{"id":"https://openalex.org/W4404509619","doi":"https://doi.org/10.1093/bioinformatics/btae689","title":"APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data","display_name":"APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data","publication_year":2024,"publication_date":"2024-11-01","ids":{"openalex":"https://openalex.org/W4404509619","doi":"https://doi.org/10.1093/bioinformatics/btae689","pmid":"https://pubmed.ncbi.nlm.nih.gov/39558592"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae689","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae689/60744093/btae689.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae689/60744093/btae689.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101790615","display_name":"Bruno Sousa","orcid":"https://orcid.org/0000-0002-3995-8545"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210147873","display_name":"Instituto de Biolog\u00eda Molecular y Celular de Rosario","ror":"https://ror.org/04x0n3178","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4141589","https://openalex.org/I4210107757","https://openalex.org/I4210123736","https://openalex.org/I4210147873","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]}],"countries":["AR","PT"],"is_corresponding":false,"raw_author_name":"Bruno Sousa","raw_affiliation_strings":["FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210147873"]},{"raw_affiliation_string":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083249426","display_name":"Maria Jo\u00e3o Bessa","orcid":"https://orcid.org/0000-0001-5357-6167"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210147873","display_name":"Instituto de Biolog\u00eda Molecular y Celular de Rosario","ror":"https://ror.org/04x0n3178","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4141589","https://openalex.org/I4210107757","https://openalex.org/I4210123736","https://openalex.org/I4210147873","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]}],"countries":["AR","PT"],"is_corresponding":false,"raw_author_name":"Maria Bessa","raw_affiliation_strings":["Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210147873"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069741202","display_name":"Filipa Lopes de Mendon\u00e7a","orcid":null},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210147873","display_name":"Instituto de Biolog\u00eda Molecular y Celular de Rosario","ror":"https://ror.org/04x0n3178","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4141589","https://openalex.org/I4210107757","https://openalex.org/I4210123736","https://openalex.org/I4210147873","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]}],"countries":["AR","PT"],"is_corresponding":false,"raw_author_name":"Filipa L de Mendon\u00e7a","raw_affiliation_strings":["Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210147873"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089291118","display_name":"Pedro G. Ferreira","orcid":"https://orcid.org/0000-0003-3838-8664"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I4210166615","display_name":"INESC TEC","ror":"https://ror.org/05fa8ka61","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210125590","https://openalex.org/I4210166615"]}],"countries":["PT","US"],"is_corresponding":false,"raw_author_name":"Pedro G Ferreira","raw_affiliation_strings":["FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","Laboratory of Artificial Intelligence and Decision Support, Institute for Systems and Computer Engineering Technology and Science , Porto, 4200-465,","FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto,","Laboratory of Artificial Intelligence and Decision Support, Institute for Systems and Computer Engineering, Technology and Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Laboratory of Artificial Intelligence and Decision Support, Institute for Systems and Computer Engineering Technology and Science , Porto, 4200-465,","institution_ids":["https://openalex.org/I4210143601"]},{"raw_affiliation_string":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Laboratory of Artificial Intelligence and Decision Support, Institute for Systems and Computer Engineering, Technology and Science","institution_ids":["https://openalex.org/I4210166615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039265804","display_name":"Alexandra Moreira","orcid":"https://orcid.org/0000-0001-9853-7575"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210147873","display_name":"Instituto de Biolog\u00eda Molecular y Celular de Rosario","ror":"https://ror.org/04x0n3178","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4141589","https://openalex.org/I4210107757","https://openalex.org/I4210123736","https://openalex.org/I4210147873","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]}],"countries":["AR","PT"],"is_corresponding":true,"raw_author_name":"Alexandra Moreira","raw_affiliation_strings":["Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto , Porto, 4050-313,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto , Porto,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210147873"]},{"raw_affiliation_string":"ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto , Porto, 4050-313,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025712968","display_name":"Isabel Pereira\u2010Castro","orcid":"https://orcid.org/0000-0003-4149-4310"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210147873","display_name":"Instituto de Biolog\u00eda Molecular y Celular de Rosario","ror":"https://ror.org/04x0n3178","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4141589","https://openalex.org/I4210107757","https://openalex.org/I4210123736","https://openalex.org/I4210147873","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]}],"countries":["AR","PT"],"is_corresponding":true,"raw_author_name":"Isabel Pereira-Castro","raw_affiliation_strings":["Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,"],"raw_orcid":"https://orcid.org/0000-0003-4149-4310","affiliations":[{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","institution_ids":["https://openalex.org/I4210147873"]},{"raw_affiliation_string":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto,","institution_ids":["https://openalex.org/I182534213"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5025712968","https://openalex.org/A5039265804"],"corresponding_institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210147873","https://openalex.org/I4210158732"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1617,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50742819,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9570000171661377,"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":0.9570000171661377,"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":0.007199999876320362,"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":0.00419999985024333,"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/polyadenylation","display_name":"Polyadenylation","score":0.7456169128417969},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7327860593795776},{"id":"https://openalex.org/keywords/venn-diagram","display_name":"Venn