{"id":"https://openalex.org/W4410720283","doi":"https://doi.org/10.1093/bib/bbaf225","title":"Multi-objective computational optimization of human 5\u2032 UTR sequences","display_name":"Multi-objective computational optimization of human 5\u2032 UTR sequences","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410720283","doi":"https://doi.org/10.1093/bib/bbaf225","pmid":"https://pubmed.ncbi.nlm.nih.gov/40413870"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf225","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf225/63349587/bbaf225.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/26/3/bbaf225/63349587/bbaf225.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083328565","display_name":"Keisuke Yamada","orcid":"https://orcid.org/0000-0003-1256-9299"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["JP","US"],"is_corresponding":false,"raw_author_name":"Keisuke Yamada","raw_affiliation_strings":["Department of Bioengineering, University of Pennsylvania , 210 South 33rd Street, Philadelphia, PA 19104 ,","Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Pennsylvania , 210 South 33rd Street, Philadelphia, PA 19104 ,","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":[]},{"raw_affiliation_string":"Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039787949","display_name":"Kanta Suga","orcid":null},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kanta Suga","raw_affiliation_strings":["Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":[]},{"raw_affiliation_string":"Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004924093","display_name":"Naoko Abe","orcid":"https://orcid.org/0000-0001-6062-3515"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Naoko Abe","raw_affiliation_strings":["Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004889536","display_name":"Koji Hashimoto","orcid":"https://orcid.org/0000-0001-8024-0060"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koji Hashimoto","raw_affiliation_strings":["Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","Graduate School of Arts and Sciences, The University of Tokyo , 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 ,","Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Graduate School of Arts and Sciences, The University of Tokyo , 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 ,","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Susumu Tsutsumi","orcid":null},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Susumu Tsutsumi","raw_affiliation_strings":["Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090231944","display_name":"Masahito Inagaki","orcid":"https://orcid.org/0000-0001-9556-4586"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masahito Inagaki","raw_affiliation_strings":["Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045939473","display_name":"Fumitaka Hashiya","orcid":"https://orcid.org/0000-0003-1546-4126"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Fumitaka Hashiya","raw_affiliation_strings":["Research Center for Materials Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Materials Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015530734","display_name":"Hiroshi Abe","orcid":"https://orcid.org/0000-0003-0048-3789"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Abe","raw_affiliation_strings":["Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","Institute for Glyco-core Research (iGCORE), Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Aichi ,","Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,"],"raw_orcid":"https://orcid.org/0000-0003-0048-3789","affiliations":[{"raw_affiliation_string":"Department of Chemistry , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Institute for Glyco-core Research (iGCORE), Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Aichi ,","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Nagoya University , Graduate School of Science, , Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi ,","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I80188885","display_name":"Nippon Medical School","ror":"https://ror.org/00krab219","country_code":"JP","type":"education","lineage":["https://openalex.org/I80188885"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["Cellular and Molecular Biotechnology Research Institute (CMB), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7, Aomi, Koto-ku, Tokyo 135-0064 ,","Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","Graduate School of Medicine, Nippon Medical School , 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602 ,","Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,"],"raw_orcid":"https://orcid.org/0000-0001-9466-1034","affiliations":[{"raw_affiliation_string":"Cellular and Molecular Biotechnology Research Institute (CMB), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7, Aomi, Koto-ku, Tokyo 135-0064 ,","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":[]},{"raw_affiliation_string":"Graduate School of Medicine, Nippon Medical School , 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602 ,","institution_ids":["https://openalex.org/I80188885"]},{"raw_affiliation_string":"Waseda University , Graduate School of Advanced Science and Engineering, , 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555 ,","institution_ids":["https://openalex.org/I150744194"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.2068,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.87308283,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9991999864578247,"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":0.991599977016449,"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":0.6582984328269958},{"id":"https://openalex.org/keywords/untranslated-region","display_name":"Untranslated region","score":0.6153740882873535},{"id":"https://openalex.org/keywords/prime","display_name":"Prime (order theory)","score":0.6088641285896301},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5873408913612366},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4782409071922302},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4567185640335083},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.43205684423446655},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3182781934738159},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18966424465179443},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16004565358161926},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12899670004844666},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1288750171661377},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09218937158584595}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6582984328269958},{"id":"https://openalex.org/C89604277","wikidata":"https://www.wikidata.org/wiki/Q424345","display_name":"Untranslated region","level":4,"score":0.6153740882873535},{"id":"https://openalex.org/C184992742","wikidata":"https://www.wikidata.org/wiki/Q7243229","display_name":"Prime (order theory)","level":2,"score":0.6088641285896301},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5873408913612366},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4782409071922302},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4567185640335083},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.43205684423446655},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3182781934738159},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18966424465179443},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16004565358161926},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12899670004844666},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1288750171661377},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09218937158584595},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"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":"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":"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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf225","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf225/63349587/bbaf225.