{"id":"https://openalex.org/W3080945506","doi":"https://doi.org/10.1093/bioinformatics/btaa751","title":"Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control","display_name":"Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control","publication_year":2020,"publication_date":"2020-08-18","ids":{"openalex":"https://openalex.org/W3080945506","doi":"https://doi.org/10.1093/bioinformatics/btaa751","mag":"3080945506","pmid":"https://pubmed.ncbi.nlm.nih.gov/32840568"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa751","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/963/41158126/btaa751.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/963/41158126/btaa751.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053481898","display_name":"Daniel Osorio","orcid":"https://orcid.org/0000-0003-4424-8422"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Osorio","raw_affiliation_strings":["Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843-4458, USA"],"raw_orcid":"https://orcid.org/0000-0003-4424-8422","affiliations":[{"raw_affiliation_string":"Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843-4458, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059360459","display_name":"James J. Cai","orcid":"https://orcid.org/0000-0002-8081-6725"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James J Cai","raw_affiliation_strings":["Department of Electrical & Computer Engineering, Texas A&M University , College Station, TX 77843-4458, USA","Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843-4458, USA","Interdisciplinary Program of Genetics, Texas A&M University , College Station, TX 77843-4458, USA"],"raw_orcid":"https://orcid.org/0000-0002-8081-6725","affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, Texas A&M University , College Station, TX 77843-4458, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843-4458, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Interdisciplinary Program of Genetics, Texas A&M University , College Station, TX 77843-4458, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053481898"],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.9127,"has_fulltext":true,"cited_by_count":217,"citation_normalized_percentile":{"value":0.97988658,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"37","issue":"7","first_page":"963","last_page":"967"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9965999722480774,"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":0.9965999722480774,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.0007999999797903001,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.00019999999494757503,"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/mitochondrial-dna","display_name":"Mitochondrial DNA","score":0.6391971111297607},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5962182283401489},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5775390863418579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5573469996452332},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5181980729103088},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.46345824003219604},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.46007686853408813},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4214043915271759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38542187213897705},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3522975444793701},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20554929971694946},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09648662805557251},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07927510142326355}],"concepts":[{"id":"https://openalex.org/C24586158","wikidata":"https://www.wikidata.org/wiki/Q27075","display_name":"Mitochondrial DNA","level":3,"score":0.6391971111297607},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5962182283401489},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5775390863418579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5573469996452332},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5181980729103088},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.46345824003219604},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.46007686853408813},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4214043915271759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38542187213897705},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3522975444793701},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20554929971694946},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09648662805557251},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07927510142326355},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa751","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/963/41158126/btaa751.