{"id":"https://openalex.org/W4411747996","doi":"https://doi.org/10.1093/bib/bbaf287","title":"Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data","display_name":"Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411747996","doi":"https://doi.org/10.1093/bib/bbaf287","pmid":"https://pubmed.ncbi.nlm.nih.gov/40576031"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf287","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf287","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060127864","display_name":"Maren Hackenberg","orcid":"https://orcid.org/0000-0003-4403-634X"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Maren Hackenberg","raw_affiliation_strings":["Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,"],"affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116198018","display_name":"Laia Canal Guitart","orcid":null},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Laia Canal Guitart","raw_affiliation_strings":["Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,"],"affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]},{"id":"https://openalex.org/I297664341","display_name":"Kohler (New Zealand)","ror":"https://ror.org/02jht7h37","country_code":"NZ","type":"company","lineage":["https://openalex.org/I297664341","https://openalex.org/I4210128646"]}],"countries":["DE","NZ"],"is_corresponding":false,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg , Georges-Kohler-Allee 106, 79110 Freiburg ,","Centre for Integrative Biological Signaling Studies (CIBSS) , University of Freiburg, Sch\u00e4nzlestr. 18, 79104 Freiburg im Breisgau,"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Georges-Kohler-Allee 106, 79110 Freiburg ,","institution_ids":["https://openalex.org/I161046081","https://openalex.org/I297664341"]},{"raw_affiliation_string":"Centre for Integrative Biological Signaling Studies (CIBSS) , University of Freiburg, Sch\u00e4nzlestr. 18, 79104 Freiburg im Breisgau,","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011534196","display_name":"Harald Binder","orcid":"https://orcid.org/0000-0002-5666-8662"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Harald Binder","raw_affiliation_strings":["Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg , Sch\u00e4nzlestr. 18, 79104 Freiburg im Breisgau ,","Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,"],"affiliations":[{"raw_affiliation_string":"Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg , Sch\u00e4nzlestr. 18, 79104 Freiburg im Breisgau ,","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Freiburg Center for Data Analysis, Modeling and AI, University of Freiburg , Ernst-Zermelo-Stra\u00dfe 1, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg , Stefan-Meier-Stra\u00dfe 26, 79106 Freiburg ,","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5060127864"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13755421,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9708999991416931,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.8454936742782593},{"id":"https://openalex.org/keywords/nonlinear-dimensionality-reduction","display_name":"Nonlinear dimensionality reduction","score":0.7361074686050415},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.6456519961357117},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6077627539634705},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.602440357208252},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5946919322013855},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5661000609397888},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5634685158729553},{"id":"https://openalex.org/keywords/manifold","display_name":"Manifold (fluid mechanics)","score":0.5442273616790771},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5058757662773132},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"Principal component analysis","score":0.5010087490081787},{"id":"https://openalex.org/keywords/projection","display_name":"Projection (relational algebra)","score":0.4862143099308014},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4816840589046478},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.462247371673584},{"id":"https://openalex.org/keywords/dynamical-systems-theory","display_name":"Dynamical systems theory","score":0.4475138187408447},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.426056444644928},{"id":"https://openalex.org/keywords/synthetic-data","display_name":"Synthetic data","score":0.42401692271232605},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.4142824709415436},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3160593509674072},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.26869305968284607},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0829746425151825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08048847317695618}],"concepts":[{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.8454936742782593},{"id":"https://openalex.org/C151876577","wikidata":"https://www.wikidata.org/wiki/Q7049464","display_name":"Nonlinear dimensionality reduction","level":3,"score":0.7361074686050415},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.6456519961357117},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6077627539634705},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.602440357208252},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5946919322013855},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5661000609397888},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5634685158729553},{"id":"https://openalex.org/C529865628","wikidata":"https://www.wikidata.org/wiki/Q1790740","display_name":"Manifold (fluid mechanics)","level":2,"score":0.5442273616790771},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5058757662773132},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.5010087490081787},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.4862143099308014},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4816840589046478},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.462247371673584},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.4475138187408447},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.426056444644928},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.42401692271232605},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.4142824709415436},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3160593509674072},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26869305968284607},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0829746425151825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08048847317695618},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098405","descriptor_name":"Dimensionality Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098405","descriptor_name":"Dimensionality Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098405","descriptor_name":"Dimensionality