{"id":"https://openalex.org/W3126704321","doi":"https://doi.org/10.1093/bib/bbaa433","title":"jSRC: a flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data","display_name":"jSRC: a flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data","publication_year":2020,"publication_date":"2020-12-28","ids":{"openalex":"https://openalex.org/W3126704321","doi":"https://doi.org/10.1093/bib/bbaa433","mag":"3126704321","pmid":"https://pubmed.ncbi.nlm.nih.gov/33535230"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa433","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa433","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":false,"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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7953970","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052243272","display_name":"Wenming Wu","orcid":"https://orcid.org/0000-0003-0892-2109"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenming Wu","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi\u2019an, 710071, China","School of Computer Science and Technology, Xidian University, Xi'an, 710071, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi\u2019an, 710071, China","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, 710071, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112227828","display_name":"Zaiyi Liu","orcid":"https://orcid.org/0000-0002-9307-8522"},"institutions":[{"id":"https://openalex.org/I4210153930","display_name":"Guangdong Provincial People's Hospital","ror":"https://ror.org/045kpgw45","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153930"]},{"id":"https://openalex.org/I4210145693","display_name":"Guangdong Academy of Medical Sciences","ror":"https://ror.org/0432p8t34","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210145693"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zaiyi Liu","raw_affiliation_strings":["Department of Radiology, Guangdong Provincial People\u2019s Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, 510080, China","Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, 510080, China"],"affiliations":[{"raw_affiliation_string":"Department of Radiology, Guangdong Provincial People\u2019s Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, 510080, China","institution_ids":["https://openalex.org/I4210145693","https://openalex.org/I4210153930"]},{"raw_affiliation_string":"Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, 510080, China","institution_ids":["https://openalex.org/I4210145693","https://openalex.org/I4210153930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029088205","display_name":"Xiaoke Ma","orcid":"https://orcid.org/0000-0002-5604-7137"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoke Ma","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi\u2019an, 710071, China","School of Computer Science and Technology, Xidian University, Xi'an, 710071, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi\u2019an, 710071, China","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, 710071, China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5029088205"],"corresponding_institution_ids":["https://openalex.org/I149594827"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.9056,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.86714144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"22","issue":"5","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":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/T11289","display_name":"Single-cell and spatial transcriptomics","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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/interpretability","display_name":"Interpretability","score":0.8623185157775879},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.8133848905563354},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7151046991348267},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7130243182182312},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5478070974349976},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49924254417419434},{"id":"https://openalex.org/keywords/rand-index","display_name":"Rand index","score":0.48550915718078613},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.47999900579452515},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4577052593231201},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4529435336589813},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42322149872779846}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8623185157775879},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8133848905563354},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7151046991348267},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7130243182182312},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5478070974349976},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49924254417419434},{"id":"https://openalex.org/C111442797","wikidata":"https://www.wikidata.org/wiki/Q7291446","display_name":"Rand index","level":3,"score":0.48550915718078613},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.47999900579452515},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4577052593231201},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4529435336589813},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42322149872779846},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":3,"locations":[{"id":"doi:10.1093/bib/bbaa433","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa433","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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33535230","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33535230","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:pubmedcentral.nih.gov:7953970","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7953970","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7953970","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7953970","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G4230207668","display_name":null,"funder_award_id":"61772394