{"id":"https://openalex.org/W2952877818","doi":"https://doi.org/10.1371/journal.pcbi.1003696","title":"Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells","display_name":"Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells","publication_year":2014,"publication_date":"2014-07-17","ids":{"openalex":"https://openalex.org/W2952877818","doi":"https://doi.org/10.1371/journal.pcbi.1003696","mag":"2952877818","pmid":"https://pubmed.ncbi.nlm.nih.gov/25032992"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003696","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003696","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003696&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003696&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063304924","display_name":"Andrew McDavid","orcid":"https://orcid.org/0000-0002-6581-1213"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew McDavid","raw_affiliation_strings":["Department of Statistics, University of Washington, Seattle, Washington, United States of America; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","Department of Statistics, University of Washington, Seattle, Washington, United States of America","Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071168587","display_name":"Lucas Dennis","orcid":"https://orcid.org/0000-0002-5299-8066"},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucas Dennis","raw_affiliation_strings":["NanoString Technologies, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210099129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103238929","display_name":"Patrick Danaher","orcid":"https://orcid.org/0000-0002-2844-5883"},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick Danaher","raw_affiliation_strings":["NanoString Technologies, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210099129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069196767","display_name":"Greg Finak","orcid":"https://orcid.org/0000-0003-4341-9090"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greg Finak","raw_affiliation_strings":["Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044089208","display_name":"Michael Krouse","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Krouse","raw_affiliation_strings":["NanoString Technologies, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210099129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100783314","display_name":"Alice Wang","orcid":"https://orcid.org/0000-0002-1789-8561"},"institutions":[{"id":"https://openalex.org/I4210116987","display_name":"BD Biosciences (United States)","ror":"https://ror.org/02h9td068","country_code":"US","type":"company","lineage":["https://openalex.org/I146461966","https://openalex.org/I4210116987"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alice Wang","raw_affiliation_strings":["BD Biosciences, San Jose, California, United States of America"],"affiliations":[{"raw_affiliation_string":"BD Biosciences, San Jose, California, United States of America","institution_ids":["https://openalex.org/I4210116987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108533939","display_name":"Philippa Webster","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philippa Webster","raw_affiliation_strings":["NanoString Technologies, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210099129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070065201","display_name":"Joseph Beechem","orcid":"https://orcid.org/0000-0001-8372-5899"},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Beechem","raw_affiliation_strings":["NanoString Technologies, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210099129"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005741024","display_name":"Rapha\u00ebl Gottardo","orcid":"https://orcid.org/0000-0002-3867-0232"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Raphael Gottardo","raw_affiliation_strings":["Department of Statistics, University of Washington, Seattle, Washington, United States of America; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","Department of Statistics, University of Washington, Seattle, Washington, United States of America","Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5005741024"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.1238,"has_fulltext":true,"cited_by_count":70,"citation_normalized_percentile":{"value":0.96427834,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"7","first_page":"e1003696","last_page":"e1003696"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9918000102043152,"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/cell-cycle","display_name":"Cell cycle","score":0.7099331617355347},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.6554176211357117},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.622492253780365},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.5718545913696289},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5541316270828247},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5318859219551086},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4803396463394165},{"id":"https://openalex.org/keywords/single-cell-analysis","display_name":"Single-cell analysis","score":0.43650782108306885},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.43151915073394775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36337947845458984},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3215567469596863}],"concepts":[{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.7099331617355347},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.6554176211357117},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.622492253780365},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.5718545913696289},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5541316270828247},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5318859219551086},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4803396463394165},{"id":"https://openalex.org/C2776950831","wikidata":"https://www.wikidata.org/wiki/Q15635432","display_name":"Single-cell