diagram","score":0.6324559450149536},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5610637664794922},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5088441371917725},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4661378264427185},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4562689960002899},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4284190535545349},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.19947120547294617},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19227644801139832},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14996689558029175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13271144032478333},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12102615833282471},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09920534491539001},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.07773727178573608}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7456169128417969},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7327860593795776},{"id":"https://openalex.org/C55508974","wikidata":"https://www.wikidata.org/wiki/Q190763","display_name":"Venn diagram","level":2,"score":0.6324559450149536},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5610637664794922},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5088441371917725},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4661378264427185},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4562689960002899},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4284190535545349},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.19947120547294617},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19227644801139832},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14996689558029175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13271144032478333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12102615833282471},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09920534491539001},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.07773727178573608},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C145420912","wikidata":"https://www.wikidata.org/wiki/Q853077","display_name":"Mathematics education","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D006801","descriptor_name":"Humans","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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae689","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae689/60744093/btae689.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39558592","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39558592","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:pubmedcentral.nih.gov:11601165","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11601165","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11601165/pdf/btae689.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae689","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae689","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae689/60744093/btae689.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G1483381719","display_name":null,"funder_award_id":"DL-57/2016","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G647086953","display_name":"Institute for Research and Innovation in Health","funder_award_id":"UIDB/04293/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7666823738","display_name":null,"funder_award_id":"13854","funder_id":"https://openalex.org/F4320308573","funder_display_name":"Gilead Sciences"}],"funders":[{"id":"https://openalex.org/F4320308573","display_name":"Gilead Sciences","ror":"https://ror.org/056546b03"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404509619.pdf","grobid_xml":"https://content.openalex.org/works/W4404509619.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1976007281","https://openalex.org/W2050345155","https://openalex.org/W2099915768","https://openalex.org/W2108264419","https://openalex.org/W2179438025","https://openalex.org/W2751247278","https://openalex.org/W2786594082","https://openalex.org/W2888423279","https://openalex.org/W3016836964","https://openalex.org/W3154988157","https://openalex.org/W3163200965","https://openalex.org/W3175752499","https://openalex.org/W3200242554","https://openalex.org/W4205728595","https://openalex.org/W4321769100","https://openalex.org/W4379878805","https://openalex.org/W6797786779"],"related_works":["https://openalex.org/W4306970587","https://openalex.org/W4256478115","https://openalex.org/W2338867480","https://openalex.org/W1497899451","https://openalex.org/W2744696476","https://openalex.org/W3156165154","https://openalex.org/W1517268357","https://openalex.org/W2060300418","https://openalex.org/W3100271225","https://openalex.org/W3081644756"],"abstract_inverted_index":{"SUMMARY:":[0],"APAtizer":[1,97],"is":[2],"a":[3,29],"tool":[4,15],"designed":[5],"to":[6,35,51],"analyze":[7],"alternative":[8],"polyadenylation":[9,61],"events":[10,62],"on":[11],"RNA-sequencing":[12],"data.":[13],"The":[14],"handles":[16],"different":[17],"file":[18],"formats,":[19],"including":[20,39],"BAM,":[21],"htseq,":[22],"and":[23,43,84,92],"DaPars":[24],"bedGraph":[25],"files.":[26],"It":[27],"provides":[28],"user-friendly":[30],"interface":[31],"that":[32],"allows":[33],"users":[34],"generate":[36],"informative":[37],"visualizations,":[38],"Volcano":[40],"plots,":[41],"heatmaps,":[42],"gene":[44,74,76],"lists.":[45],"These":[46],"outputs":[47],"allow":[48],"the":[49,58],"user":[50],"retrieve":[52],"useful":[53],"biological":[54,66],"insights":[55],"such":[56],"as":[57],"occurrence":[59],"of":[60,80],"when":[63],"comparing":[64],"two":[65],"conditions.":[67],"In":[68],"addition,":[69],"it":[70],"can":[71],"perform":[72],"differential":[73],"expression,":[75],"ontology":[77],"analysis,":[78],"visualization":[79],"Venn":[81],"diagram":[82],"intersections,":[83],"correlation":[85],"analysis.":[86],"AVAILABILITY":[87],"AND":[88],"IMPLEMENTATION:":[89],"Source":[90],"code":[91],"example":[93],"case":[94],"studies":[95],"for":[96],"are":[98],"available":[99],"at":[100],"https://github.com/GeneRegulationi3S/APAtizer/.":[101]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
