{"id":"https://openalex.org/W3004715719","doi":"https://doi.org/10.1109/bibm47256.2019.8983123","title":"A deconvolution method for predicting cell abundance based on single cell RNA-seq data","display_name":"A deconvolution method for predicting cell abundance based on single cell RNA-seq data","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004715719","doi":"https://doi.org/10.1109/bibm47256.2019.8983123","mag":"3004715719"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983123","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983123","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084343474","display_name":"Jiajie Peng","orcid":"https://orcid.org/0000-0002-3857-7927"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajie Peng","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100625412","display_name":"Lu Han","orcid":"https://orcid.org/0000-0001-9759-1537"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lu Han","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an City,Shaanxi Province,China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an City, Shaanxi Province, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1769","last_page":"1773"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9983000159263611,"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9983000159263611,"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/deconvolution","display_name":"Deconvolution","score":0.6417914032936096},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5212950706481934},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.4819197952747345},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.47798389196395874},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.47643786668777466},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4618801772594452},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4557771682739258},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45439982414245605},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.4434766173362732},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.42726951837539673},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41168174147605896},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.332452654838562},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2761368155479431},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1785857081413269},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15738922357559204},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10062184929847717},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.07432180643081665}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.6417914032936096},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5212950706481934},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.4819197952747345},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.47798389196395874},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.47643786668777466},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4618801772594452},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4557771682739258},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45439982414245605},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.4434766173362732},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.42726951837539673},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41168174147605896},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.332452654838562},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2761368155479431},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1785857081413269},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15738922357559204},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10062184929847717},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.07432180643081665},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983123","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983123","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1491459594","https://openalex.org/W1983951224","https://openalex.org/W1985987855","https://openalex.org/W2016895073","https://openalex.org/W2158549544","https://openalex.org/W2507880739","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2921330004","https://openalex.org/W2950779253","https://openalex.org/W2952240309","https://openalex.org/W4237910213"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2127804977","https://openalex.org/W2108418243","https://openalex.org/W164103134","https://openalex.org/W4250106855","https://openalex.org/W2040545019","https://openalex.org/W2037261263","https://openalex.org/W612792751"],"abstract_inverted_index":{"It":[0],"is":[1,47,65,109,120],"important":[2],"to":[3,30,67,71,77,124,144,212,221],"understand":[4],"the":[5,19,73,79,84,88,92,97,106,176,186,189,194,203,230],"cell-type":[6],"composition":[7,35,82],"and":[8,36,49,118,169,182,229],"its":[9],"proportion":[10,37],"in":[11,24,53,83,188,193,227,238],"tissues.":[12],"Some":[13],"previous":[14],"experiments":[15],"have":[16],"shown":[17],"that":[18,234],"variation":[20],"of":[21,60,87,116,179,191],"gene":[22,100,130,166,171],"expression":[23,101,131,167,172],"certain":[25],"cell":[26,33,80,98,128,146,196,214,239],"types":[27,115],"may":[28],"lead":[29],"disease.":[31],"Although":[32],"type":[34,81,197,215,240],"can":[38],"be":[39,51],"obtained":[40],"by":[41,206],"single-cell":[42,170],"RNA-sequencing":[43],"(scRNA-sq),":[44],"using":[45,207],"scRNA-sq":[46],"expensive":[48],"cannot":[50],"applied":[52],"clinical":[54],"studies":[55],"involving":[56],"a":[57,69,126,139,223],"large":[58],"number":[59],"subjects":[61],"currently.":[62],"Therefore,":[63],"it":[64,119],"urgent":[66],"develop":[68],"method":[70],"deconvolute":[72],"Bulk":[74,180],"RNA-Seq":[75,181],"data":[76],"obtain":[78],"tissue.":[85],"Most":[86],"existing":[89,244],"methods":[90],"require":[91],"signature":[93,107,225],"matrix,":[94,173],"which":[95],"provides":[96],"type-specific":[99,129],"profile,":[102],"as":[103],"input.":[104],"However,":[105],"matrix":[108,168,226],"not":[110,121,219],"always":[111,122],"available":[112],"for":[113],"some":[114],"tissue,":[117],"possible":[123],"find":[125],"suitable":[127,224],"profile.":[132],"To":[133],"solve":[134],"this":[135],"problem,":[136],"we":[137],"propose":[138],"novel":[140],"method,":[141],"named":[142],"DCap,":[143],"predict":[145,213],"abundance.":[147,216],"Different":[148],"from":[149,185],"non-negative":[150,209],"least":[151,160,210],"squares,":[152],"DCap":[153,174,201,217,235],"performs":[154,236],"weighted":[155,208],"iterative":[156],"calculation":[157],"based":[158],"on":[159],"squares.":[161],"By":[162],"weighting":[163],"bulk":[164],"tissue":[165],"minimizes":[175],"measurement":[177],"error":[178,183],"resulting":[184],"difference":[187],"amount":[190],"genes":[192],"same":[195],"among":[198],"different":[199],"samples.":[200],"solves":[202],"deconvolution":[204],"problem":[205],"squares":[211],"does":[218],"need":[220],"prepare":[222],"advance,":[228],"evaluation":[231],"test":[232],"shows":[233],"better":[237],"abundance":[241],"prediction":[242],"than":[243],"methods.":[245]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
