{"id":"https://openalex.org/W2134223330","doi":"https://doi.org/10.1093/bioinformatics/btt034","title":"RNA-eXpress annotates novel transcript features in RNA-seq data","display_name":"RNA-eXpress annotates novel transcript features in RNA-seq data","publication_year":2013,"publication_date":"2013-02-08","ids":{"openalex":"https://openalex.org/W2134223330","doi":"https://doi.org/10.1093/bioinformatics/btt034","mag":"2134223330","pmid":"https://pubmed.ncbi.nlm.nih.gov/23396121"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/810/48901649/bioinformatics_29_6_810.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/29/6/810/48901649/bioinformatics_29_6_810.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004051536","display_name":"Samuel C. Forster","orcid":"https://orcid.org/0000-0003-4144-2537"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]},{"id":"https://openalex.org/I60733029","display_name":"Monash Institute of Medical Research","ror":"https://ror.org/05p96ba03","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I60733029"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Samuel C. Forster","raw_affiliation_strings":["Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168"],"affiliations":[{"raw_affiliation_string":"Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168","institution_ids":["https://openalex.org/I60733029","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009501314","display_name":"Alexander M. Finkel","orcid":null},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]},{"id":"https://openalex.org/I60733029","display_name":"Monash Institute of Medical Research","ror":"https://ror.org/05p96ba03","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I60733029"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Alexander M. Finkel","raw_affiliation_strings":["Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168"],"affiliations":[{"raw_affiliation_string":"Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168","institution_ids":["https://openalex.org/I60733029","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069350946","display_name":"Jodee A. Gould","orcid":null},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]},{"id":"https://openalex.org/I60733029","display_name":"Monash Institute of Medical Research","ror":"https://ror.org/05p96ba03","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I60733029"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jodee A. Gould","raw_affiliation_strings":["Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168"],"affiliations":[{"raw_affiliation_string":"Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168","institution_ids":["https://openalex.org/I60733029","https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035018866","display_name":"Paul J. Hertzog","orcid":"https://orcid.org/0000-0002-1373-8472"},"institutions":[{"id":"https://openalex.org/I60733029","display_name":"Monash Institute of Medical Research","ror":"https://ror.org/05p96ba03","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I60733029"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Paul J. Hertzog","raw_affiliation_strings":["Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168"],"affiliations":[{"raw_affiliation_string":"Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia, 3168","institution_ids":["https://openalex.org/I60733029","https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5004051536"],"corresponding_institution_ids":["https://openalex.org/I56590836","https://openalex.org/I60733029"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.794,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.85090519,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"6","first_page":"810","last_page":"812"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9994999766349792,"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":0.9994000196456909,"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/annotation","display_name":"Annotation","score":0.668300211429596},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6245520710945129},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5353076457977295},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5329638123512268},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4643191993236542},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45282042026519775},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.45180171728134155},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25991278886795044},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19099676609039307},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10756188631057739}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.668300211429596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6245520710945129},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5353076457977295},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5329638123512268},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4643191993236542},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45282042026519775},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.45180171728134155},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25991278886795044},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19099676609039307},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10756188631057739},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","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":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btt034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/810/48901649/bioinformatics_29_6_810.