Reduction","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf287","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40576031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40576031","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:freidok.uni-freiburg.de:268472","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/268472","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in bioinformatics. - 26, 3 (2025) , bbaf287, ISSN: 1477-4054","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12203088","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12203088","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf287","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":76,"referenced_works":["https://openalex.org/W1979283544","https://openalex.org/W2071128523","https://openalex.org/W2072319015","https://openalex.org/W2116516955","https://openalex.org/W2120575449","https://openalex.org/W2158131535","https://openalex.org/W2225156818","https://openalex.org/W2295124130","https://openalex.org/W2460637143","https://openalex.org/W2518828632","https://openalex.org/W2800392236","https://openalex.org/W2800912249","https://openalex.org/W2809365568","https://openalex.org/W2889326414","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2911279170","https://openalex.org/W2916020270","https://openalex.org/W2949067670","https://openalex.org/W2949237386","https://openalex.org/W2949272108","https://openalex.org/W2951381561","https://openalex.org/W2951444558","https://openalex.org/W2952840385","https://openalex.org/W2953852587","https://openalex.org/W2978541146","https://openalex.org/W2985298191","https://openalex.org/W2989747508","https://openalex.org/W2990138404","https://openalex.org/W2990509304","https://openalex.org/W2996274328","https://openalex.org/W3001040093","https://openalex.org/W3012143780","https://openalex.org/W3041242936","https://openalex.org/W3041869364","https://openalex.org/W3043327744","https://openalex.org/W3043574641","https://openalex.org/W3084428275","https://openalex.org/W3129866267","https://openalex.org/W3138308628","https://openalex.org/W3158064698","https://openalex.org/W3164448939","https://openalex.org/W3194520274","https://openalex.org/W3194560548","https://openalex.org/W3197209004","https://openalex.org/W4200538065","https://openalex.org/W4205861571","https://openalex.org/W4210403261","https://openalex.org/W4210587306","https://openalex.org/W4225981439","https://openalex.org/W4226162659","https://openalex.org/W4233620411","https://openalex.org/W4252782584","https://openalex.org/W4285013409","https://openalex.org/W4306750481","https://openalex.org/W4322768301","https://openalex.org/W4379521442","https://openalex.org/W4381795323","https://openalex.org/W4382447931","https://openalex.org/W4385945347","https://openalex.org/W4388207900","https://openalex.org/W4388915239","https://openalex.org/W4391824133","https://openalex.org/W4392162689","https://openalex.org/W4401586123","https://openalex.org/W4406715779","https://openalex.org/W6640963894","https://openalex.org/W6682962330","https://openalex.org/W6697018724","https://openalex.org/W6718521567","https://openalex.org/W6748124529","https://openalex.org/W6765271542","https://openalex.org/W6784024758","https://openalex.org/W6785344246","https://openalex.org/W6793943280","https://openalex.org/W6852816297"],"related_works":["https://openalex.org/W2375574759","https://openalex.org/W2383239174","https://openalex.org/W3088634662","https://openalex.org/W117517268","https://openalex.org/W3162910294","https://openalex.org/W2539700568","https://openalex.org/W1995622179","https://openalex.org/W1484111231","https://openalex.org/W4391160746","https://openalex.org/W2166963679"],"abstract_inverted_index":{"There":[0],"are":[1],"various":[2],"dimensionality":[3,114],"reduction":[4,115],"techniques":[5,44,162],"for":[6,71,142,201],"visually":[7],"inspecting":[8],"dynamical":[9,54,88,157,195],"patterns":[10,89,209],"in":[11,36,50,91,182,210],"time-series":[12,79,211],"single-cell":[13,132],"RNA-sequencing":[14],"(scRNA-seq)":[15],"data.":[16,213],"However,":[17,56],"the":[18,51,138,170,185,192],"lack":[19],"of":[20,42,53,59,160],"one-to-one":[21],"correspondence":[22],"between":[23],"cells":[24],"across":[25],"time":[26],"points":[27],"makes":[28],"it":[29],"difficult":[30],"to":[31,48,145,165,187,206],"uniquely":[32],"uncover":[33],"temporal":[34,98],"structure":[35],"a":[37,92,106,199],"low-dimensional":[38,93,148],"manifold.":[39],"The":[40,57,86],"use":[41],"different":[43,113,152,156],"may":[45,175],"thus":[46],"lead":[47],"discrepancies":[49,61,75],"representation":[52],"patterns.":[55,158],"extent":[58,147],"these":[60,161],"remains":[62],"unclear.":[63],"To":[64],"investigate":[65],"this,":[66],"we":[67],"propose":[68],"an":[69],"approach":[70,140,197],"reasoning":[72,143],"about":[73,144],"such":[74,100,117],"based":[76],"on":[77],"synthetic":[78,87,194],"scRNA-seq":[80,212],"data":[81],"generated":[82],"by":[83],"variational":[84,133],"autoencoders.":[85],"induced":[90],"manifold":[94,127],"reflect":[95],"biologically":[96],"plausible":[97],"patterns,":[99],"as":[101,118],"dividing":[102],"cell":[103],"clusters":[104],"during":[105],"differentiation":[107],"process.":[108],"We":[109,135],"consider":[110],"manifolds":[111],"from":[112,151],"techniques,":[116,153],"principal":[119],"component":[120],"analysis,":[121],"t-distributed":[122],"stochastic":[123],"neighbor":[124],"embedding,":[125],"uniform":[126],"approximation,":[128],"and":[129,131,169],"projection":[130],"inference.":[134],"illustrate":[136],"how":[137],"proposed":[139,193],"allows":[141],"what":[146],"manifolds,":[149],"obtained":[150],"can":[154],"capture":[155],"None":[159],"was":[163],"found":[164],"be":[166],"consistently":[167],"superior":[168],"results":[171],"indicate":[172],"that":[173],"they":[174],"not":[176],"reliably":[177],"represent":[178],"dynamics":[179],"when":[180],"used":[181],"isolation,":[183],"underscoring":[184],"need":[186],"compare":[188],"multiple":[189],"perspectives.":[190],"Thus,":[191],"pattern":[196],"provides":[198],"foundation":[200],"guiding":[202],"future":[203],"methods":[204],"development":[205],"detect":[207],"complex":[208]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}