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32840568","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32840568","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8599307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8599307","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa751","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/963/41158126/btaa751.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"},{"score":0.5,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310164","display_name":"Texas A and M University","ror":"https://ror.org/01f5ytq51"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3080945506.pdf","grobid_xml":"https://content.openalex.org/works/W3080945506.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2020247204","https://openalex.org/W2069089843","https://openalex.org/W2076687510","https://openalex.org/W2108738634","https://openalex.org/W2154598603","https://openalex.org/W2159482845","https://openalex.org/W2170819005","https://openalex.org/W2190545194","https://openalex.org/W2207646908","https://openalex.org/W2286142055","https://openalex.org/W2540833380","https://openalex.org/W2885673883","https://openalex.org/W2886347923","https://openalex.org/W2891898226","https://openalex.org/W2945104282","https://openalex.org/W2949237386","https://openalex.org/W2951158909","https://openalex.org/W2979778359","https://openalex.org/W4294216483","https://openalex.org/W6728888212","https://openalex.org/W6869026298"],"related_works":["https://openalex.org/W2326369733","https://openalex.org/W4308441232","https://openalex.org/W2567787466","https://openalex.org/W2022430805","https://openalex.org/W2068493848","https://openalex.org/W2433011597","https://openalex.org/W2058866756","https://openalex.org/W1990401969","https://openalex.org/W2387480278","https://openalex.org/W4244613333"],"abstract_inverted_index":{"MOTIVATION:":[0],"Quality":[1],"control":[2],"(QC)":[3],"is":[4,35,41,140,149,265],"a":[5,44,57,69,82,93,237],"critical":[6],"step":[7],"in":[8,53,71,84,119,124,134,144,220],"single-cell":[9,99],"RNA-seq":[10],"(scRNA-seq)":[11],"data":[12,77,136,272],"analysis.":[13],"Low-quality":[14],"cells":[15,117,219],"are":[16,273],"removed":[17],"from":[18],"the":[19,22,29,36,54,89,125,131,153,158,170,187,203,231,259,263],"analysis":[20],"during":[21],"QC":[23,33,233],"process":[24],"to":[25,46,156,192,212,243,255],"avoid":[26],"misinterpretation":[27],"of":[28,59,91,169,175,180,223,247],"data.":[30,159,249],"An":[31],"important":[32],"metric":[34],"mitochondrial":[37],"proportion":[38],"(mtDNA%),":[39],"which":[40],"used":[42,67,155,254],"as":[43,68,81,209],"threshold":[45,58,95,189,205,240],"filter":[47,234],"out":[48],"low-quality":[49,197,218],"cells.":[50,198],"Early":[51],"publications":[52],"field":[55],"established":[56],"5%":[60,188,204],"and":[61,79,102,128,177,196,217,261],"since":[62],"then,":[63],"it":[64,210],"has":[65,105],"been":[66,107],"default":[70],"several":[72],"software":[73],"packages":[74],"for":[75,172,184,200],"scRNA-seq":[76,86,135,248],"analysis,":[78],"adopted":[80],"standard":[83],"many":[85],"studies.":[87],"However,":[88,199],"validity":[90],"using":[92],"uniform":[94],"across":[96,137],"different":[97],"species,":[98],"technologies,":[100],"tissues":[101,139,174,179,225],"cell":[103],"types":[104],"not":[106,150],"adequately":[108],"assessed.":[109],"RESULTS:":[110],"We":[111,227],"systematically":[112],"analyzed":[113],"5":[114],"530":[115],"106":[116],"reported":[118],"1349":[120],"annotated":[121],"datasets":[122],"available":[123,266,274],"PanglaoDB":[126],"database":[127],"found":[129],"that":[130,229],"average":[132],"mtDNA%":[133,171,232,239],"human":[138,201],"significantly":[141],"higher":[142],"than":[143],"mouse":[145,176,185],"tissues.":[146],"This":[147],"difference":[148],"confounded":[151],"by":[152],"platform":[154],"generate":[157],"Based":[160],"on":[161],"this":[162],"finding,":[163],"we":[164],"propose":[165],"new":[166],"reference":[167],"values":[168],"121":[173],"44":[178],"humans.":[181],"In":[182],"general,":[183],"tissues,":[186,202],"performs":[190],"well":[191],"distinguish":[193],"between":[194,215],"healthy":[195,216],"should":[206],"be":[207],"reconsidered":[208],"fails":[211],"accurately":[213],"discriminate":[214],"29.5%":[221],"(13":[222],"44)":[224],"analyzed.":[226],"conclude":[228],"omitting":[230],"or":[235],"adopting":[236],"suboptimal":[238],"may":[241],"lead":[242],"erroneous":[244],"biological":[245],"interpretations":[246],"AVAILABILITYAND":[250],"IMPLEMENTATION:":[251],"The":[252],"code":[253],"download":[256],"datasets,":[257],"perform":[258],"analyzes":[260],"produce":[262],"figures":[264],"at":[267,275],"https://github.com/dosorio/mtProportion.":[268],"SUPPLEMENTARY":[269],"INFORMATION:":[270],"Supplementary":[271],"Bioinformatics":[276],"online.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":72},{"year":2023,"cited_by_count":37},{"year":2022,"cited_by_count":29},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":3}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}
