{"id":"https://openalex.org/W4225926369","doi":"https://doi.org/10.1371/journal.pcbi.1009626","title":"Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies","display_name":"Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies","publication_year":2021,"publication_date":"2021-12-30","ids":{"openalex":"https://openalex.org/W4225926369","doi":"https://doi.org/10.1371/journal.pcbi.1009626","pmid":"https://pubmed.ncbi.nlm.nih.gov/34968384"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009626&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.1009626&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101682562","display_name":"Phuc Nguyen","orcid":"https://orcid.org/0000-0003-1679-723X"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phuc Nguyen","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103953534","display_name":"Sylvia Chien","orcid":null},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sylvia Chien","raw_affiliation_strings":["Division of Hematology, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Hematology, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103189403","display_name":"Jin Dai","orcid":"https://orcid.org/0000-0002-1947-7410"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin Dai","raw_affiliation_strings":["Division of Hematology, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Hematology, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061090065","display_name":"Raymond J. Monnat","orcid":"https://orcid.org/0000-0001-7638-7393"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Raymond J. Monnat","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America","Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051018931","display_name":"Pamela S. Becker","orcid":"https://orcid.org/0000-0001-6235-9463"},"institutions":[{"id":"https://openalex.org/I169071179","display_name":"Cancer Research Institute","ror":"https://ror.org/02f3xk561","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I169071179"]},{"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/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"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":"Pamela S. Becker","raw_affiliation_strings":["Chao Family Comprehensive Cancer Center Cancer Research Institute, University of California, Irvine, California, United States of America","Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","Division of Hematology, University of Washington, Seattle, Washington, United States of America","Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6235-9463","affiliations":[{"raw_affiliation_string":"Chao Family Comprehensive Cancer Center Cancer Research Institute, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I169071179","https://openalex.org/I204250578"]},{"raw_affiliation_string":"Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Division of Hematology, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079150594","display_name":"Hao Yuan Kueh","orcid":"https://orcid.org/0000-0001-6272-6673"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hao Yuan Kueh","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America","Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6272-6673","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5051018931","https://openalex.org/A5061090065","https://openalex.org/A5079150594"],"corresponding_institution_ids":["https://openalex.org/I169071179","https://openalex.org/I201448701","https://openalex.org/I204250578","https://openalex.org/I4210089486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6343,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.86721382,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"17","issue":"12","first_page":"e1009626","last_page":"e1009626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.998199999332428,"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9291999936103821,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.674958348274231},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6372607350349426},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5909302234649658},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.5594599843025208},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5181750059127808},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5070502758026123},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.4571220576763153},{"id":"https://openalex.org/keywords/unsupervised-learning","display_name":"Unsupervised learning","score":0.4568922519683838},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4391614496707916},{"id":"https://openalex.org/keywords/phenotypic-screening","display_name":"Phenotypic screening","score":0.435258150100708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.424679696559906},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4108259975910187},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30626073479652405},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1759728491306305},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.092399001121521},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08475524187088013}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.674958348274231},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6372607350349426},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5909302234649658},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.5594599843025208},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5181750059127808},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5070502758026123},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4571220576763153},{"id":"https://openalex.org/C8038995","wikidata":"https://www.wikidata.org/wiki/Q1152135","display_name":"Unsupervised learning","level":2,"score":0.4568922519683838},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4391614496707916},{"id":"https://openalex.org/C6555983","wikidata":"https://www.wikidata.org/wiki/Q7181398","display_name":"Phenotypic screening","level":4,"score":0.435258150100708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.424679696559906},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4108259975910187},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30626073479652405},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1759728491306305},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.092399001121521},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08475524187088013},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001773","descriptor_name":"Blood Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008027","descriptor_name":"Light","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008027","descriptor_name":"Light","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008027","descriptor_name":"Light","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008027","descriptor_name":"Light","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015470","descriptor_name":"Leukemia, Myeloid, Acute","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D059008","descriptor_name":"Time-Lapse Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059008","descriptor_name":"Time-Lapse Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059008","descriptor_name":"Time-Lapse Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059008","descriptor_name":"Time-Lapse Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009626&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:34968384","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34968384","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:doaj.org/article:6a86ed4571f04203a16e11a0d87ddd1e","is_oa":true,"landing_page_url":"https://doaj.org/article/6a86ed4571f04203a16e11a0d87ddd1e","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":"PLoS