{"id":"https://openalex.org/W2106352274","doi":"https://doi.org/10.1093/bioinformatics/btv488","title":"Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data","display_name":"Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data","publication_year":2015,"publication_date":"2015-09-03","ids":{"openalex":"https://openalex.org/W2106352274","doi":"https://doi.org/10.1093/bioinformatics/btv488","mag":"2106352274","pmid":"https://pubmed.ncbi.nlm.nih.gov/26338770"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3938/50307104/bioinformatics_31_24_3938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3938/50307104/bioinformatics_31_24_3938.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015451664","display_name":"Katharina E. Hayer","orcid":"https://orcid.org/0000-0002-1463-3111"},"institutions":[{"id":"https://openalex.org/I4210125521","display_name":"Translational Therapeutics (United States)","ror":"https://ror.org/02z3rcy16","country_code":"US","type":"company","lineage":["https://openalex.org/I4210125521"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katharina E. Hayer","raw_affiliation_strings":["1 University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I4210125521","https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026998349","display_name":"Angel Pizarro","orcid":"https://orcid.org/0000-0003-2263-2255"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Angel Pizarro","raw_affiliation_strings":["2 Scientific Computing at Amazon Web Services, Seattle, WA 98108,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Scientific Computing at Amazon Web Services, Seattle, WA 98108,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015403792","display_name":"Nicholas F. Lahens","orcid":"https://orcid.org/0000-0002-3965-5624"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas F. Lahens","raw_affiliation_strings":["3 Department of Pharmacology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Pharmacology and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035012559","display_name":"John B. Hogenesch","orcid":"https://orcid.org/0000-0002-9138-8973"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John B. Hogenesch","raw_affiliation_strings":["3 Department of Pharmacology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Pharmacology and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068257910","display_name":"Gregory R. Grant","orcid":"https://orcid.org/0000-0002-0139-7658"},"institutions":[{"id":"https://openalex.org/I4210125521","display_name":"Translational Therapeutics (United States)","ror":"https://ror.org/02z3rcy16","country_code":"US","type":"company","lineage":["https://openalex.org/I4210125521"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory R. Grant","raw_affiliation_strings":["1 University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104,","4 Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I4210125521","https://openalex.org/I79576946"]},{"raw_affiliation_string":"4 Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015451664"],"corresponding_institution_ids":["https://openalex.org/I4210125521","https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.7774,"has_fulltext":true,"cited_by_count":101,"citation_normalized_percentile":{"value":0.9753147,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"31","issue":"24","first_page":"3938","last_page":"3945"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.7059999704360962,"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/T10604","display_name":"RNA Research and Splicing","score":0.7059999704360962,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.09529999643564224,"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":0.04470000043511391,"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/benchmark","display_name":"Benchmark (surveying)","score":0.6498520374298096},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6280813217163086},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.6091656684875488},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5927368402481079},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5450910925865173},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5192623138427734},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5023632049560547},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4709243178367615},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3348965644836426},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16571646928787231},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13975441455841064},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10873553156852722},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1052977442741394},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.09117245674133301}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6498520374298096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6280813217163086},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.6091656684875488},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5927368402481079},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5450910925865173},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5192623138427734},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5023632049560547},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4709243178367615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3348965644836426},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16571646928787231},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13975441455841064},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10873553156852722},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1052977442741394},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.09117245674133301},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3938/50307104/bioinformatics_31_24_3938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