{"id":"https://openalex.org/W2161397498","doi":"https://doi.org/10.1109/embc.2013.6609583","title":"Benchmarking RNA-Seq quantification tools","display_name":"Benchmarking RNA-Seq quantification tools","publication_year":2013,"publication_date":"2013-07-01","ids":{"openalex":"https://openalex.org/W2161397498","doi":"https://doi.org/10.1109/embc.2013.6609583","mag":"2161397498","pmid":"https://pubmed.ncbi.nlm.nih.gov/24109770"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2013.6609583","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6609583","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","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/5003039","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005230766","display_name":"Raghu Chandramohan","orcid":null},"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":"Raghu Chandramohan","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"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":["School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074230084","display_name":"John H. Phan","orcid":"https://orcid.org/0000-0002-4670-2660"},"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":"John H. Phan","raw_affiliation_strings":["Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Institute of Technology, 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/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, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":2.3599,"has_fulltext":false,"cited_by_count":47,"citation_normalized_percentile":{"value":0.89019275,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2013","issue":null,"first_page":"647","last_page":"650"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10604","display_name":"RNA Research and Splicing","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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9979000091552734,"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/benchmarking","display_name":"Benchmarking","score":0.8462716341018677},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.583105742931366},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5162224769592285},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3627520501613617},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12072116136550903},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1081618070602417},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.09453228116035461}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8462716341018677},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.583105742931366},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5162224769592285},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3627520501613617},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12072116136550903},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1081618070602417},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.09453228116035461},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/embc.2013.6609583","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6609583","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:24109770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24109770","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5003039","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5003039","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":"Conf Proc IEEE Eng Med Biol Soc","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5003039","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5003039","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":"Conf Proc IEEE Eng Med Biol Soc","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2030844469","display_name":null,"funder_award_id":"RC2 CA148265","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5634960583","display_name":null,"funder_award_id":"U01 HL080711","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6053241097","display_name":null,"funder_award_id":"U54 CA119338","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6738851939","display_name":null,"funder_award_id":"U54CA119338","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7850144365","display_name":null,"funder_award_id":"NHLBI 5U01HL080711","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G903501388","display_name":null,"funder_award_id":"1RC2CA148265","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1984708728","https://openalex.org/W1999574084","https://openalex.org/W2010637767","https://openalex.org/W2044010294","https://openalex.org/W2055770801","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2121211805","https://openalex.org/W2124985265","https://openalex.org/W2141458291","https://openalex.org/W2154431984","https://openalex.org/W2155705877","https://openalex.org/W2155804510"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W1971332228"],"abstract_inverted_index":{"RNA-Seq,":[0,37],"a":[1,8],"deep":[2],"sequencing":[3],"technique,":[4],"promises":[5],"to":[6,11,27,43,81,108,133],"be":[7],"potential":[9],"successor":[10],"microarrays":[12],"for":[13],"studying":[14],"the":[15,61,104,113,135],"transcriptome.":[16],"One":[17],"of":[18,21,25,57,88,106,119,122],"many":[19],"aspects":[20],"transcriptomics":[22],"that":[23,94],"are":[24,39],"interest":[26],"researchers":[28],"is":[29],"gene":[30,45,64],"expression":[31,65,84,97,125,160],"estimation.":[32],"With":[33],"rapid":[34],"development":[35],"in":[36,103,117],"there":[38],"numerous":[40],"tools":[41,59],"available":[42],"estimate":[44],"expression,":[46],"each":[47],"producing":[48],"different":[49],"results.":[50],"However,":[51],"we":[52,70,92,130,139],"do":[53],"not":[54,148],"know":[55],"which":[56],"these":[58,89],"produces":[60],"most":[62],"accurate":[63],"estimates.":[66],"In":[67],"this":[68,73],"study":[69],"have":[71],"addressed":[72],"issue":[74],"using":[75],"Cufflinks,":[76,143],"IsoEM,":[77],"HTSeq,":[78],"and":[79,145],"RSEM":[80],"quantify":[82],"RNA-Seq":[83,95,123],"profiles.":[85],"Comparing":[86],"results":[87],"quantification":[90],"tools,":[91],"observe":[93],"relative":[96,124],"estimates":[98,126],"correlate":[99,149],"with":[100,110,154,162],"RT-qPCR":[101,128,155],"measurements":[102],"range":[105],"0.85":[107],"0.89,":[109],"HTSeq":[111,132,153],"exhibiting":[112],"highest":[114],"correlation.":[115],"But,":[116],"terms":[118],"root-mean-square":[120],"deviation":[121],"from":[127],"measurements,":[129,156],"find":[131],"produce":[134,159],"greatest":[136],"deviation.":[137],"Therefore,":[138],"conclude":[140],"that,":[141],"though":[142],"RSEM,":[144],"IsoEM":[146],"might":[147],"as":[150,152],"well":[151],"they":[157],"may":[158],"values":[161],"higher":[163],"accuracy.":[164]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