Computational Biology, Vol 17, Iss 12, p e1009626 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8754342","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8754342","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009626&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":[{"id":"https://openalex.org/G1515311804","display_name":null,"funder_award_id":"P30 CA015704","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G333237308","display_name":null,"funder_award_id":"R00 HL119638","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3603863188","display_name":null,"funder_award_id":"P30CA015704","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3721675486","display_name":null,"funder_award_id":"R01 HL146478","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G4140001643","display_name":null,"funder_award_id":"P30CA015704","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4389467698","display_name":null,"funder_award_id":"P01 CA077852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4563728084","display_name":null,"funder_award_id":"P01CA077852","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5392160296","display_name":null,"funder_award_id":"5R00HL119638","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5498668318","display_name":null,"funder_award_id":"R01HL146478","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5550659646","display_name":null,"funder_award_id":"R01HL146478","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6765839665","display_name":null,"funder_award_id":"P01CA077852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7912029183","display_name":null,"funder_award_id":"5R00HL119638","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320307115","display_name":"Bristol-Myers Squibb","ror":"https://ror.org/00gtmwv55"},{"id":"https://openalex.org/F4320311916","display_name":"John H. Tietze Foundation Trust","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225926369.pdf","grobid_xml":"https://content.openalex.org/works/W4225926369.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W117096852","https://openalex.org/W601258952","https://openalex.org/W1224195541","https://openalex.org/W1959608418","https://openalex.org/W1983641075","https://openalex.org/W1984270031","https://openalex.org/W1996241893","https://openalex.org/W2009886857","https://openalex.org/W2020671440","https://openalex.org/W2040568539","https://openalex.org/W2047601088","https://openalex.org/W2050845614","https://openalex.org/W2051850537","https://openalex.org/W2071010503","https://openalex.org/W2079698917","https://openalex.org/W2081409454","https://openalex.org/W2093144236","https://openalex.org/W2107554012","https://openalex.org/W2131681506","https://openalex.org/W2131935275","https://openalex.org/W2140099710","https://openalex.org/W2154112975","https://openalex.org/W2316088817","https://openalex.org/W2582033455","https://openalex.org/W2591514928","https://openalex.org/W2599354622","https://openalex.org/W2750796620","https://openalex.org/W2786672974","https://openalex.org/W2890462169","https://openalex.org/W2914570111","https://openalex.org/W2916458303","https://openalex.org/W2916620152","https://openalex.org/W2942915404","https://openalex.org/W2949493305","https://openalex.org/W2950214765","https://openalex.org/W2963373786","https://openalex.org/W2963761396","https://openalex.org/W2971686199","https://openalex.org/W2974146427","https://openalex.org/W3033098366","https://openalex.org/W3094802395","https://openalex.org/W3097417633","https://openalex.org/W3099768174","https://openalex.org/W3165467680","https://openalex.org/W4293568373","https://openalex.org/W6640963894","https://openalex.org/W6718379498","https://openalex.org/W6780248173","https://openalex.org/W7063556251"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4220926404","https://openalex.org/W2806873178","https://openalex.org/W3123344745","https://openalex.org/W2770818364","https://openalex.org/W2965146396"],"abstract_inverted_index":{"Identification":[0],"of":[1,11,133,163,170],"cell":[2,58,77,95,123,171],"phenotypic":[3,31,59],"states":[4,78,146],"within":[5],"heterogeneous":[6,127],"populations,":[7],"along":[8],"with":[9],"elucidation":[10],"their":[12,80],"switching":[13],"dynamics,":[14],"is":[15],"a":[16,52,126],"central":[17],"challenge":[18],"in":[19,125,176],"modern":[20],"biology.":[21],"Conventional":[22],"single-cell":[23],"analysis":[24],"methods":[25],"typically":[26],"provide":[27,40,51],"only":[28],"indirect,":[29],"static":[30],"readouts.":[32],"Transmitted":[33],"light":[34,84,165],"images,":[35],"on":[36],"the":[37,88,150,161],"other":[38],"hand,":[39],"direct":[41],"morphological":[42,145],"readouts":[43],"and":[44,79,108,154,174,178],"can":[45],"be":[46],"acquired":[47],"over":[48],"time":[49],"to":[50,92,153],"rich":[53],"data":[54],"source":[55],"for":[56,75,101,105,113,167],"dynamic":[57],"state":[60,102,172],"identification.":[61],"Here,":[62],"we":[63,119,141],"describe":[64],"an":[65],"end-to-end":[66],"deep":[67],"learning":[68],"platform,":[69],"UPSIDE":[70,86,158],"(Unsupervised":[71],"Phenotypic":[72],"State":[73],"IDEntification),":[74],"discovering":[76],"dynamics":[81,175],"from":[82,139,155],"transmitted":[83,164],"movies.":[85],"uses":[87],"variational":[89],"auto-encoder":[90],"architecture":[91],"learn":[93],"latent":[94],"representations,":[96],"which":[97,140],"are":[98],"then":[99,130],"clustered":[100],"identification,":[103],"decoded":[104],"feature":[106],"interpretation,":[107],"linked":[109],"across":[110],"movie":[111],"frames":[112],"transition":[114,151],"rate":[115],"inference.":[116],"Using":[117],"UPSIDE,":[118],"identified":[120,142],"distinct":[121],"blood":[122],"types":[124],"dataset.":[128],"We":[129],"analyzed":[131],"movies":[132,166],"patient-derived":[134],"acute":[135],"myeloid":[136],"leukemia":[137],"cells,":[138],"stem-cell":[143],"associated":[144],"as":[147,149],"well":[148],"rates":[152],"these":[156],"states.":[157],"opens":[159],"up":[160],"use":[162],"systematic":[168],"exploration":[169],"heterogeneity":[173],"biology":[177],"medicine.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
