{"id":"https://openalex.org/W3008782137","doi":"https://doi.org/10.1109/access.2020.2977106","title":"A Non-Negative Matrix Factorization-Based Framework for the Analysis of Multi-Class Time-Series Single-Cell RNA-Seq Data","display_name":"A Non-Negative Matrix Factorization-Based Framework for the Analysis of Multi-Class Time-Series Single-Cell RNA-Seq Data","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3008782137","doi":"https://doi.org/10.1109/access.2020.2977106","mag":"3008782137"},"language":"en","primary_location":{"id":"doi:10.1109/access.2020.2977106","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2977106","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09018223.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09018223.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004249952","display_name":"Inuk Jung","orcid":"https://orcid.org/0000-0003-0675-4244"},"institutions":[{"id":"https://openalex.org/I31419693","display_name":"Kyungpook National University","ror":"https://ror.org/040c17130","country_code":"KR","type":"education","lineage":["https://openalex.org/I31419693"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Inuk Jung","raw_affiliation_strings":["Department of Computer Science and Engineering, Kyungpook National University, Daegu, South Korea"],"raw_orcid":"https://orcid.org/0000-0003-0675-4244","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Kyungpook National University, Daegu, South Korea","institution_ids":["https://openalex.org/I31419693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080551816","display_name":"Joung Min Choi","orcid":"https://orcid.org/0000-0003-2090-3330"},"institutions":[{"id":"https://openalex.org/I31766871","display_name":"Sookmyung Women's University","ror":"https://ror.org/00vvvt117","country_code":"KR","type":"education","lineage":["https://openalex.org/I31766871"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Joungmin Choi","raw_affiliation_strings":["Department of Computer Science, Sookmyung Women\u2019s University, Seoul, South Korea","Department of Computer Science, Sookmyung Women's University, Seoul, South Korea"],"raw_orcid":"https://orcid.org/0000-0003-2090-3330","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sookmyung Women\u2019s University, Seoul, South Korea","institution_ids":["https://openalex.org/I31766871"]},{"raw_affiliation_string":"Department of Computer Science, Sookmyung Women's University, Seoul, South Korea","institution_ids":["https://openalex.org/I31766871"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101608081","display_name":"Heejoon Chae","orcid":"https://orcid.org/0000-0002-0960-5829"},"institutions":[{"id":"https://openalex.org/I31766871","display_name":"Sookmyung Women's University","ror":"https://ror.org/00vvvt117","country_code":"KR","type":"education","lineage":["https://openalex.org/I31766871"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Heejoon Chae","raw_affiliation_strings":["Department of Computer Science, Sookmyung Women\u2019s University, Seoul, South Korea","Department of Computer Science, Sookmyung Women's University, Seoul, South Korea"],"raw_orcid":"https://orcid.org/0000-0002-0960-5829","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sookmyung Women\u2019s University, Seoul, South Korea","institution_ids":["https://openalex.org/I31766871"]},{"raw_affiliation_string":"Department of Computer Science, Sookmyung Women's University, Seoul, South Korea","institution_ids":["https://openalex.org/I31766871"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2075,"currency":"USD","value_usd":2075},"apc_paid":{"value":2075,"currency":"USD","value_usd":2075},"fwci":0.2247,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.47839318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"8","issue":null,"first_page":"42342","last_page":"42348"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9584000110626221,"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/rna-seq","display_name":"RNA-Seq","score":0.5892460346221924},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5591259598731995},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5560462474822998},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5265141725540161},{"id":"https://openalex.org/keywords/snapshot","display_name":"Snapshot (computer storage)","score":0.507267415523529},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5025820732116699},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4680618345737457},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4340643882751465},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.4335383176803589},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42616602778434753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42408448457717896},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.34773892164230347},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26733118295669556}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5892460346221924},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5591259598731995},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5560462474822998},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5265141725540161},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.507267415523529},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5025820732116699},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4680618345737457},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4340643882751465},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.4335383176803589},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42616602778434753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42408448457717896},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.34773892164230347},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26733118295669556},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2020.2977106","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2977106","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09018223.