[79,111],"usually).":[80],"RESULTS:":[81],"We":[82,114,135],"approach":[83,239],"problem":[85],"analytically,":[86],"assuming":[87],"reflect":[91],"only":[92],"heterogeneity":[94],"(what":[95],"we":[96,157,163,195],"seek":[97],"characterize),":[99],"transcriptional":[100],"(temporal":[102],"fluctuations":[103],"randomly":[104],"distributed":[105],"across":[106],"cells),":[107],"sampling":[109],"error":[110],"Poisson":[112],"noise).":[113],"analyze":[115],"without":[118,203],"normalization-a":[119],"step":[120],"skews":[122],"distributions,":[123],"particularly":[124],"sparse":[126],"data-and":[127],"calculate":[128],"p":[129],"values":[130],"associated":[131],"key":[133],"statistics.":[134],"develop":[136],"improved":[138],"method":[139],"selecting":[141],"features":[142],"clustering":[145],"identifying":[147],"gene-gene":[148,244],"correlations,":[149],"both":[150],"positive":[151],"negative.":[153],"Using":[154],"simulated":[155],"data,":[156],"show":[158],"method,":[161],"call":[164],"BigSur":[165,185],"(Basic":[166],"Informatics":[167],"Gene":[169],"Statistics":[170],"Unnormalized":[172],"Reads),":[173],"captures":[174],"even":[175],"weak":[176],"yet":[177],"significant":[178],"correlation":[179],"structures":[180],"data.":[183],"Applying":[184],"clonal":[190],"human":[191],"melanoma":[192],"line,":[194],"identify":[196],"thousands":[197],"correlations":[199],"that,":[200],"when":[201],"clustered":[202],"supervision":[204],"communities,":[207],"align":[208],"known":[210],"cellular":[211],"components":[212],"processes,":[215],"highlight":[217],"potentially":[218],"novel":[219],"relationships.":[222],"CONCLUSIONS:":[223],"New":[224],"insights":[225],"functionally":[227],"relevant":[228],"networks":[231],"can":[232],"obtained":[234],"using":[235],"statistically":[237],"grounded":[238],"identification":[242],"correlations.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}