{"id":"https://openalex.org/W2121883846","doi":"https://doi.org/10.1109/gensips.2012.6507729","title":"Improving the flexibility of RNA-Seq data analysis pipelines","display_name":"Improving the flexibility of RNA-Seq data analysis pipelines","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2121883846","doi":"https://doi.org/10.1109/gensips.2012.6507729","mag":"2121883846","pmid":"https://pubmed.ncbi.nlm.nih.gov/27536420"},"language":"en","primary_location":{"id":"doi:10.1109/gensips.2012.6507729","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2012.6507729","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","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/A5074230084","display_name":"John H. Phan","orcid":"https://orcid.org/0000-0002-4670-2660"},"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":true,"raw_author_name":"John H. Phan","raw_affiliation_strings":["Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA","Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA, jhphan@gatech.edu"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666","https://openalex.org/I130701444"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA, jhphan@gatech.edu","institution_ids":[]}]},{"author_position":"middle","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":false,"raw_author_name":"Po-Yen Wu","raw_affiliation_strings":["Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta, GA, USA","Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA, leoboki@gmail.com"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA, leoboki@gmail.com","institution_ids":[]}]},{"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 Institute of Technology and Emory University Atlanta, GA, USA","Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA, aywang@bme.gatech.edu"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666","https://openalex.org/I130701444"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA, aywang@bme.gatech.edu","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074230084"],"corresponding_institution_ids":["https://openalex.org/I130701444","https://openalex.org/I150468666"],"apc_list":null,"apc_paid":null,"fwci":0.1342,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53467842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2012","issue":null,"first_page":"70","last_page":"73"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T11482","display_name":"RNA modifications and cancer","score":0.9943000078201294,"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":0.9941999912261963,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6020903587341309},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.586808443069458},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5766087770462036},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.520807147026062},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3573668599128723},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3299451470375061},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1441740095615387},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.113178551197052},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09971848130226135},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09558075666427612},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08534324169158936},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06972566246986389},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06771373748779297}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6020903587341309},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.586808443069458},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5766087770462036},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.520807147026062},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3573668599128723},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3299451470375061},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1441740095615387},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.113178551197052},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09971848130226135},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09558075666427612},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08534324169158936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06972566246986389},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06771373748779297},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/gensips.2012.6507729","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2012.6507729","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"},{"id":"pmid:27536420","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27536420","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 International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics","raw_type":null},{"id":"pmh:oai:europepmc.org:3945599","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4985025","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1981509058","https://openalex.org/W2049628752","https://openalex.org/W2096173343","https://openalex.org/W2096441981","https://openalex.org/W2097065948","https://openalex.org/W2100448568","https://openalex.org/W2141458291","https://openalex.org/W2154431984","https://openalex.org/W2158717244","https://openalex.org/W2168909179","https://openalex.org/W2170551349","https://openalex.org/W4210347168"],"related_works":["https://openalex.org/W1995889332","https://openalex.org/W3104163240","https://openalex.org/W4200033037","https://openalex.org/W2626808643","https://openalex.org/W2004064826","https://openalex.org/W3103727510","https://openalex.org/W3143779693","https://openalex.org/W97045569","https://openalex.org/W3213655218","https://openalex.org/W4293054118"],"abstract_inverted_index":{"Accurate":[0],"quantification":[1,35,100,142,173],"of":[2,13,32,79,95,115,138,156],"gene":[3,139],"or":[4,140],"isoform":[5,26,141,167],"expression":[6],"with":[7],"RNA-Seq":[8,34,40,148,159],"depends":[9],"on":[10,102],"complete":[11,18],"knowledge":[12],"the":[14,33,77,86,113,127,136],"transcriptome.":[15],"Because":[16],"a":[17,38,43,54,80,103,109,157],"genomic":[19],"annotation":[20],"does":[21],"not":[22],"yet":[23],"exist,":[24],"novel":[25,166],"discovery":[27,168],"is":[28],"an":[29,154],"important":[30],"component":[31],"process.":[36],"Thus,":[37,106],"typical":[39],"pipeline":[41,160],"includes":[42],"transcriptome":[44,87,116],"mapping":[45,57,82,91,96,120],"step":[46,58],"to":[47,59,126],"quantify":[48],"known":[49],"genes":[50,62],"and":[51,53,63,88,117,169],"isoforms,":[52],"reference":[55,89,118],"genome":[56,90,119],"discover":[60],"new":[61],"isoforms.":[64],"Several":[65],"tools":[66],"implement":[67],"this":[68],"approach,":[69],"but":[70],"are":[71],"limited":[72],"in":[73],"that":[74,111,123],"they":[75,124],"force":[76],"use":[78],"single":[81],"algorithm":[83,97],"at":[84],"both":[85],"stages.":[92],"The":[93],"choice":[94],"could":[98,133],"affect":[99],"accuracy":[101,137],"per-dataset":[104],"basis.":[105],"we":[107],"describe":[108],"method":[110],"enables":[112],"merging":[114],"stages":[121],"provided":[122],"conform":[125],"standard":[128],"SAM/BAM":[129],"format.":[130],"This":[131],"procedure":[132],"potentially":[134],"improve":[135],"by":[143,161,170],"increasing":[144],"flexibility":[145],"when":[146],"selecting":[147],"data":[149],"analysis":[150],"pipelines.":[151],"We":[152],"demonstrate":[153],"example":[155],"flexible":[158],"assessing":[162],"its":[163,172],"potential":[164],"for":[165],"validating":[171],"performance":[174],"using":[175],"qRT-PCR.":[176]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