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:b65ebfd2e99640c4a9da5e3ffaf06051","is_oa":true,"landing_page_url":"https://doaj.org/article/b65ebfd2e99640c4a9da5e3ffaf06051","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":"IEEE Access, Vol 8, Pp 42342-42348 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2020.2977106","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2977106","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09018223.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321272","display_name":"Kyungpook National University","ror":"https://ror.org/040c17130"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3008782137.pdf","grobid_xml":"https://content.openalex.org/works/W3008782137.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W1522301498","https://openalex.org/W1596717185","https://openalex.org/W1902027874","https://openalex.org/W1967327758","https://openalex.org/W1984883254","https://openalex.org/W2036055444","https://openalex.org/W2060724738","https://openalex.org/W2068881679","https://openalex.org/W2095705004","https://openalex.org/W2106462080","https://openalex.org/W2118258530","https://openalex.org/W2130410032","https://openalex.org/W2131263031","https://openalex.org/W2134526812","https://openalex.org/W2135029798","https://openalex.org/W2169456326","https://openalex.org/W2184331293","https://openalex.org/W2373831850","https://openalex.org/W2407916594","https://openalex.org/W2416402039","https://openalex.org/W2579728701","https://openalex.org/W2582033455","https://openalex.org/W2620352414","https://openalex.org/W2784188716","https://openalex.org/W2884607428","https://openalex.org/W6610017368","https://openalex.org/W6631190155","https://openalex.org/W6674330103","https://openalex.org/W6680012447"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4394365953"],"abstract_inverted_index":{"The":[0,140],"development":[1],"of":[2,41,133,137,144,157],"single-cell":[3,15],"RNA":[4,27],"sequencing":[5,28],"(scRNA-seq)":[6],"has":[7],"enabled":[8],"gene":[9,88,119,141,238],"expression":[10,89,120,142,241],"to":[11,21,78,92,178,233],"be":[12,93],"quantified":[13],"at":[14,65],"resolution.":[16],"Such":[17,213],"advancement":[18],"is":[19],"expected":[20],"solve":[22],"important":[23],"issues":[24],"that":[25,122,175,199],"bulk":[26],"could":[29],"not":[30],"fully":[31],"answer,":[32],"such":[33,56],"as":[34],"inferring":[35],"cell":[36,45,49,160,186,200,211],"population":[37],"heterogeneity,":[38],"genetic":[39],"variability":[40],"cells,":[42],"detecting":[43,118],"rare":[44],"types,":[46],"accurately":[47],"predicting":[48],"states":[50],"and":[51,111,155,191,215,240],"their":[52],"localization.":[53],"However,":[54],"analyzing":[55],"large":[57],"scale":[58],"data,":[59],"especially":[60],"when":[61,87],"they":[62],"are":[63,91],"sampled":[64],"multiple":[66,101],"time":[67,112],"points,":[68],"brings":[69],"new":[70],"challenges":[71],"in":[72],"data":[73,107],"mining":[74],"informative":[75],"genes,":[76],"compared":[77],"single":[79],"snapshot":[80],"samples.":[81,247],"It":[82],"becomes":[83],"even":[84],"more":[85],"complicated":[86],"patterns":[90,121,242],"mined":[94],"from":[95,100,149,219,243],"time-series":[96,130,146,245],"scRNA-seq":[97,131,147,246],"datasets":[98,132],"generated":[99],"conditions,":[102],"which":[103],"will":[104],"constitute":[105],"a":[106],"with":[108,224],"gene,":[109],"condition":[110,171],"dimensions.":[113],"Here,":[114],"we":[115,197],"focused":[116],"on":[117],"well":[123],"capture":[124],"the":[125,184,189,209,225,229],"underlying":[126],"biological":[127,236],"differences":[128],"between":[129,183,208],"three":[134,185,210],"different":[135],"types":[136,161],"stem":[138,152],"cells.":[139],"profile":[143],"2,128":[145],"samples":[148],"long-term":[150],"hematopoietic":[151],"cells":[153],"(LT-HSC)":[154],"two":[156],"its":[158],"progenitor":[159],"were":[162,176,222],"analyzed":[163],"using":[164],"our":[165,195,220],"framework.":[166],"We":[167],"have":[168],"successfully":[169,234],"detected":[170,193,218],"specific":[172],"feature":[173],"genes":[174,190,203],"able":[177,232],"achieve":[179],"90.03%":[180],"classification":[181],"accuracy":[182],"types.":[187,212],"Investigating":[188],"clusters":[192],"by":[194],"framework,":[196],"found":[198],"cycle":[201],"related":[202],"showed":[204],"significantly":[205],"high":[206],"variance":[207],"results":[214],"transcriptomic":[216],"characters":[217],"analysis":[221],"consistent":[223],"original":[226],"study.":[227],"Collectively,":[228],"framework":[230],"was":[231],"detect":[235],"meaningful":[237],"sets":[239],"multi-condition":[244]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