26338770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26338770","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:europepmc.org:3652331","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4673975","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/24/3938","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/24/3938","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv488","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3938/50307104/bioinformatics_31_24_3938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2783897811","display_name":null,"funder_award_id":"5UL1TR000003","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G5333873862","display_name":null,"funder_award_id":"DARPA-D12AP00025","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G5902410746","display_name":null,"funder_award_id":"U54HL117798","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7035006519","display_name":null,"funder_award_id":"D12AP00025","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G7479834065","display_name":null,"funder_award_id":"R01 NS054794","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G7578655654","display_name":null,"funder_award_id":"P30 ES013508","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G836761610","display_name":null,"funder_award_id":"1R01NS054794-06","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G84984283","display_name":null,"funder_award_id":"U54 HL117798","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320308109","display_name":"Pennsylvania Department of Health","ror":"https://ror.org/00ra1fg11"},{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320310180","display_name":"Institute for Translational Medicine and Therapeutics","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106352274.pdf","grobid_xml":"https://content.openalex.org/works/W2106352274.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1988245212","https://openalex.org/W1999574084","https://openalex.org/W2000875411","https://openalex.org/W2008183439","https://openalex.org/W2054576015","https://openalex.org/W2093253451","https://openalex.org/W2094492214","https://openalex.org/W2096173343","https://openalex.org/W2098809361","https://openalex.org/W2098937968","https://openalex.org/W2102813686","https://openalex.org/W2104005232","https://openalex.org/W2110392562","https://openalex.org/W2112232553","https://openalex.org/W2112888168","https://openalex.org/W2117688129","https://openalex.org/W2126419817","https://openalex.org/W2126766730","https://openalex.org/W2128016314","https://openalex.org/W2133459862","https://openalex.org/W2133918896","https://openalex.org/W2134526812","https://openalex.org/W2135592053","https://openalex.org/W2136101247","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2151464048","https://openalex.org/W2155705877","https://openalex.org/W2156841387","https://openalex.org/W2161397498","https://openalex.org/W2166820820","https://openalex.org/W2169456326","https://openalex.org/W2998575373","https://openalex.org/W6673948768","https://openalex.org/W6683523447"],"related_works":["https://openalex.org/W2568580722","https://openalex.org/W2911288319","https://openalex.org/W4301305631","https://openalex.org/W2950986437","https://openalex.org/W2134014174","https://openalex.org/W2399707041","https://openalex.org/W2255292617","https://openalex.org/W4224216279","https://openalex.org/W2112067162","https://openalex.org/W2157770058"],"abstract_inverted_index":{"MOTIVATION:":[0],"Because":[1],"of":[2,5,36,42,93],"the":[3,157],"advantages":[4],"RNA":[6],"sequencing":[7,141],"(RNA-Seq)":[8],"over":[9],"microarrays,":[10],"it":[11,55],"is":[12,25,90,131],"gaining":[13],"widespread":[14],"popularity":[15],"for":[16,48,160],"highly":[17,132],"parallel":[18],"gene":[19],"expression":[20],"analysis.":[21],"For":[22],"example,":[23],"RNA-Seq":[24],"expected":[26],"to":[27,30,72,75,111,156],"be":[28,174],"able":[29],"provide":[31],"accurate":[32,133],"identification":[33],"and":[34,63,81,95,107,127,147,169],"quantification":[35],"full-length":[37],"splice":[38,136],"forms.":[39],"A":[40],"number":[41],"informatics":[43],"packages":[44],"have":[45],"been":[46],"developed":[47],"this":[49],"purpose,":[50],"but":[51],"short":[52],"reads":[53],"make":[54],"a":[56,91],"difficult":[57],"problem":[58],"in":[59],"principle.":[60],"Sequencing":[61],"error":[62],"polymorphisms":[64],"add":[65],"further":[66,161],"complications.":[67],"It":[68],"has":[69],"become":[70],"necessary":[71],"perform":[73,79,86],"studies":[74],"determine":[76],"which":[77,82],"algorithms":[78,85],"best":[80],"if":[83],"any":[84],"adequately.":[87],"However,":[88],"there":[89],"dearth":[92],"independent":[94],"unbiased":[96],"benchmarking":[97],"studies.":[98],"Here":[99],"we":[100],"take":[101],"an":[102],"approach":[103],"using":[104,124],"both":[105],"simulated":[106],"experimental":[108],"benchmark":[109],"data":[110,181],"evaluate":[112],"their":[113],"accuracy.":[114],"RESULTS:":[115],"We":[116],"conclude":[117],"that":[118,128],"most":[119],"methods":[120],"are":[121,151,182],"inaccurate":[122],"even":[123],"idealized":[125],"data,":[126],"no":[129],"method":[130],"once":[134],"multiple":[135],"forms,":[137],"polymorphisms,":[138],"intron":[139],"signal,":[140],"errors,":[142,144],"alignment":[143],"annotation":[145],"errors":[146],"other":[148,170],"complicating":[149],"factors":[150],"present.":[152],"These":[153],"results":[154],"point":[155],"pressing":[158],"need":[159],"algorithm":[162],"development.":[163],"AVAILABILITY":[164],"AND":[165],"IMPLEMENTATION:":[166],"Simulated":[167],"datasets":[168],"supporting":[171],"information":[172],"can":[173],"found":[175],"at":[176,184],"http://bioinf.itmat.upenn.edu/BEERS/bp2.":[177],"SUPPLEMENTARY":[178],"INFORMATION:":[179],"Supplementary":[180],"available":[183],"Bioinformatics":[185],"online.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
