{"id":"https://openalex.org/W7125832659","doi":"https://doi.org/10.1186/s12859-025-06298-8","title":"Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples","display_name":"Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples","publication_year":2026,"publication_date":"2026-01-27","ids":{"openalex":"https://openalex.org/W7125832659","doi":"https://doi.org/10.1186/s12859-025-06298-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/41593502"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06298-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06298-8","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://doi.org/10.1186/s12859-025-06298-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123912778","display_name":"Samuel Hamilton","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel Hamilton","raw_affiliation_strings":["Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051729012","display_name":"Gaurav Gadhvi","orcid":"https://orcid.org/0000-0002-4379-2824"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gaurav Gadhvi","raw_affiliation_strings":["Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099026900","display_name":"Tyler Therron","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tyler Therron","raw_affiliation_strings":["Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076358987","display_name":"Deborah R. Winter","orcid":"https://orcid.org/0000-0003-1806-673X"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deborah R. Winter","raw_affiliation_strings":["Center for Human Immunobiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. deborah.winter@northwestern.edu","Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA. deborah.winter@northwestern.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Human Immunobiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. deborah.winter@northwestern.edu","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, 240 East Huron Street, M300, Chicago, IL, 60611, USA. deborah.winter@northwestern.edu","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124031156","display_name":"SCRIPT Investigators","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"SCRIPT Investigators","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5123912778"],"corresponding_institution_ids":["https://openalex.org/I111979921"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15209159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.24879999458789825,"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":0.24879999458789825,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.21850000321865082,"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":0.17470000684261322,"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/pipeline","display_name":"Pipeline (software)","score":0.746399998664856},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.675599992275238},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.546500027179718},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.538100004196167},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.5339999794960022},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4377000033855438},{"id":"https://openalex.org/keywords/quality-assurance","display_name":"Quality assurance","score":0.39340001344680786},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.36739999055862427}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.746399998664856},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7365000247955322},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.675599992275238},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6516000032424927},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.546500027179718},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.538100004196167},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.5339999794960022},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4377000033855438},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40059998631477356},{"id":"https://openalex.org/C106436119","wikidata":"https://www.wikidata.org/wiki/Q836575","display_name":"Quality assurance","level":3,"score":0.39340001344680786},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.36739999055862427},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.34689998626708984},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.3452000021934509},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3244999945163727},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.3149999976158142},{"id":"https://openalex.org/C82214349","wikidata":"https://www.wikidata.org/wiki/Q657339","display_name":"Software metric","level":5,"score":0.3089999854564667},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.2944999933242798},{"id":"https://openalex.org/C21080849","wikidata":"https://www.wikidata.org/wiki/Q13611879","display_name":"Data point","level":2,"score":0.2842999994754791},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.2840999960899353},{"id":"https://openalex.org/C168820333","wikidata":"https://www.wikidata.org/wiki/Q448889","display_name":"Visual inspection","level":2,"score":0.2766000032424927},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.27459999918937683},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.273499995470047},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.25540000200271606},{"id":"https://openalex.org/C2779346075","wikidata":"https://www.wikidata.org/wiki/Q7268763","display_name":"Quality Score","level":3,"score":0.2540999948978424}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06298-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06298-8","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41593502","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41593502","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:pubmedcentral.nih.gov:12964923","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12964923/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12964923/pdf/12859_2025_Article_6298.