{"id":"https://openalex.org/W2343312926","doi":"https://doi.org/10.1109/bhi.2016.7455839","title":"The selection of quantification pipelines for Illumina RNA-seq data using a subsampling approach","display_name":"The selection of quantification pipelines for Illumina RNA-seq data using a subsampling approach","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W2343312926","doi":"https://doi.org/10.1109/bhi.2016.7455839","mag":"2343312926","pmid":"https://pubmed.ncbi.nlm.nih.gov/28133637"},"language":"en","primary_location":{"id":"doi:10.1109/bhi.2016.7455839","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2016.7455839","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5267345","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050846682","display_name":"Po-Yen Wu","orcid":"https://orcid.org/0000-0002-3552-5152"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Po-Yen Wu","raw_affiliation_strings":["School of Electrical and Computer Engineering, Georgia Tech, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Georgia Tech, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030096887","display_name":"May D. Wang","orcid":"https://orcid.org/0000-0003-3961-3608"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]},{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"May D. Wang","raw_affiliation_strings":["Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444","https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050846682"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.01983619,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2016","issue":null,"first_page":"78","last_page":"81"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955000281333923,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955000281333923,"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":0.9901999831199646,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9876000285148621,"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":0.8369994759559631},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.7280879616737366},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6880186796188354},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6196904182434082},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5499347448348999},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5230330228805542},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5124052166938782},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4573253393173218},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4249211251735687},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31804773211479187},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2299262285232544},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22383499145507812},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17486786842346191},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1343008279800415},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10060137510299683},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09761902689933777}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8369994759559631},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.7280879616737366},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6880186796188354},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6196904182434082},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5499347448348999},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5230330228805542},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5124052166938782},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4573253393173218},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4249211251735687},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31804773211479187},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2299262285232544},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22383499145507812},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17486786842346191},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1343008279800415},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10060137510299683},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09761902689933777},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bhi.2016.7455839","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2016.7455839","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"},{"id":"pmid:28133637","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28133637","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":"... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5267345","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5267345","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":"IEEE EMBS Int Conf Biomed Health Inform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5267345","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5267345","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":"IEEE EMBS Int Conf Biomed Health Inform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1508938177","https://openalex.org/W1990293955","https://openalex.org/W1999574084","https://openalex.org/W2013990566","https://openalex.org/W2058140004","https://openalex.org/W2064397275","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2100305481","https://openalex.org/W2116445108","https://openalex.org/W2124985265","https://openalex.org/W2129916363","https://openalex.org/W2134526812","https://openalex.org/W2138773756","https://openalex.org/W2141458291","https://openalex.org/W2152239989","https://openalex.org/W2159730169","https://openalex.org/W2161106528","https://openalex.org/W2952535963","https://openalex.org/W4297828318","https://openalex.org/W6680267820","https://openalex.org/W6843190129"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"RNA":[0],"sequencing,":[1],"or":[2],"(RNA-seq":[3],"for":[4,12,25,86,115],"short,,":[5],"is":[6,31,149],"a":[7,35,66,87,150],"widely":[8],"applied":[9,92],"technology":[10],"that":[11,37,69,105,138,147],"extractings":[13],"gene":[14,47],"and":[15,77,98,103],"transcript":[16,49],"expression":[17,106],"from":[18,109,118],"biological":[19],"samples.":[20],"Given":[21],"numerous":[22],"quantification":[23,126,156],"pipelines":[24,54,127],"RNA-seq":[26,89,101,160],"data,":[27],"one":[28,96],"fundamental":[29],"challenge":[30],"to":[32,64,95,153],"determine":[33],"identify":[34],"pipeline":[36,75,83,157],"can":[38,70],"produce":[39],"the":[40,44,74,79,123,130,141],"most":[41,45],"accurate":[42,46],"estimate":[43],"and/or":[48],"expression.":[50],"Exploring":[51],"all":[52],"available":[53],"requires":[55],"tremendous":[56],"extensive":[57],"computational":[58],"resources,":[59],"so.":[60],"Therefore,":[61,144],"we":[62,145],"propose":[63],"use":[65],"subsampling":[67,148],"approach":[68,94,152],"improve":[71],"speed":[72],"up":[73],"evaluation":[76,85],"selection":[78,158],"efficiency":[80],"process":[81],"of":[82,125],"performance":[84],"given":[88],"dataset.":[90],"We":[91],"our":[93],"simulated":[97],"two":[99],"real":[100],"datasets":[102],"found":[104],"estimates":[107],"derived":[108,117],"subsampled":[110,131],"data":[111,132],"are":[112],"close":[113],"surrogates":[114],"those":[116],"original":[119,142],"data.":[120,143,161],"In":[121],"addition,":[122],"ranking":[124],"based":[128,139],"on":[129,140],"was":[133],"highly":[134],"correlated":[135],"concordant":[136],"with":[137],"conclude":[146],"valid":[151],"facilitating":[154],"efficient":[155],"using":[159]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
