{"id":"https://openalex.org/W4297493876","doi":"https://doi.org/10.1186/s12859-022-04939-w","title":"APA-Scan: detection and visualization of 3\u2032-UTR alternative polyadenylation with RNA-seq and 3\u2032-end-seq data","display_name":"APA-Scan: detection and visualization of 3\u2032-UTR alternative polyadenylation with RNA-seq and 3\u2032-end-seq data","publication_year":2022,"publication_date":"2022-09-28","ids":{"openalex":"https://openalex.org/W4297493876","doi":"https://doi.org/10.1186/s12859-022-04939-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/36171568"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04939-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04939-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04939-w","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","license_id":"https://openalex.org/licenses/cc-by","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04939-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071466514","display_name":"Naima Ahmed Fahmi","orcid":"https://orcid.org/0000-0003-2745-2130"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naima Ahmed Fahmi","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074491379","display_name":"Khandakar Tanvir Ahmed","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Khandakar Tanvir Ahmed","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111920578","display_name":"Jae\u2010Woong Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jae-Woong Chang","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081202549","display_name":"Heba Nassereddeen","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heba Nassereddeen","raw_affiliation_strings":["Department of Computer Engineering, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047916979","display_name":"Deliang Fan","orcid":"https://orcid.org/0000-0002-7989-6297"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deliang Fan","raw_affiliation_strings":["School of Electrical, Computer and Energy Engineering, Arizona State University, 650 E Tyler Mall, Tempe, AZ, 85287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical, Computer and Energy Engineering, Arizona State University, 650 E Tyler Mall, Tempe, AZ, 85287, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010172507","display_name":"Jeongsik Yong","orcid":"https://orcid.org/0000-0002-2758-0450"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210101327","display_name":"Twin Cities Orthopedics","ror":"https://ror.org/01en4s460","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101327"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeongsik Yong","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA. jyong@umn.edu","Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA. jyong@umn.edu","institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210101327"]},{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 420 Washington Ave. S.E., Minneapolis, MN, 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100441789","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0003-3605-9373"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA. wzhang.cs@ucf.edu","Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA"],"raw_orcid":"https://orcid.org/0000-0003-3605-9373","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA. wzhang.cs@ucf.edu","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5010172507","https://openalex.org/A5100441789"],"corresponding_institution_ids":["https://openalex.org/I106165777","https://openalex.org/I130238516","https://openalex.org/I4210101327"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.213,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.78235859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"23","issue":"S3","first_page":"396","last_page":"396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9970999956130981,"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":0.9970999956130981,"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":0.0005000000237487257,"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":0.0005000000237487257,"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":0.9276896119117737},{"id":"https://openalex.org/keywords/untranslated-region","display_name":"Untranslated region","score":0.674791157245636},{"id":"https://openalex.org/keywords/three-prime-untranslated-region","display_name":"Three prime untranslated region","score":0.6373603940010071},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6066185832023621},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47182804346084595},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4371928870677948},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.39999839663505554},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.36851775646209717}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.9276896119117737},{"id":"https://openalex.org/C89604277","wikidata":"https://www.wikidata.org/wiki/Q424345","display_name":"Untranslated region","level":4,"score":0.674791157245636},{"id":"https://openalex.org/C22667442","wikidata":"https://www.wikidata.org/wiki/Q3272830","display_name":"Three prime untranslated region","level":5,"score":0.6373603940010071},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6066185832023621},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47182804346084595},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4371928870677948},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39999839663505554},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.36851775646209717}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"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":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012322","descriptor_name":"RNA Precursors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012322","descriptor_name":"RNA Precursors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012322","descriptor_name":"RNA Precursors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012322","descriptor_name":"RNA Precursors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04939-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04939-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04939-w","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36171568","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36171568","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:doaj.org/article:73aa49f2544e4f40a4dc1ad28ac37c2c","is_oa":true,"landing_page_url":"https://doaj.org/article/73aa49f2544e4f40a4dc1ad28ac37c2c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss S3, Pp 1-14 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9520800","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9520800","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04939-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04939-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04939-w","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","license_id":"https://openalex.org/licenses/cc-by","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/G1005616485","display_name":null,"funder_award_id":"U24 