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d47aa9ef67db47b99764d48d2c15fc1d","is_oa":true,"landing_page_url":"https://doaj.org/article/d47aa9ef67db47b99764d48d2c15fc1d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06298-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06298-8","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4623726010322571}],"awards":[{"id":"https://openalex.org/G3458703199","display_name":null,"funder_award_id":"U19AI135964","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5781740001","display_name":null,"funder_award_id":"5T32LM012203-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1575174146","https://openalex.org/W1696199194","https://openalex.org/W1805019014","https://openalex.org/W1967180093","https://openalex.org/W1981509058","https://openalex.org/W1983426138","https://openalex.org/W1995070233","https://openalex.org/W1996543077","https://openalex.org/W2009458183","https://openalex.org/W2009783955","https://openalex.org/W2014677321","https://openalex.org/W2018604728","https://openalex.org/W2030677229","https://openalex.org/W2035618305","https://openalex.org/W2036897871","https://openalex.org/W2053408266","https://openalex.org/W2060075610","https://openalex.org/W2069638100","https://openalex.org/W2070564311","https://openalex.org/W2074871118","https://openalex.org/W2079958213","https://openalex.org/W2082704080","https://openalex.org/W2096976625","https://openalex.org/W2097065948","https://openalex.org/W2108234281","https://openalex.org/W2117608012","https://openalex.org/W2130383124","https://openalex.org/W2131271579","https://openalex.org/W2134526812","https://openalex.org/W2137586531","https://openalex.org/W2138207763","https://openalex.org/W2143051000","https://openalex.org/W2145126338","https://openalex.org/W2163553106","https://openalex.org/W2168342464","https://openalex.org/W2169456326","https://openalex.org/W2276748084","https://openalex.org/W2287064828","https://openalex.org/W2432815617","https://openalex.org/W2681631427","https://openalex.org/W2765281411","https://openalex.org/W2790830776","https://openalex.org/W2795686629","https://openalex.org/W2904478560","https://openalex.org/W2911964244","https://openalex.org/W2984505311","https://openalex.org/W3035517615","https://openalex.org/W3120857229","https://openalex.org/W3134285609","https://openalex.org/W3197001456","https://openalex.org/W4200410169","https://openalex.org/W4221110333","https://openalex.org/W4296162355","https://openalex.org/W4307230656","https://openalex.org/W4319333703","https://openalex.org/W4390509564","https://openalex.org/W4400651671"],"related_works":[],"abstract_inverted_index":{"With":[0],"the":[1,14,48,89,128,156,168,184,189,212,220,238,265],"rise":[2],"of":[3,62,103,121,153,179,192,214,240,268],"RNA-seq":[4,68,101,269],"as":[5,29],"an":[6,67,83,206],"essential":[7],"and":[8,70,124,137,148,233,255],"ubiquitous":[9],"tool":[10],"for":[11,16],"biomedical":[12],"research,":[13],"need":[15],"guidelines":[17],"on":[18,183,205,237],"quality":[19,197],"control":[20],"(QC)":[21],"is":[22,227],"pressing.":[23],"Specifically,":[24],"there":[25],"remains":[26],"limited":[27,228],"data":[28],"to":[30,56,78,88,115,187,195,263],"which":[31,259],"technical":[32],"metrics":[33,64,123,134,165,194,242],"are":[34],"most":[35,129],"informative":[36],"in":[37,93,211,229],"identifying":[38],"low-quality":[39],"samples.":[40],"Here,":[41],"we":[42,85,111],"addressed":[43],"this":[44,113],"issue":[45],"by":[46,66],"developing":[47],"Quality":[49],"Control":[50],"Diagnostic":[51],"Renderer":[52],"(QC-DR),":[53],"software":[54,258],"designed":[55],"simultaneously":[57],"visualize":[58],"a":[59,79,98,119,177],"comprehensive":[60],"panel":[61],"QC":[63,122,133,164,193,215,225,244,257],"generated":[65],"pipeline":[69,132],"flag":[71],"samples":[72],"with":[73,243],"aberrant":[74],"values":[75],"when":[76,203],"compared":[77],"reference":[80],"dataset.":[81],"As":[82],"example,":[84],"applied":[86],"QC-DR":[87],"Successful":[90],"Clinical":[91],"Response":[92],"Pneumonia":[94],"Therapy":[95],"(SCRIPT)":[96],"dataset,":[97],"large":[99],"clinical":[100],"dataset":[102,114,186,208],"sequenced":[104],"alveolar":[105],"macrophages":[106],"(n":[107],"=":[108],"252).":[109],"Next,":[110],"used":[112,262],"assess":[116],"relationships":[117],"between":[118],"variety":[120],"sample":[125,196],"quality.":[126],"Among":[127],"highly":[130],"correlated":[131],"were":[135,170],"%":[136,142],"#":[138,145],"Uniquely":[139],"Aligned":[140],"Reads,":[141],"rRNA":[143],"reads,":[144],"Detected":[146],"Genes,":[147],"our":[149,248],"newly":[150],"developed":[151],"metric":[152,226],"Area":[154],"Under":[155],"Gene":[157],"Body":[158],"Coverage":[159],"Curve":[160],"(AUC-GBC),":[161],"while":[162],"experimental":[163],"derived":[166],"from":[167],"lab":[169],"not":[171],"significantly":[172],"correlated.":[173],"We":[174],"then":[175],"trained":[176],"set":[178],"machine":[180],"learning":[181],"models":[182],"SCRIPT":[185],"evaluate":[188],"relative":[190],"contribution":[191],"prediction.":[198],"Our":[199,217],"model":[200],"performs":[201],"well":[202],"tested":[204],"independent":[207],"despite":[209],"differences":[210],"distribution":[213],"metrics.":[216],"results":[218],"support":[219],"conclusion":[221],"that":[222],"any":[223],"individual":[224],"its":[230],"predictive":[231],"value":[232],"suggests":[234],"approaches":[235],"based":[236],"integration":[239],"multiple":[241],"thresholds.":[245],"In":[246],"summary,":[247],"work":[249],"provides":[250],"new":[251],"insights,":[252],"practical":[253],"guidance,":[254],"novel":[256],"can":[260],"be":[261],"improve":[264],"methodological":[266],"rigor":[267],"studies.":[270]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-01-28T00:00:00"}
