{"id":"https://openalex.org/W3032989484","doi":"https://doi.org/10.1093/bib/bbaa112","title":"Proper imputation of missing values in proteomics datasets for differential expression analysis","display_name":"Proper imputation of missing values in proteomics datasets for differential expression analysis","publication_year":2020,"publication_date":"2020-05-13","ids":{"openalex":"https://openalex.org/W3032989484","doi":"https://doi.org/10.1093/bib/bbaa112","mag":"3032989484","pmid":"https://pubmed.ncbi.nlm.nih.gov/32520347"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa112","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa112","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000026020","display_name":"Mingyi Liu","orcid":"https://orcid.org/0000-0002-8101-8522"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mingyi Liu","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8101-8522","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5083287881","display_name":"Ashok Dongre","orcid":"https://orcid.org/0000-0001-9624-4584"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ashok Dongre","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5000026020"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.6139,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.96441212,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.98089998960495,"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/imputation","display_name":"Imputation (statistics)","score":0.873397707939148},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7313758730888367},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.7272594571113586},{"id":"https://openalex.org/keywords/shotgun-proteomics","display_name":"Shotgun proteomics","score":0.6121095418930054},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5510039925575256},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.35933318734169006},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.22234675288200378},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12555456161499023}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.873397707939148},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7313758730888367},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.7272594571113586},{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.6121095418930054},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5510039925575256},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.35933318734169006},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.22234675288200378},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12555456161499023},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa112","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa112","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:32520347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32520347","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1965806060","https://openalex.org/W2000403772","https://openalex.org/W2053089337","https://openalex.org/W2087481305","https://openalex.org/W2103165230","https://openalex.org/W2106839391","https://openalex.org/W2125419939","https://openalex.org/W2135581618","https://openalex.org/W2146512944","https://openalex.org/W2170776626","https://openalex.org/W2278988761","https://openalex.org/W2582743722","https://openalex.org/W2603189578","https://openalex.org/W2619796081","https://openalex.org/W2623259478","https://openalex.org/W2900687966","https://openalex.org/W2951837249","https://openalex.org/W4254687493"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549","https://openalex.org/W3179858851","https://openalex.org/W3123177881"],"abstract_inverted_index":{"Label-free":[0],"shotgun":[1],"proteomics":[2],"is":[3,18],"an":[4],"important":[5],"tool":[6],"in":[7,92,133],"biomedical":[8,111],"research,":[9],"where":[10],"tandem":[11],"mass":[12],"spectrometry":[13],"with":[14],"data-dependent":[15],"acquisition":[16],"(DDA)":[17],"frequently":[19],"used":[20,52],"for":[21,53,109,177],"protein":[22],"identification":[23],"and":[24,86],"quantification.":[25],"However,":[26,68],"the":[27,54,69,84,97,129,142,153,161],"DDA":[28,121,182],"datasets":[29,73,122,139],"contain":[30],"a":[31],"significant":[32],"number":[33],"of":[34,57,77,90,99,123,131,145,155,163],"missing":[35,59,64],"values":[36],"(MVs)":[37],"that":[38,46,140],"severely":[39],"hinders":[40],"proper":[41,88],"analysis.":[42],"Existing":[43],"literature":[44],"suggests":[45],"different":[47],"imputation":[48,89,100,158,173],"methods":[49,101,159],"should":[50],"be":[51],"two":[55],"types":[56,126],"MVs:":[58],"completely":[60],"at":[61,66],"random":[62],"or":[63,71],"not":[65],"random.":[67],"simulated":[70,138],"biased":[72],"utilized":[74],"by":[75],"most":[76],"such":[78,149],"studies":[79],"offer":[80],"few":[81],"clues":[82],"about":[83],"composition":[85,130],"thus":[87],"MVs":[91,132],"real-life":[93,146],"proteomic":[94,178],"datasets.":[95,147,183],"Moreover,":[96],"impact":[98,154],"on":[102,160,171],"downstream":[103],"differential":[104],"expression":[105],"analysis-a":[106],"critical":[107],"goal":[108],"many":[110],"projects-is":[112],"largely":[113],"undetermined.":[114],"In":[115],"this":[116],"study,":[117],"we":[118,151,168],"investigated":[119],"public":[120],"various":[124,156],"tissue/sample":[125],"to":[127,175],"determine":[128],"them.":[134],"We":[135],"then":[136],"developed":[137],"imitate":[141],"MV":[143],"profile":[144],"Using":[148],"datasets,":[150],"compared":[152],"popular":[157],"analysis":[162],"differentially":[164],"expressed":[165],"proteins.":[166],"Finally,":[167],"make":[169],"recommendations":[170],"which":[172],"method(s)":[174],"use":[176],"data":[179],"beyond":[180],"just":[181]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