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40413870","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40413870","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12103902","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12103902","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf225","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf225/63349587/bbaf225.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1408967043","display_name":null,"funder_award_id":"JP22ama121055","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G1760691466","display_name":null,"funder_award_id":"24gm0010008","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G2576085165","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G342479731","display_name":"Platform for Advanced Genome Science","funder_award_id":"22H04925","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3909598355","display_name":null,"funder_award_id":"JP21ae0121049","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5111648280","display_name":null,"funder_award_id":"22H04925","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5303493250","display_name":null,"funder_award_id":"JPMJCR21F1","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G5613566846","display_name":null,"funder_award_id":"JPMJCR21F1","funder_id":"https://openalex.org/F4320317041","funder_display_name":"Collaborative Research in Engineering, Science and Technology Centre"},{"id":"https://openalex.org/G5722676322","display_name":"Overview and Systematic Understanding of Biological Phase Separation Based on RNA-Centric Molecular Networks","funder_award_id":"23H00509","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7669804585","display_name":"Elucidation of the function of long non-coding RNAs based on de novo discovery of repeat elements","funder_award_id":"20H00624","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8516532660","display_name":null,"funder_award_id":"JPMJCR23B3","funder_id":"https://openalex.org/F4320317041","funder_display_name":"Collaborative Research in Engineering, Science and Technology Centre"},{"id":"https://openalex.org/G8941101309","display_name":"RNA\u30ea\u30a4\u30f3\u30ab\u30cd\u30fc\u30b7\u30e7\u30f3","funder_award_id":"24K21326","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8943419055","display_name":null,"funder_award_id":"JPMJCR23B3","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320317041","display_name":"Collaborative Research in Engineering, Science and Technology Centre","ror":null},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410720283.pdf","grobid_xml":"https://content.openalex.org/works/W4410720283.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1538766821","https://openalex.org/W1583837637","https://openalex.org/W1906706885","https://openalex.org/W1986178107","https://openalex.org/W2037313242","https://openalex.org/W2058647478","https://openalex.org/W2074613554","https://openalex.org/W2109491705","https://openalex.org/W2124351063","https://openalex.org/W2145768602","https://openalex.org/W2427010553","https://openalex.org/W2521176812","https://openalex.org/W2747329762","https://openalex.org/W2750779823","https://openalex.org/W2792094507","https://openalex.org/W2810403368","https://openalex.org/W2908433735","https://openalex.org/W2952390442","https://openalex.org/W2955231772","https://openalex.org/W2983889514","https://openalex.org/W3011313923","https://openalex.org/W3017349264","https://openalex.org/W3037592148","https://openalex.org/W3045414875","https://openalex.org/W3111255098","https://openalex.org/W3113734454","https://openalex.org/W3127238141","https://openalex.org/W3185007959","https://openalex.org/W3190118369","https://openalex.org/W3200792349","https://openalex.org/W3205470891","https://openalex.org/W4200232768","https://openalex.org/W4220991830","https://openalex.org/W4310895557","https://openalex.org/W4311486625","https://openalex.org/W4367681391","https://openalex.org/W4376223644","https://openalex.org/W4386863222","https://openalex.org/W4394823561","https://openalex.org/W4399848621","https://openalex.org/W6636658889","https://openalex.org/W6755207826","https://openalex.org/W6779450718","https://openalex.org/W6796250220","https://openalex.org/W6801712475","https://openalex.org/W6810389141","https://openalex.org/W6845970670","https://openalex.org/W6852575741"],"related_works":["https://openalex.org/W2002886563","https://openalex.org/W2016832127","https://openalex.org/W1979226940","https://openalex.org/W2063674507","https://openalex.org/W2037244830","https://openalex.org/W2073834597","https://openalex.org/W2101281838","https://openalex.org/W1970755891","https://openalex.org/W2413745830","https://openalex.org/W2211593851"],"abstract_inverted_index":{"The":[0],"computational":[1,69,99],"design":[2,46,100],"of":[3,33,41,47,101],"messenger":[4],"RNA":[5],"(mRNA)":[6],"sequences":[7,51,77],"is":[8],"a":[9,68,79],"critical":[10],"technology":[11],"for":[12,107],"both":[13],"scientific":[14],"research":[15],"and":[16,23,31,87],"industrial":[17],"applications.":[18],"Recent":[19],"advances":[20],"in":[21,78,96],"prediction":[22],"optimization":[24,32],"models":[25],"have":[26],"enabled":[27],"the":[28,97,105],"automatic":[29],"scoring":[30],"$5^\\prime":[34,48,74],"$":[35,49,75],"UTR":[36,50,76],"sequences,":[37,103],"key":[38],"upstream":[39],"elements":[40],"mRNA.":[42],"However,":[43],"fully":[44],"automated":[45],"with":[52],"more":[53,108],"than":[54],"two":[55],"objective":[56],"scores":[57],"has":[58],"not":[59],"yet":[60],"been":[61],"explored.":[62],"In":[63],"this":[64],"study,":[65],"we":[66],"present":[67],"pipeline":[70],"that":[71],"optimizes":[72],"human":[73],"multi-objective":[80,98],"framework,":[81],"addressing":[82],"up":[83],"to":[84],"four":[85],"distinct":[86],"conflicting":[88],"objectives.":[89],"Our":[90],"work":[91],"represents":[92],"an":[93],"important":[94],"advancement":[95],"mRNA":[102,110],"paving":[104],"way":[106],"sophisticated":[109],"engineering.":[111]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}