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:23396121","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23396121","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:jupiter.its.unimelb.edu.au:11343/272023","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/272023","pdf_url":"http://hdl.handle.net/11343/272023","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:monash.edu:publications/9e945c6b-71be-469b-8bba-86f17c5e394a","is_oa":true,"landing_page_url":"https://research.monash.edu/en/publications/9e945c6b-71be-469b-8bba-86f17c5e394a","pdf_url":null,"source":{"id":"https://openalex.org/S4306402625","display_name":"Monash University Research Portal (Monash University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56590836","host_organization_name":"Monash University","host_organization_lineage":["https://openalex.org/I56590836"],"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":"Forster, S, Finkel, A M, Gould, J A & Hertzog, P J 2013, 'RNA-eXpress annotates novel transcript features in RNA-seq data', Bioinformatics, vol. 29, no. 6, pp. 810 - 812. https://doi.org/10.1093/bioinformatics/btt034","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2596310","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3597146","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:monash.edu:Publications/9e945c6b-71be-469b-8bba-86f17c5e394a","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402625","display_name":"Monash University Research Portal (Monash University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56590836","host_organization_name":"Monash University","host_organization_lineage":["https://openalex.org/I56590836"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/810/48901649/bioinformatics_29_6_810.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":[],"funders":[{"id":"https://openalex.org/F4320322858","display_name":"State Government of Victoria","ror":"https://ror.org/02xvc5r05"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134223330.pdf","grobid_xml":"https://content.openalex.org/works/W2134223330.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W1981509058","https://openalex.org/W2000875411","https://openalex.org/W2100305481","https://openalex.org/W2108234281"],"related_works":["https://openalex.org/W1892467659","https://openalex.org/W1529400504","https://openalex.org/W2998403542","https://openalex.org/W2808586768","https://openalex.org/W4248817909","https://openalex.org/W4367048510","https://openalex.org/W2164324468","https://openalex.org/W2469937864","https://openalex.org/W2333703843","https://openalex.org/W4293076875"],"abstract_inverted_index":{"Next-generation":[0],"sequencing":[1],"is":[2,162],"rapidly":[3],"becoming":[4],"the":[5,62,138],"approach":[6],"of":[7,51,92,121,130,190],"choice":[8],"for":[9,68,103],"transcriptional":[10,127],"analysis":[11],"experiments.":[12],"Substantial":[13],"advances":[14],"have":[15],"been":[16],"achieved":[17],"in":[18,137,150],"computational":[19,44],"approaches":[20,26],"to":[21,164,172,184],"support":[22],"these":[23],"technologies.":[24],"These":[25],"typically":[27],"rely":[28],"on":[29,49],"existing":[30,97],"transcript":[31],"annotations,":[32],"introducing":[33],"a":[34,109,146],"bias":[35],"towards":[36],"known":[37],"genes,":[38],"require":[39],"specific":[40],"experimental":[41],"design":[42],"and":[43,78,90,112,123,126,144,157],"resources,":[45],"or":[46,188],"focus":[47],"only":[48],"identification":[50,120,189],"splice":[52],"variants":[53],"(ignoring":[54],"other":[55,124],"biologically":[56],"relevant":[57,72],"transcribed":[58,73],"features":[59,74,128],"contained":[60],"within":[61],"data":[63],"that":[64,118],"may":[65],"be":[66,165],"important":[67],"downstream":[69],"analysis).":[70],"Biologically":[71],"also":[75],"include":[76],"large":[77],"small":[79],"non-coding":[80],"RNA,":[81],"new":[82,174],"transcription":[83],"start":[84],"sites,":[85],"alternative":[86],"promoters,":[87],"RNA":[88],"editing":[89],"processing":[91],"coding":[93],"transcripts.":[94],"Also,":[95],"many":[96],"solutions":[98],"lack":[99],"accessible":[100,167],"interfaces":[101],"required":[102],"wide":[104],"scale":[105],"adoption.":[106],"We":[107],"present":[108],"user-friendly,":[110],"rapid":[111],"computation-efficient":[113],"feature":[114,148,158,186,192],"annotation":[115,149],"framework":[116,161],"(RNA-eXpress)":[117],"enables":[119],"transcripts":[122],"genomic":[125],"independently":[129],"current":[131],"annotations.":[132],"RNA-eXpress":[133],"accepts":[134],"mapped":[135],"reads":[136],"standard":[139],"binary":[140],"alignment":[141],"(BAM)":[142],"format":[143],"produces":[145],"study-specific":[147,191],"GTF":[151],"format,":[152],"comparison":[153],"statistics,":[154],"sequence":[155],"extraction":[156],"counts.":[159],"The":[160],"designed":[163],"easily":[166],"while":[168],"allowing":[169],"advanced":[170],"users":[171],"integrate":[173],"feature-identification":[175],"algorithms":[176],"through":[177],"simple":[178],"class":[179],"extension,":[180],"thus":[181],"facilitating":[182],"expansion":[183],"novel":[185],"types":[187],"types.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2025-10-10T00:00:00"}