","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1759518109","https://openalex.org/W1813068103","https://openalex.org/W1967489571","https://openalex.org/W1978088258","https://openalex.org/W1979283544","https://openalex.org/W2009411635","https://openalex.org/W2025828346","https://openalex.org/W2069089843","https://openalex.org/W2120205807","https://openalex.org/W2129812935","https://openalex.org/W2146353910","https://openalex.org/W2159600984","https://openalex.org/W2164278908","https://openalex.org/W2187089797","https://openalex.org/W2193667971","https://openalex.org/W2195294260","https://openalex.org/W2286281449","https://openalex.org/W2306630387","https://openalex.org/W2307567449","https://openalex.org/W2315452447","https://openalex.org/W2523620612","https://openalex.org/W2530672181","https://openalex.org/W2559821250","https://openalex.org/W2562266966","https://openalex.org/W2598326928","https://openalex.org/W2606771561","https://openalex.org/W2609473806","https://openalex.org/W2615253071","https://openalex.org/W2736547131","https://openalex.org/W2742415671","https://openalex.org/W2747447040","https://openalex.org/W2748637762","https://openalex.org/W2750867444","https://openalex.org/W2788348358","https://openalex.org/W2792915048","https://openalex.org/W2800392236","https://openalex.org/W2885712366","https://openalex.org/W2887761828","https://openalex.org/W2890450226","https://openalex.org/W2894687190","https://openalex.org/W2896882268","https://openalex.org/W2902652978","https://openalex.org/W2905703306","https://openalex.org/W2907783748","https://openalex.org/W2928665623","https://openalex.org/W2948850940","https://openalex.org/W2949067670","https://openalex.org/W2949236943","https://openalex.org/W2949272108","https://openalex.org/W2949329924","https://openalex.org/W2949471597","https://openalex.org/W2951506174","https://openalex.org/W2952303649","https://openalex.org/W2953251392","https://openalex.org/W2971398276","https://openalex.org/W2973034691","https://openalex.org/W2973455289","https://openalex.org/W2977438002","https://openalex.org/W2982577914","https://openalex.org/W2997470228","https://openalex.org/W3001118548","https://openalex.org/W3002476014","https://openalex.org/W3003444384","https://openalex.org/W3009281473","https://openalex.org/W3014610125","https://openalex.org/W3021145032","https://openalex.org/W3024643080","https://openalex.org/W3135480207","https://openalex.org/W4235169531","https://openalex.org/W4292363360","https://openalex.org/W6773313107","https://openalex.org/W6774738330","https://openalex.org/W7052812575"],"related_works":["https://openalex.org/W2112801327","https://openalex.org/W4312201980","https://openalex.org/W1537413002","https://openalex.org/W2949329924","https://openalex.org/W4205940116","https://openalex.org/W2000077490","https://openalex.org/W4386467284","https://openalex.org/W2752973482","https://openalex.org/W4319303001","https://openalex.org/W2032713750"],"abstract_inverted_index":{"Single-cell":[0],"RNA-sequencing":[1],"(scRNA-seq)":[2],"explores":[3],"the":[4,16,59,91,104,113,122,130,149,154,170,175],"transcriptome":[5],"of":[6,20,57,64,115,140,156,172,177,199,235],"genes":[7],"at":[8],"cell":[9,21,44,230],"level,":[10],"which":[11],"sheds":[12],"light":[13],"on":[14,135],"revealing":[15],"heterogeneity":[17],"and":[18,38,46,62,87,95,106,146,164,215,240,256],"dynamics":[19],"populations.":[22],"Advances":[23],"in":[24,197],"biotechnologies":[25],"make":[26],"it":[27],"possible":[28],"to":[29,42,55,152,168,183,246],"generate":[30],"scRNA-seq":[31,141,159,219,248],"profiles":[32],"for":[33,103,259],"large-scale":[34],"cells,":[35],"requiring":[36],"effective":[37,244],"efficient":[39,214],"clustering":[40,56,88,96,139],"algorithms":[41,66],"identify":[43],"types":[45,231],"informative":[47],"genes.":[48],"Although":[49],"great":[50],"efforts":[51],"have":[52,125],"been":[53],"devoted":[54],"scRNA-seq,":[58],"accuracy,":[60],"scalability":[61,105],"interpretability":[63,114],"available":[65],"are":[67,97,166],"not":[68],"desirable.":[69],"In":[70],"this":[71],"study,":[72],"we":[73,117],"solve":[74],"these":[75],"problems":[76],"by":[77,205],"developing":[78],"a":[79],"joint":[80,107],"learning":[81,108],"algorithm":[82],"[a.k.a.":[83],"joints":[84],"sparse":[85,131],"representation":[86,132],"(jSRC)],":[89],"where":[90,129,174],"dimension":[92],"reduction":[93],"(DR)":[94],"integrated.":[98],"Specifically,":[99],"DR":[100],"is":[101,133,213,252,257],"employed":[102],"improves":[109],"accuracy.":[110],"To":[111],"increase":[112],"patterns,":[116,128],"assume":[118],"that":[119,190],"cells":[120,179],"within":[121],"same":[123],"type":[124],"similar":[126],"expression":[127],"imposed":[134],"features.":[136],"We":[137],"transform":[138],"into":[142],"an":[143,243],"optimization":[144],"problem":[145],"then":[147],"derive":[148],"update":[150],"rules":[151],"optimize":[153],"objective":[155],"jSRC.":[157],"Fifteen":[158],"datasets":[160,220],"from":[161,181,221],"various":[162,200,222],"tissues":[163],"organisms":[165],"adopted":[167],"validate":[169],"performance":[171],"jSRC,":[173],"number":[176],"single":[178],"varies":[180],"49":[182],"110":[184],"824.":[185],"The":[186,237],"experimental":[187],"results":[188],"demonstrate":[189],"jSRC":[191,212,225],"significantly":[192],"outperforms":[193],"12":[194],"state-of-the-art":[195],"methods":[196,241],"terms":[198],"measurements":[201],"(on":[202],"average":[203],"20.29%":[204],"improvement)":[206],"with":[207,233],"fewer":[208],"running":[209],"time.":[210],"Furthermore,":[211],"robust":[216],"across":[217],"different":[218],"tissues.":[223],"Finally,":[224],"also":[226],"accurately":[227],"identifies":[228],"dynamic":[229],"associated":[232],"progression":[234],"COVID-19.":[236],"proposed":[238],"model":[239],"provide":[242],"strategy":[245],"analyze":[247],"data":[249],"(the":[250],"software":[251],"coded":[253],"using":[254],"MATLAB":[255],"free":[258],"academic":[260],"purposes;":[261],"https://github.com/xkmaxidian/jSRC).":[262]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}