{"id":"https://openalex.org/W4410357313","doi":"https://doi.org/10.1145/3672608.3707762","title":"RepAs: Iterative Refinement for Predicting Polyadenylation Site Usage","display_name":"RepAs: Iterative Refinement for Predicting Polyadenylation Site Usage","publication_year":2025,"publication_date":"2025-03-31","ids":{"openalex":"https://openalex.org/W4410357313","doi":"https://doi.org/10.1145/3672608.3707762"},"language":"en","primary_location":{"id":"doi:10.1145/3672608.3707762","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3672608.3707762","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3672608.3707762","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM/SIGAPP Symposium on Applied Computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3672608.3707762","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092247175","display_name":"Eleni Giovanoudi","orcid":"https://orcid.org/0009-0000-8580-9367"},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Eleni Giovanoudi","raw_affiliation_strings":["University of Thessaly, Volos, Greece"],"affiliations":[{"raw_affiliation_string":"University of Thessaly, Volos, Greece","institution_ids":["https://openalex.org/I145722265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034151597","display_name":"Dimitrios Rafailidis","orcid":"https://orcid.org/0000-0002-7366-3716"},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Dimitrios Rafailidis","raw_affiliation_strings":["University of Thessaly, Volos, Greece"],"affiliations":[{"raw_affiliation_string":"University of Thessaly, Volos, Greece","institution_ids":["https://openalex.org/I145722265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5092247175"],"corresponding_institution_ids":["https://openalex.org/I145722265"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11505136,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"161","last_page":"168"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10604","display_name":"RNA Research and Splicing","score":0.9995999932289124,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9966999888420105,"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/computer-science","display_name":"Computer science","score":0.6259410381317139},{"id":"https://openalex.org/keywords/polyadenylation","display_name":"Polyadenylation","score":0.5946889519691467},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07962581515312195},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07337924838066101}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6259410381317139},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.5946889519691467},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07962581515312195},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07337924838066101},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3672608.3707762","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3672608.3707762","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3672608.3707762","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM/SIGAPP Symposium on Applied Computing","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3672608.3707762","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3672608.3707762","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3672608.3707762","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM/SIGAPP Symposium on Applied Computing","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410357313.pdf","grobid_xml":"https://content.openalex.org/works/W4410357313.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1975707733","https://openalex.org/W1984397453","https://openalex.org/W1985267020","https://openalex.org/W2015663091","https://openalex.org/W2026663202","https://openalex.org/W2075054758","https://openalex.org/W2077940776","https://openalex.org/W2099305989","https://openalex.org/W2099915768","https://openalex.org/W2101852192","https://openalex.org/W2129429612","https://openalex.org/W2133019267","https://openalex.org/W2272187370","https://openalex.org/W2582462755","https://openalex.org/W2763864472","https://openalex.org/W2790178665","https://openalex.org/W2790970997","https://openalex.org/W2888955024","https://openalex.org/W2902896987","https://openalex.org/W2919633911","https://openalex.org/W2940943632","https://openalex.org/W2948558658","https://openalex.org/W2949671734","https://openalex.org/W2955517832","https://openalex.org/W2963430933","https://openalex.org/W3159968191"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1976007281","https://openalex.org/W195216885","https://openalex.org/W1968152888","https://openalex.org/W2081082232","https://openalex.org/W4205787488","https://openalex.org/W2065213545","https://openalex.org/W2082559221"],"abstract_inverted_index":{"Alternative":[0],"Polyadenylation":[1],"is":[2,13,18],"an":[3],"essential":[4],"post-transcriptional":[5],"process.":[6],"By":[7],"selecting":[8],"which":[9],"polyadenylation":[10],"(poly(A))":[11],"site":[12,79],"cleaved,":[14],"a":[15,66,81,91,122,127],"single":[16],"gene":[17],"enabled":[19],"to":[20,48,111,131],"generate":[21],"multiple":[22],"transcript":[23],"isoforms":[24],"with":[25,44,126],"different":[26],"3\u2032":[27],"untranslated":[28],"regions.":[29],"However,":[30],"previous":[31,105],"studies":[32],"have":[33],"focused":[34],"on":[35,142],"the":[36,50,58,73,87,101,104,108,114,134,147,150,164],"identification":[37],"of":[38,53,76,136,149,166],"poly(A)":[39,55,78,96,137],"sites":[40,56,106],"within":[41,80,107],"genomic":[42],"sequences,":[43],"limited":[45],"research":[46],"dedicated":[47],"quantifying":[49],"usage":[51,74,92],"level":[52,75],"alternative":[54],"in":[57],"same":[59,109],"gene.":[60],"In":[61,85],"this":[62],"paper,":[63],"we":[64,162],"propose":[65],"novel":[67],"Iterative":[68],"Refinement":[69],"model":[70,88],"for":[71,94,103,113,159],"predicting":[72],"each":[77,95],"gene,":[82,110],"namely":[83],"RepAs.":[84],"particular,":[86],"iteratively":[89],"predicts":[90],"value":[93],"site,":[97],"while":[98],"simultaneously":[99],"refining":[100],"predictions":[102],"account":[112],"competing":[115],"interactions":[116],"between":[117],"them.":[118],"Furthermore,":[119],"RepAs":[120,167],"integrates":[121],"feature":[123],"refinement":[124],"process":[125],"custom":[128],"attention":[129],"mechanism":[130],"progressively":[132],"improve":[133],"representation":[135],"site-related":[138],"features.":[139],"Our":[140],"experiments":[141],"publicly":[143,168],"available":[144,169],"datasets":[145],"demonstrate":[146],"effectiveness":[148],"proposed":[151],"approach,":[152],"outperforming":[153],"other":[154],"state-of-the":[155],"art":[156],"methods.":[157],"Finally,":[158],"reproduction":[160],"purposes,":[161],"make":[163],"implementation":[165],"at":[170],"https://github.com/egiovanoudi/RepAs.":[171]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}