{"id":"https://openalex.org/W4391385140","doi":"https://doi.org/10.1214/23-aoas1761","title":"RZiMM-scRNA: A regularized zero-inflated mixture model framework for single-cell RNA-seq data","display_name":"RZiMM-scRNA: A regularized zero-inflated mixture model framework for single-cell RNA-seq data","publication_year":2024,"publication_date":"2024-01-31","ids":{"openalex":"https://openalex.org/W4391385140","doi":"https://doi.org/10.1214/23-aoas1761"},"language":"en","primary_location":{"id":"doi:10.1214/23-aoas1761","doi":"https://doi.org/10.1214/23-aoas1761","is_oa":false,"landing_page_url":"https://doi.org/10.1214/23-aoas1761","pdf_url":null,"source":{"id":"https://openalex.org/S112778392","display_name":"The Annals of Applied Statistics","issn_l":"1932-6157","issn":["1932-6157","1941-7330"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","cwts-core","dongbi-c","doyens","jufo-3","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319881","host_organization_name":"Institute of Mathematical Statistics","host_organization_lineage":["https://openalex.org/P4310319881"],"host_organization_lineage_names":["Institute of Mathematical Statistics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Annals of Applied Statistics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2110.12964","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049572543","display_name":"Xinlei Mi","orcid":"https://orcid.org/0000-0002-2966-3217","observed_orcids":["https://orcid.org/0000-0002-2966-3217"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinlei Mi","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091254294","display_name":"William Bekerman","orcid":"https://orcid.org/0000-0002-6957-6863","observed_orcids":["https://orcid.org/0000-0002-6957-6863"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Bekerman","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023539776","display_name":"Anil K. Rustgi","orcid":"https://orcid.org/0000-0002-6439-6919","observed_orcids":["https://orcid.org/0000-0002-6439-6919"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anil K. Rustgi","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066080208","display_name":"Peter A. Sims","orcid":"https://orcid.org/0000-0002-3921-4837","observed_orcids":["https://orcid.org/0000-0002-3921-4837"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter A. Sims","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046673359","display_name":"Peter Canoll","orcid":"https://orcid.org/0000-0002-7001-0226","observed_orcids":["https://orcid.org/0000-0002-7001-0226"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D. Canoll","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100781688","display_name":"Jianhua Hu","orcid":"https://orcid.org/0000-0002-3306-6722","observed_orcids":["https://orcid.org/0000-0002-3306-6722","https://orcid.org/0000-0002-0773-9348"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianhua Hu","raw_affiliation_strings":["Department of Biostatistics, Columbia University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":null,"apc_paid":null,"fwci":0.5914,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.57000629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"18","issue":"1","first_page":"1","last_page":"22"},"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":0.0,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.9079999923706055},{"id":"https://openalex.org/keywords/cell-clustering","display_name":"cell clustering","score":0.6330000162124634},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.8009999990463257},{"id":"https://openalex.org/keywords/dropout-rates","display_name":"dropout rates","score":0.7110000252723694},{"id":"https://openalex.org/keywords/batch-effects","display_name":"batch effects","score":0.9940000176429749},{"id":"https://openalex.org/keywords/cell-heterogeneity","display_name":"cellular heterogeneity","score":0.8180000185966492},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"biomarker discovery","score":0.7739999890327454},{"id":"https://openalex.org/keywords/glioblastoma","display_name":"glioblastoma","score":0.9100000262260437},{"id":"https://openalex.org/keywords/astrocytoma","display_name":"astrocytoma","score":0.9509999752044678},{"id":"https://openalex.org/keywords/brain-tumors","display_name":"brain tumors","score":0.5040000081062317},{"id":"https://openalex.org/keywords/camk2b","display_name":"CAMK2B","score":0.6859999895095825}],"concepts":[{"id":"https://openalex.org/C2780813799","wikidata":"https://www.wikidata.org/wiki/Q3274237","display_name":"Zero (linguistics)","level":2,"score":0.5174658894538879},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.4721802771091461},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4112219214439392},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3984617590904236},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.39605265855789185},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3353230059146881},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.1193922758102417},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.10098659992218018}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1214/23-aoas1761","doi":"https://doi.org/10.1214/23-aoas1761","is_oa":false,"landing_page_url":"https://doi.org/10.1214/23-aoas1761","pdf_url":null,"source":{"id":"https://openalex.org/S112778392","display_name":"The Annals of Applied Statistics","issn_l":"1932-6157","issn":["1932-6157","1941-7330"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","cwts-core","dongbi-c","doyens","jufo-3","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319881","host_organization_name":"Institute of Mathematical Statistics","host_organization_lineage":["https://openalex.org/P4310319881"],"host_organization_lineage_names":["Institute of Mathematical Statistics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Annals of Applied Statistics","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2110.12964","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2110.12964","pdf_url":"https://arxiv.org/pdf/2110.12964","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2110.12964","doi":"https://doi.org/10.48550/arxiv.2110.12964","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2110.12964","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2110.12964","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2110.12964","pdf_url":"https://arxiv.org/pdf/2110.12964","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6240000128746033,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1619152892","display_name":"Mechanisms of Esophageal Carcinogenesis","funder_award_id":"P01CA098101","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6903084428","display_name":"Novel analysis of association between microbiome and treatment infection in AML","funder_award_id":"R01AI143886","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000916142","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA013696","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391385140.pdf","grobid_xml":"https://content.openalex.org/works/W4391385140.grobid-xml"},"referenced_works_count":85,"referenced_works":["https://openalex.org/W101836494","https://openalex.org/W116844149","https://openalex.org/W1505314979","https://openalex.org/W1540655326","https://openalex.org/W1544991924","https://openalex.org/W1579416850","https://openalex.org/W1813068103","https://openalex.org/W1941492958","https://openalex.org/W1966896038","https://openalex.org/W1970667811","https://openalex.org/W1974063010","https://openalex.org/W1987971958","https://openalex.org/W1988391018","https://openalex.org/W1999574084","https://openalex.org/W2004598677","https://openalex.org/W2011477876","https://openalex.org/W2035829209","https://openalex.org/W2050031210","https://openalex.org/W2063623990","https://openalex.org/W2067530950","https://openalex.org/W2068767807","https://openalex.org/W2068881679","https://openalex.org/W2079516663","https://openalex.org/W2081451334","https://openalex.org/W2085994329","https://openalex.org/W2086277161","https://openalex.org/W2087708981","https://openalex.org/W2089510792","https://openalex.org/W2107665951","https://openalex.org/W2118258530","https://openalex.org/W2141817630","https://openalex.org/W2149691534","https://openalex.org/W2152692691","https://openalex.org/W2173732482","https://openalex.org/W2292721147","https://openalex.org/W2316095770","https://openalex.org/W2324487575","https://openalex.org/W2409157550","https://openalex.org/W2507161011","https://openalex.org/W2526187074","https://openalex.org/W2534463354","https://openalex.org/W2598326928","https://openalex.org/W2603523955","https://openalex.org/W2605152472","https://openalex.org/W2607278153","https://openalex.org/W2612502013","https://openalex.org/W2620943949","https://openalex.org/W2740711073","https://openalex.org/W2783187175","https://openalex.org/W2783644856","https://openalex.org/W2790003308","https://openalex.org/W2791380365","https://openalex.org/W2791403841","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2806548241","https://openalex.org/W2809588124","https://openalex.org/W2882972013","https://openalex.org/W2883808647","https://openalex.org/W2902634143","https://openalex.org/W2905317377","https://openalex.org/W2907783748","https://openalex.org/W2917173367","https://openalex.org/W2942659065","https://openalex.org/W2947761852","https://openalex.org/W2951638683","https://openalex.org/W2952303649","https://openalex.org/W2955621471","https://openalex.org/W2959736753","https://openalex.org/W2960663647","https://openalex.org/W2968607401","https://openalex.org/W2974352293","https://openalex.org/W2974646711","https://openalex.org/W2977083349","https://openalex.org/W2979541460","https://openalex.org/W2984698492","https://openalex.org/W2985422085","https://openalex.org/W3007113358","https://openalex.org/W3007573310","https://openalex.org/W3080730578","https://openalex.org/W3088048367","https://openalex.org/W3089531905","https://openalex.org/W3134771351","https://openalex.org/W4235169531","https://openalex.org/W4248081355"],"related_works":["https://openalex.org/W4386609690","https://openalex.org/W3005815617","https://openalex.org/W3126694418","https://openalex.org/W7162773748","https://openalex.org/W4409211490","https://openalex.org/W2980819072","https://openalex.org/W4375853972","https://openalex.org/W3022825011","https://openalex.org/W3108294659","https://openalex.org/W2937917790"],"abstract_inverted_index":{"Applications":[0],"of":[1,30,49,110,154,169,176,205,247],"single-cell":[2],"RNA":[3],"sequencing":[4],"in":[5,104,213,231,255,261],"various":[6,170],"biomedical":[7,214],"research":[8],"areas":[9],"have":[10],"been":[11],"blooming.":[12],"This":[13],"new":[14,225],"technology":[15],"provides":[16],"unprecedented":[17],"opportunities":[18],"to":[19,76,141,186],"study":[20],"disease":[21],"heterogeneity":[22,189],"at":[23],"the":[24,47,108,152,173,232,242],"cellular":[25],"level.":[26],"However,":[27],"unique":[28],"characteristics":[29],"scRNA-seq":[31,73],"data,":[32],"including":[33,119,172,235],"large":[34],"dimensionality,":[35],"high":[36],"dropout":[37],"rates,":[38],"and":[39,81,96,112,123,135,190,238,244,257,259,266],"possibly":[40],"batch":[41,97],"effects,":[42],"bring":[43],"great":[44],"difficulty":[45],"into":[46],"analysis":[48],"such":[50],"data.":[51],"Not":[52],"appropriately":[53],"addressing":[54],"these":[55,196],"issues":[56],"obstructs":[57],"true":[58],"scientific":[59],"discovery.":[60],"Herein":[61],"we":[62,106],"propose":[63],"a":[64,88,202],"unified":[65],"Regularized":[66],"Zero-inflated":[67],"Mixture":[68],"Model":[69],"framework,":[70],"designed":[71],"for":[72,93],"data":[74],"(RZiMM-scRNA),":[75],"simultaneously":[77],"detect":[78],"cell":[79,146,188],"subgroups":[80,147],"identify":[82,191],"gene":[83],"differential":[84],"expression":[85],"based":[86],"on":[87,161,216],"developed":[89],"importance":[90],"score,":[91],"accounting":[92],"both":[94],"dropouts":[95],"effects.":[98],"We":[99],"conduct":[100],"extensive":[101],"simulation":[102],"studies":[103,165],"which":[105,208,227,252],"evaluate":[107],"performance":[109,134],"RZiMM-scRNA":[111,130],"compare":[113],"it":[114],"with":[115,167,195,241],"several":[116,224],"popular":[117],"methods,":[118,143],"Seurat,":[120],"SC3,":[121],"K-means,":[122],"hierarchical":[124],"clustering.":[125],"Simulation":[126],"results":[127],"show":[128],"that":[129],"demonstrates":[131],"superior":[132],"clustering":[133],"enhanced":[136],"biomarker":[137],"detection":[138],"accuracy,":[139],"compared":[140],"alternative":[142],"especially":[144],"when":[145],"are":[148,228],"less":[149],"distinct,":[150],"verifying":[151],"robustness":[153],"our":[155,221],"method.":[156],"Our":[157,183],"empirical":[158],"investigations":[159],"focus":[160],"two":[162],"brain":[163,178,217,263],"tumor":[164],"dealing":[166],"astrocytoma":[168],"grades,":[171],"most":[174],"malignant":[175,245],"all":[177],"tumors,":[179],"glioblastoma":[180],"multiforme":[181],"(GBM).":[182],"goal":[184],"is":[185,253],"delineate":[187],"driving":[192],"biomarkers":[193,226],"associated":[194,240],"tumors.":[197],"Notably,":[198],"RZiMM-scNRA":[199],"successfully":[200],"identifies":[201],"small":[203],"group":[204],"oligodendrocyte":[206],"cells,":[207],"has":[209],"drawn":[210],"much":[211],"attention":[212],"literature":[215],"cancers.":[218],"In":[219],"addition,":[220],"method":[222],"discovers":[223],"not":[229],"discussed":[230],"original":[233],"studies,":[234],"PLP1,":[236],"BCAN,":[237],"PTPRZ1\u2014all":[239],"development":[243],"growth":[246],"glioma\u2014as":[248],"well":[249],"as":[250],"CAMK2B,":[251],"downregulated":[254],"glioma":[256],"GBM":[258],"implicated":[260],"neurodevelopment,":[262],"function,":[264],"learning":[265],"memory":[267],"processes.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2024-02-01T00:00:00"}