analysis","level":3,"score":0.43650782108306885},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.43151915073394775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36337947845458984},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3215567469596863}],"mesh":[{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018816","descriptor_name":"Genes, cdc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018816","descriptor_name":"Genes, cdc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018816","descriptor_name":"Genes, cdc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1003696","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003696","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003696&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25032992","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25032992","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:figshare.com:article/1108664","is_oa":true,"landing_page_url":null,"pdf_url":"https://figshare.com/articles/dataset/_Modeling_Bi_modality_Improves_Characterization_of_Cell_Cycle_on_Gene_Expression_in_Single_Cells_/1108664","source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003696","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003696","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:f75e10c6c2c84238aa7dc9f80ad9a852","is_oa":true,"landing_page_url":"https://doaj.org/article/f75e10c6c2c84238aa7dc9f80ad9a852","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 7, p e1003696 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3074063","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4102402","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003696","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003696","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003696&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952877818.pdf","grobid_xml":"https://content.openalex.org/works/W2952877818.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1973332790","https://openalex.org/W1974858978","https://openalex.org/W1976332738","https://openalex.org/W1978319180","https://openalex.org/W1991988184","https://openalex.org/W1995830102","https://openalex.org/W1998161495","https://openalex.org/W2010824638","https://openalex.org/W2012990108","https://openalex.org/W2015457120","https://openalex.org/W2019490156","https://openalex.org/W2033457416","https://openalex.org/W2033995502","https://openalex.org/W2035951788","https://openalex.org/W2042829929","https://openalex.org/W2051331875","https://openalex.org/W2058744048","https://openalex.org/W2080205501","https://openalex.org/W2087242711","https://openalex.org/W2097360283","https://openalex.org/W2097581234","https://openalex.org/W2099618343","https://openalex.org/W2101617798","https://openalex.org/W2102158172","https://openalex.org/W2105712639","https://openalex.org/W2107665951","https://openalex.org/W2110768394","https://openalex.org/W2114390747","https://openalex.org/W2114870653","https://openalex.org/W2125179305","https://openalex.org/W2137460766","https://openalex.org/W2142460132","https://openalex.org/W2144139554","https://openalex.org/W2148541040","https://openalex.org/W2154290889","https://openalex.org/W2155372791","https://openalex.org/W2161791847","https://openalex.org/W2169187183","https://openalex.org/W2171280873","https://openalex.org/W2419024714","https://openalex.org/W3098834468","https://openalex.org/W3141065972","https://openalex.org/W4253120075","https://openalex.org/W4294541781","https://openalex.org/W6682342736"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2023641020","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2188530857","https://openalex.org/W2041199873","https://openalex.org/W1971081588","https://openalex.org/W1964194222"],"abstract_inverted_index":{"Advances":[0],"in":[1,46,53,78,208,214,233,235,278],"high-throughput,":[2],"single":[3,47,132,199,236,243,282],"cell":[4,11,19,24,40,61,133,159,164,200,226,244,250,256,267,283],"gene":[5,29,44,86,201],"expression":[6,30,45,93,134,215,245,262],"are":[7],"allowing":[8],"interrogation":[9],"of":[10,22,28,39,80,94,117,173,188,242,261,280],"heterogeneity.":[12],"However,":[13],"there":[14],"is":[15,98,109],"concern":[16],"that":[17,122,181,207,254,265],"the":[18,32,37,92,147,171,186,240,249,255,266,281],"cycle":[20,41,160,227,257,268],"phase":[21,42,67],"a":[23,76,88,141,274],"might":[25],"bias":[26],"characterizations":[27],"at":[31],"single-cell":[33,189],"level.":[34],"We":[35,63,83,191,238,252],"assess":[36],"effect":[38],"on":[43,146],"cells":[48,55],"by":[49],"measuring":[50],"333":[51],"genes":[52,97,156,177,228],"930":[54],"across":[56,162],"three":[57,60,163],"phases":[58],"and":[59,72,113,151],"lines.":[62,165],"determine":[64],"each":[65],"cell's":[66],"non-invasively":[68],"without":[69],"chemical":[70],"arrest":[71],"use":[73,152,192],"it":[74,123,153],"as":[75],"covariate":[77],"tests":[79],"differential":[81],"expression.":[82],"observe":[84],"bi-modal":[85],"expression,":[87],"previously-described":[89],"phenomenon,":[90],"wherein":[91],"otherwise":[95],"abundant":[96],"either":[99],"strongly":[100],"positive,":[101],"or":[102],"undetectable":[103],"within":[104],"individual":[105],"cells.":[106,237],"This":[107],"bi-modality":[108,187],"likely":[110],"both":[111],"biologically":[112],"technically":[114],"driven.":[115],"Irrespective":[116],"its":[118],"source,":[119],"we":[120,139],"show":[121],"should":[124],"be":[125,231,273],"modeled":[126],"to":[127,154,179,197,210,230,248,272],"draw":[128],"accurate":[129],"inferences":[130],"from":[131],"experiments.":[135],"To":[136],"this":[137],"end,":[138],"propose":[140],"semi-continuous":[142,194],"modeling":[143],"framework":[144,169,196],"based":[145],"generalized":[148],"linear":[149],"model,":[150],"characterize":[155],"with":[157],"consistent":[158],"effects":[161],"Our":[166],"new":[167],"computational":[168],"improves":[170],"detection":[172],"previously":[174],"characterized":[175],"cell-cycle":[176],"compared":[178],"approaches":[180],"do":[182],"not":[183,223,270],"account":[184],"for":[185],"data.":[190],"our":[193],"modelling":[195],"estimate":[198,239],"co-expression":[202],"networks.":[203],"These":[204],"networks":[205],"suggest":[206],"addition":[209],"having":[211],"phase-dependent":[212],"shifts":[213],"(when":[216],"averaged":[217],"over":[218],"many":[219],"cells),":[220],"some,":[221],"but":[222],"all,":[224],"canonical":[225],"tend":[229,271],"co-expressed":[232],"groups":[234],"amount":[241],"variability":[246],"attributable":[247],"cycle.":[251],"find":[253],"explains":[258],"only":[259],"5%-17%":[260],"variability,":[263],"suggesting":[264],"will":[269],"large":[275],"nuisance":[276],"factor":[277],"analysis":[279],"transcriptome.":[284]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":12}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}