DK097771","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G1019699972","display_name":null,"funder_award_id":"09&apos","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G1316583835","display_name":null,"funder_award_id":"R01 GM113952","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2817000484","display_name":null,"funder_award_id":"FET2003749","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2987990644","display_name":null,"funder_award_id":"2&apos","funder_id":"https://openalex.org/F4320332169","funder_display_name":"Directorate for Computer and Information Science and Engineering"},{"id":"https://openalex.org/G3476934849","display_name":null,"funder_award_id":"2'003749","funder_id":"https://openalex.org/F4320332169","funder_display_name":"Directorate for Computer and Information Science and Engineering"},{"id":"https://openalex.org/G6782162763","display_name":null,"funder_award_id":"09'7771","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G8018275787","display_name":null,"funder_award_id":"003749","funder_id":"https://openalex.org/F4320332169","funder_display_name":"Directorate for Computer and Information Science and Engineering"},{"id":"https://openalex.org/G8169943893","display_name":null,"funder_award_id":"DK097771","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332169","display_name":"Directorate for Computer and Information Science and Engineering","ror":"https://ror.org/025kzpk63"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4297493876.pdf","grobid_xml":"https://content.openalex.org/works/W4297493876.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1964727443","https://openalex.org/W1967637890","https://openalex.org/W1985267020","https://openalex.org/W2036065307","https://openalex.org/W2053057991","https://openalex.org/W2061537056","https://openalex.org/W2099915768","https://openalex.org/W2105879579","https://openalex.org/W2108234281","https://openalex.org/W2118031210","https://openalex.org/W2123285201","https://openalex.org/W2124985265","https://openalex.org/W2137307000","https://openalex.org/W2140729960","https://openalex.org/W2144137440","https://openalex.org/W2151866777","https://openalex.org/W2254187956","https://openalex.org/W2283446040","https://openalex.org/W2461965332","https://openalex.org/W2612122212","https://openalex.org/W2750490914","https://openalex.org/W2790970997","https://openalex.org/W2799303691"],"related_works":["https://openalex.org/W2157467537","https://openalex.org/W2073461718","https://openalex.org/W2019107363","https://openalex.org/W2750747499","https://openalex.org/W2773320331","https://openalex.org/W1535356260","https://openalex.org/W2025227979","https://openalex.org/W2069993237","https://openalex.org/W3216855095","https://openalex.org/W1990741123"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,280,297,325],"eukaryotic":[2],"genome":[3,310],"is":[4,58,226,314],"capable":[5],"of":[6,26,51,164,185,189,201,211,271,282],"producing":[7],"multiple":[8],"isoforms":[9],"from":[10],"a":[11,39,65,91,126,155,233,315,342],"gene":[12,69,141],"by":[13,287],"alternative":[14],"polyadenylation":[15,103,152,158],"(APA)":[16],"during":[17],"pre-mRNA":[18],"processing.":[19],"APA":[20,57,84,109,132,195,273,306,323],"in":[21,81,170,176,228],"the":[22,49,52,72,136,162,171,182,186,193,199,202,222,269,277,338],"3'-untranslated":[23],"region":[24],"(3'-UTR)":[25],"mRNA":[27,53],"produces":[28],"transcripts":[29,169],"with":[30,140,215,256,341],"shorter":[31],"or":[32,148],"longer":[33],"3'-UTR.":[34],"Often,":[35],"3'-UTR":[36,56,83,108,131,168,187,216,223,272,305,322],"serves":[37],"as":[38,154],"binding":[40],"platform":[41],"for":[42,157],"microRNAs":[43],"and":[44,63,90,134,160,166,197,218,232,250,254,262,290,308,330,334],"RNA-binding":[45],"proteins,":[46],"which":[47],"affect":[48],"fate":[50],"transcript.":[54],"Thus,":[55],"known":[59],"to":[60,67,87,247,276,319],"modulate":[61],"translation":[62],"provides":[64],"mean":[66],"regulate":[68],"expression":[70],"at":[71,240],"post-transcriptional":[73],"level.":[74],"Current":[75],"bioinformatics":[76,97],"pipelines":[77,98],"have":[78],"limited":[79],"capability":[80],"profiling":[82],"events":[85,133,203,307,340],"due":[86],"incomplete":[88],"annotations":[89],"low-resolution":[92],"analyzing":[93],"power:":[94],"widely":[95,258],"available":[96,239],"do":[99],"not":[100],"reference":[101,156],"actionable":[102,151],"(cleavage)":[104],"sites":[105,159,196],"but":[106],"simulate":[107],"only":[110],"using":[111],"RNA-seq":[112,137,172,252,329],"read":[113,183,219],"coverage,":[114],"causing":[115],"false":[116],"positive":[117],"identifications.":[118],"To":[119],"overcome":[120],"these":[121],"limitations,":[122],"we":[123],"developed":[124],"APA-Scan,":[125],"robust":[127],"program":[128],"that":[129,300],"identifies":[130],"visualizes":[135],"short-read":[138],"coverage":[139,184,220,346],"annotations.":[142],"METHODS:":[143],"APA-Scan":[144,174,225,244,266,283,301,313],"utilizes":[145],"either":[146],"predicted":[147],"experimentally":[149],"validated":[150,286],"signals":[153],"calculates":[161],"quantity":[163],"long":[165],"short":[167,344],"data.":[173],"works":[175],"three":[177],"major":[178],"steps:":[179],"(i)":[180],"calculate":[181],"regions":[188],"genes;":[190],"(ii)":[191],"identify":[192,337],"potential":[194],"evaluate":[198],"significance":[200],"among":[204],"two":[205,257],"biological":[206],"conditions;":[207],"(iii)":[208],"graphical":[209],"representation":[210],"user":[212],"specific":[213],"event":[214],"annotation":[217],"on":[221,292],"regions.":[224],"implemented":[227],"Python3.":[229],"Source":[230],"code":[231],"comprehensive":[234,316],"user's":[235],"manual":[236],"are":[237],"freely":[238],"https://github.com/compbiolabucf/APA-Scan":[241],".":[242],"RESULT:":[243],"was":[245,284],"applied":[246],"both":[248,328],"simulated":[249],"real":[251],"datasets":[253],"compared":[255,275],"used":[259],"baselines":[260],"DaPars":[261],"APAtrap.":[263],"In":[264],"simulation":[265],"significantly":[267],"improved":[268],"accuracy":[270],"identification":[274],"other":[278],"baselines.":[279],"performance":[281],"also":[285],"3'-end-seq":[288,331],"data":[289,332],"qPCR":[291],"mouse":[293],"embryonic":[294],"fibroblast":[295],"cells.":[296],"experiments":[298],"confirm":[299],"can":[302,335],"detect":[303,320],"unannotated":[304],"improve":[309],"annotation.":[311],"CONCLUSION:":[312],"computational":[317],"pipeline":[318,326],"transcriptome-wide":[321],"events.":[324],"integrates":[327],"information":[333],"efficiently":[336],"significant":[339],"high-resolution":[343],"reads":[345],"plots.":[347]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}