{"id":"https://openalex.org/W7125279003","doi":"https://doi.org/10.1186/s12859-026-06368-5","title":"CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool","display_name":"CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool","publication_year":2026,"publication_date":"2026-01-21","ids":{"openalex":"https://openalex.org/W7125279003","doi":"https://doi.org/10.1186/s12859-026-06368-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/41566196"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06368-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06368-5","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-026-06368-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5099988496","display_name":"Gilles Sireta","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210103002","display_name":"University of Clermont Auvergne","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210103002"]},{"id":"https://openalex.org/I4210123221","display_name":"Sigma Clermont","ror":"https://ror.org/02n5evf44","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214","https://openalex.org/I4210123221","https://openalex.org/I4387154249"]},{"id":"https://openalex.org/I4210143836","display_name":"Clermont Universit\u00e9","ror":"https://ror.org/03yf5zr20","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210143836"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gilles Sireta","raw_affiliation_strings":["Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210123221","https://openalex.org/I154526488","https://openalex.org/I4210103002","https://openalex.org/I4210143836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059275846","display_name":"Gwendal CUEFF","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210137075","display_name":"Centre de Recherche en Nutrition Humaine d'Auvergne","ror":"https://ror.org/03rzyjb72","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210137075"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gwendal Cueff","raw_affiliation_strings":["UMR 1019, INRAE, Unit\u00e9 de Nutrition Humaine, Universit\u00e9 Clermont Auvergne, 63000, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR 1019, INRAE, Unit\u00e9 de Nutrition Humaine, Universit\u00e9 Clermont Auvergne, 63000, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I4210137075","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123520098","display_name":"Vincent Darbot","orcid":null},"institutions":[{"id":"https://openalex.org/I129162050","display_name":"TBS Education","ror":"https://ror.org/0349y2q65","country_code":"FR","type":"education","lineage":["https://openalex.org/I129162050","https://openalex.org/I4405263209"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Darbot","raw_affiliation_strings":["Aviwell SAS, TWB Campus, 31077, Toulouse, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aviwell SAS, TWB Campus, 31077, Toulouse, France","institution_ids":["https://openalex.org/I129162050"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123513888","display_name":"Marie Lefebvre","orcid":null},"institutions":[{"id":"https://openalex.org/I198244214","display_name":"Universit\u00e9 Clermont Auvergne","ror":"https://ror.org/01a8ajp46","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marie Lefebvre","raw_affiliation_strings":["Universit\u00e9 Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du M\u00e9tabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du M\u00e9tabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I4210088668","https://openalex.org/I198244214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034162926","display_name":"Simon Amiard","orcid":"https://orcid.org/0000-0002-0427-1647"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210103002","display_name":"University of Clermont Auvergne","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210103002"]},{"id":"https://openalex.org/I4210123221","display_name":"Sigma Clermont","ror":"https://ror.org/02n5evf44","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214","https://openalex.org/I4210123221","https://openalex.org/I4387154249"]},{"id":"https://openalex.org/I4210143836","display_name":"Clermont Universit\u00e9","ror":"https://ror.org/03yf5zr20","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210143836"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Simon Amiard","raw_affiliation_strings":["Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210123221","https://openalex.org/I154526488","https://openalex.org/I4210103002","https://openalex.org/I4210143836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020455495","display_name":"Aline V. Probst","orcid":"https://orcid.org/0000-0001-9534-8058"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210103002","display_name":"University of Clermont Auvergne","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210103002"]},{"id":"https://openalex.org/I4210123221","display_name":"Sigma Clermont","ror":"https://ror.org/02n5evf44","country_code":"FR","type":"education","lineage":["https://openalex.org/I198244214","https://openalex.org/I4210123221","https://openalex.org/I4387154249"]},{"id":"https://openalex.org/I4210143836","display_name":"Clermont Universit\u00e9","ror":"https://ror.org/03yf5zr20","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210143836"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Aline V. Probst","raw_affiliation_strings":["Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210123221","https://openalex.org/I154526488","https://openalex.org/I4210103002","https://openalex.org/I4210143836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042995991","display_name":"Christophe Tatout","orcid":"https://orcid.org/0000-0001-5215-2338"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210103002","display_name":"University of Clermont Auvergne","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210103002"]},{"id":"https://openalex.org/I4210143836","display_name":"Clermont Universit\u00e9","ror":"https://ror.org/03yf5zr20","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210143836"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Christophe Tatout","raw_affiliation_strings":["Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France. christophe.tatout@uca.fr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France. christophe.tatout@uca.fr","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210103002","https://openalex.org/I4210143836","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5042995991"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210103002","https://openalex.org/I4210143836"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11556631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"43","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.6133000254631042,"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":0.6133000254631042,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.07729999721050262,"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/T12610","display_name":"RNA regulation and disease","score":0.06759999692440033,"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/scalability","display_name":"Scalability","score":0.6234999895095825},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.428600013256073},{"id":"https://openalex.org/keywords/element","display_name":"Element (criminal law)","score":0.33090001344680786},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.31839999556541443},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3176000118255615}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6790000200271606},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6234999895095825},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.428600013256073},{"id":"https://openalex.org/C200288055","wikidata":"https://www.wikidata.org/wiki/Q2621792","display_name":"Element (criminal law)","level":2,"score":0.33090001344680786},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.31839999556541443},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3176000118255615},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3172000050544739},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.2946999967098236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.29409998655319214},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2865999937057495},{"id":"https://openalex.org/C129119673","wikidata":"https://www.wikidata.org/wiki/Q4418003","display_name":"Network element","level":2,"score":0.25450000166893005},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.2540999948978424},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.25279998779296875}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","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":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"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":6,"locations":[{"id":"doi:10.1186/s12859-026-06368-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06368-5","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41566196","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41566196","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-05598122v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-05598122","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics, 2026, 27 (1), pp.43. &#x27E8;10.1186/s12859-026-06368-5&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:15f4f3020b0b454d9a1e98091c07a452","is_oa":true,"landing_page_url":"https://doaj.org/article/15f4f3020b0b454d9a1e98091c07a452","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11702992","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12895761","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12895761","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12895761/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06368-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06368-5","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8504063463","display_name":null,"funder_award_id":"16IDEX0001 CAP 2025 CIR 1","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W2066231767","https://openalex.org/W2110417468","https://openalex.org/W2118458682","https://openalex.org/W2155115337","https://openalex.org/W2161645441","https://openalex.org/W2167262093","https://openalex.org/W2302501749","https://openalex.org/W2323326409","https://openalex.org/W2406493898","https://openalex.org/W2530385183","https://openalex.org/W2556763090","https://openalex.org/W2560726917","https://openalex.org/W2572857085","https://openalex.org/W2592811885","https://openalex.org/W2605897695","https://openalex.org/W2612976808","https://openalex.org/W2799170276","https://openalex.org/W2915489249","https://openalex.org/W2921922051","https://openalex.org/W2949513937","https://openalex.org/W3006653136","https://openalex.org/W3012529551","https://openalex.org/W3017119031","https://openalex.org/W3093580068","https://openalex.org/W3110764155","https://openalex.org/W3115957378","https://openalex.org/W3122109253","https://openalex.org/W4200099322","https://openalex.org/W4313488537","https://openalex.org/W4362596286","https://openalex.org/W4362656986","https://openalex.org/W4392111189","https://openalex.org/W4392446671","https://openalex.org/W4410278703"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Traditional":[1],"short-read":[2],"RNA-Seq":[3,103],"analysis":[4,117,165],"pipelines":[5],"predominantly":[6],"focus":[7],"on":[8,218,239,253],"protein-coding":[9,194],"genes,":[10,195],"often":[11],"overlooking":[12],"other":[13],"genomic":[14],"sequences":[15],"such":[16],"as":[17,191],"transposable":[18],"elements":[19],"(TEs)":[20],"and":[21,25,43,65,87,101,115,127,197],"non-coding":[22],"RNA":[23],"dynamics":[24,70],"do":[26],"not":[27],"usually":[28],"investigate":[29],"splicing":[30,200],"events":[31,201],"or":[32,166,222],"transcript":[33,125],"usage.":[34],"To":[35,76],"fully":[36,99],"capture":[37],"the":[38,41,72,113,148,151,175,180,188],"complexity":[39],"of":[40,68,96,112,118,139,154],"transcriptome,":[42],"in":[44,71,172],"particular":[45],"transcriptomic":[46,268],"regulation,":[47],"it":[48,214],"is":[49,262,271],"crucial":[50],"to":[51,143,234,248],"adopt":[52],"a":[53,62,92,98,163,169,219,223,227,232,242,263],"comprehensive":[54,102,267],"approach":[55],"that":[56,213],"integrates":[57,106],"these":[58,78],"diverse":[59],"aspects,":[60],"providing":[61],"more":[63],"complete":[64,164],"nuanced":[66],"understanding":[67],"expression":[69],"studied":[73],"organism.":[74],"RESULTS:":[75],"address":[77],"limitations,":[79],"we":[80],"present":[81],"CRESCENT":[82,105,183,210,261],"(Comprehensive":[83],"RNA-seq":[84],"Expression,":[85],"Splicing,":[86],"Coding/non-coding":[88],"Element":[89],"Network":[90],"Tool),":[91],"Snakemake":[93,141],"workflow":[94,114,136,184],"capable":[95],"performing":[97],"automated":[100],"analysis.":[104],"multiple":[107,140],"tools":[108],"at":[109,274],"each":[110],"step":[111],"enables":[116],"differential":[119,121,124,198],"expression,":[120],"alternative":[122,199],"splicing,":[123],"usage,":[126],"gene":[128],"ontology-based":[129],"functional":[130],"enrichment":[131],"for":[132,147,162,167,266],"all":[133],"three.":[134],"The":[135,182],"takes":[137],"advantage":[138],"wrappers":[142],"minimize":[144],"required":[145],"installations":[146],"user,":[149],"integrating":[150],"latest":[152],"versions":[153],"popular":[155],"bioinformatic":[156],"tools.":[157],"It":[158,270],"can":[159,215],"be":[160,216],"run":[161,217],"only":[168],"specific":[170],"part":[171],"accordance":[173],"with":[174,204],"configuration":[176],"file":[177],"provided":[178],"by":[179],"user.":[181],"was":[185],"validated,":[186],"demonstrating":[187],"pipeline's":[189],"reliability,":[190],"differentially":[192],"expressed":[193],"TEs":[196],"were":[202],"consistent":[203],"previously":[205],"published":[206],"datasets.":[207],"Finally,":[208],"benchmarking":[209],"performance":[211],"indicated":[212],"personal":[220],"computer":[221],"remote":[224],"server,":[225],"including":[226],"high-performance":[228],"computing":[229],"cluster,":[230],"allowing":[231],"user":[233],"process":[235],"small":[236,243],"single-end":[237],"sequencing":[238,252],"species":[240,255],"possessing":[241],"genome":[244],"like":[245,256],"Arabidopsis":[246],"thaliana":[247],"very":[249],"large":[250],"paired-end":[251],"polyploid":[254],"wheat.":[257],"CONCLUSION":[258],"AND":[259],"AVAILABILITY:":[260],"scalable":[264],"solution":[265],"profiling.":[269],"freely":[272],"available":[273],"https://github.com/gilless429/crescent":[275],".":[276]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-01-22T00:00:00"}
