{"id":"https://openalex.org/W3203219085","doi":"https://doi.org/10.1186/s12859-021-04385-0","title":"A targeted solution for estimating the cell-type composition of bulk samples","display_name":"A targeted solution for estimating the cell-type composition of bulk samples","publication_year":2021,"publication_date":"2021-09-26","ids":{"openalex":"https://openalex.org/W3203219085","doi":"https://doi.org/10.1186/s12859-021-04385-0","mag":"3203219085","pmid":"https://pubmed.ncbi.nlm.nih.gov/34565346"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04385-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04385-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04385-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04385-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019911642","display_name":"Edwin J. C. G. van den Oord","orcid":"https://orcid.org/0000-0003-2701-4405"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edwin J. C. G. van den Oord","raw_affiliation_strings":["Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101487016","display_name":"Lin Xie","orcid":"https://orcid.org/0000-0001-5425-1356"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Y. Xie","raw_affiliation_strings":["Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005757002","display_name":"Charles J. Tran","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles J. Tran","raw_affiliation_strings":["Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101595055","display_name":"Min Zhao","orcid":"https://orcid.org/0000-0001-8382-3050"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Min Zhao","raw_affiliation_strings":["Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049988542","display_name":"Karolina A. \u00c5berg","orcid":"https://orcid.org/0000-0001-6103-5168"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Karolina A. Aberg","raw_affiliation_strings":["Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA. kaaberg@vcu.edu","Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA"],"raw_orcid":"https://orcid.org/0000-0001-6103-5168","affiliations":[{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA. kaaberg@vcu.edu","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049988542"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6514,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67369579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"462","last_page":"462"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.2721000015735626,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.2721000015735626,"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":0.25679999589920044,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.09889999777078629,"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/estimator","display_name":"Estimator","score":0.7759851217269897},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.6991958618164062},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.6495686173439026},{"id":"https://openalex.org/keywords/standard-deviation","display_name":"Standard deviation","score":0.6280224919319153},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.4921109080314636},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.450567364692688},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4428614377975464},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.4171140491962433},{"id":"https://openalex.org/keywords/type-i-and-type-ii-errors","display_name":"Type I and type II errors","score":0.4137556552886963},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3893952965736389},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.2224874198436737},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1896991729736328},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08940666913986206},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07767277956008911}],"concepts":[{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.7759851217269897},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.6991958618164062},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.6495686173439026},{"id":"https://openalex.org/C22679943","wikidata":"https://www.wikidata.org/wiki/Q159375","display_name":"Standard deviation","level":2,"score":0.6280224919319153},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.4921109080314636},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.450567364692688},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4428614377975464},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.4171140491962433},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.4137556552886963},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3893952965736389},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.2224874198436737},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1896991729736328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08940666913986206},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07767277956008911},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04385-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04385-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04385-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34565346","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34565346","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5c00df12d99840e9bb04d3d5e34fa68f","is_oa":true,"landing_page_url":"https://doaj.org/article/5c00df12d99840e9bb04d3d5e34fa68f","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":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-9 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7367142","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8474864","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8474864","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8474864","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04385-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04385-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04385-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1099972009","display_name":null,"funder_award_id":"R01MH104576","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G7504826364","display_name":null,"funder_award_id":"R01MH109525","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3203219085.pdf","grobid_xml":"https://content.openalex.org/works/W3203219085.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1967937330","https://openalex.org/W1985987855","https://openalex.org/W2029033394","https://openalex.org/W2065355024","https://openalex.org/W2104142691","https://openalex.org/W2113611401","https://openalex.org/W2127829299","https://openalex.org/W2137605677","https://openalex.org/W2155388222","https://openalex.org/W2169556367","https://openalex.org/W2170551349","https://openalex.org/W2523620612","https://openalex.org/W2579184152","https://openalex.org/W2735049306","https://openalex.org/W2772142671","https://openalex.org/W2792843627","https://openalex.org/W2798933487","https://openalex.org/W2919386822","https://openalex.org/W2949548034","https://openalex.org/W2952240309","https://openalex.org/W2989382642","https://openalex.org/W2990893338","https://openalex.org/W3008983522"],"related_works":["https://openalex.org/W2995118009","https://openalex.org/W2786748503","https://openalex.org/W2011298649","https://openalex.org/W1966203981","https://openalex.org/W1919212819","https://openalex.org/W2077117870","https://openalex.org/W3201428053","https://openalex.org/W2070136414","https://openalex.org/W2188658106","https://openalex.org/W2329496086"],"abstract_inverted_index":{"BACKGROUND:":[0],"To":[1],"avoid":[2],"false-positive":[3,186],"findings":[4,187],"and":[5,12,74,101,135,158,188,202],"detect":[6],"cell-type":[7,41,77,167,193,208],"specific":[8,194],"associations":[9],"in":[10,169,178],"methylation":[11,49],"transcription":[13],"investigations":[14],"with":[15,57],"bulk":[16,170],"samples,":[17],"it":[18],"is":[19,99,129,198],"critical":[20],"to":[21,206],"know":[22],"the":[23,26,63,68,72,75,82,89,97,102,106,113,117,122,149,182],"proportions":[24,42,78,168,209],"of":[25,40,105,116,132,184,192],"major":[27],"cell-types.":[28],"RESULTS:":[29],"We":[30],"present":[31],"a":[32,45,130],"novel":[33],"approach":[34,150,164,197],"that":[35,96,148,154],"allows":[36,172],"for":[37,66,165,173,190,210],"precise":[38],"estimation":[39],"using":[43,62],"only":[44],"few":[46],"highly":[47,159],"informative":[48],"markers.":[50],"The":[51,196],"most":[52],"reliable":[53,152],"estimates":[54,83,107,118,153],"were":[55,79,84],"obtained":[56],"17":[58],"amplicons":[59],"(34":[60],"CpGs)":[61],"MuSiC":[64],"estimator,":[65],"which":[67,128,177],"average":[69],"correlations":[70],"between":[71],"estimated":[73],"true":[76,90],"0.889.":[80],"Furthermore,":[81],"not":[85],"significantly":[86],"different":[87],"from":[88],"values":[91],"(P":[92],"=":[93,141],"0.95)":[94],"indicating":[95],"estimator":[98],"unbiased":[100,157],"standard":[103],"deviation":[104],"further":[108],"indicate":[109,147],"high":[110],"precision.":[111],"Moreover,":[112],"overall":[114],"variability":[115],"as":[119],"measured":[120],"by":[121],"Root":[123],"Mean":[124],"Squared":[125],"Error":[126],"(RMSE),":[127],"function":[131],"both":[133,156],"bias":[134],"precision,":[136],"was":[137],"low":[138],"(mean":[139],"RMSE":[140],"0.038).":[142],"Taken":[143],"together,":[144],"these":[145],"results":[146],"produced":[151],"are":[155],"precise.":[160],"CONCLUSION:":[161],"This":[162],"cost-effective":[163],"estimating":[166],"samples":[171],"enhanced":[174],"targeted":[175],"analysis,":[176],"turn":[179],"will":[180],"minimize":[181],"risk":[183],"reporting":[185],"allowing":[189],"detection":[191],"associations.":[195],"applicable":[199],"across":[200],"platforms":[201],"can":[203],"be":[204],"extended":[205],"assess":[207],"various":[211],"tissues.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
