{"id":"https://openalex.org/W7117885468","doi":"https://doi.org/10.1093/bib/bbaf701","title":"From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling","display_name":"From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W7117885468","doi":"https://doi.org/10.1093/bib/bbaf701","pmid":"https://pubmed.ncbi.nlm.nih.gov/41470045"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf701","pdf_url":null,"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://doi.org/10.1093/bib/bbaf701","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101472868","display_name":"Fatemeh Safari","orcid":"https://orcid.org/0000-0003-4218-4496"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Fatemeh Safari","raw_affiliation_strings":["School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,","UNSW Biomedical AI, University of New South Wales , Sydney, NSW 2052 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]},{"raw_affiliation_string":"UNSW Biomedical AI, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060479152","display_name":"Jai J. Tree","orcid":"https://orcid.org/0000-0001-8233-0975"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jai J Tree","raw_affiliation_strings":["School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090363651","display_name":"Fatemeh Vafaee","orcid":"https://orcid.org/0000-0002-7521-2417"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Fatemeh Vafaee","raw_affiliation_strings":["School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,","UNSW AI Institute, University of New South Wales , Sydney, NSW 2052 ,","UNSW Biomedical AI, University of New South Wales , Sydney, NSW 2052 ,"],"raw_orcid":"https://orcid.org/0000-0002-7521-2417","affiliations":[{"raw_affiliation_string":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]},{"raw_affiliation_string":"UNSW AI Institute, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]},{"raw_affiliation_string":"UNSW Biomedical AI, University of New South Wales , Sydney, NSW 2052 ,","institution_ids":["https://openalex.org/I31746571"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090363651"],"corresponding_institution_ids":["https://openalex.org/I31746571"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.55596789,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"6","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":0.895799994468689,"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":0.895799994468689,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07109999656677246,"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":0.007699999958276749,"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/interpretability","display_name":"Interpretability","score":0.8827999830245972},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.6122000217437744},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5748999714851379},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.5734000205993652},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.46230000257492065},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.398499995470047}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8827999830245972},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7405999898910522},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6122000217437744},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5748999714851379},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.5734000205993652},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5486000180244446},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.46230000257492065},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4339999854564667},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.398499995470047},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38440001010894775},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.36899998784065247},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.35519999265670776},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.33000001311302185},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.31220000982284546},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.2989000082015991},{"id":"https://openalex.org/C101814296","wikidata":"https://www.wikidata.org/wiki/Q5439685","display_name":"Feature model","level":3,"score":0.2565000057220459}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf701","pdf_url":null,"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:41470045","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41470045","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:12753313","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12753313/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12753313/pdf/bbaf701.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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:11563894","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12753313","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf701","pdf_url":null,"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":105,"referenced_works":["https://openalex.org/W652664929","https://openalex.org/W1494484168","https://openalex.org/W1920564293","https://openalex.org/W1943237984","https://openalex.org/W1984385688","https://openalex.org/W1994958179","https://openalex.org/W1995168985","https://openalex.org/W1997730991","https://openalex.org/W2001168095","https://openalex.org/W2004132756","https://openalex.org/W2004945910","https://openalex.org/W2006898727","https://openalex.org/W2009818318","https://openalex.org/W2014933335","https://openalex.org/W2016143109","https://openalex.org/W2024213282","https://openalex.org/W2034070267","https://openalex.org/W2044955175","https://openalex.org/W2048194168","https://openalex.org/W2051713039","https://openalex.org/W2054697783","https://openalex.org/W2063599993","https://openalex.org/W2068881314","https://openalex.org/W2082436128","https://openalex.org/W2082599328","https://openalex.org/W2086561953","https://openalex.org/W2089852843","https://openalex.org/W2098571862","https://openalex.org/W2105349784","https://openalex.org/W2113816707","https://openalex.org/W2124303320","https://openalex.org/W2132247880","https://openalex.org/W2134065368","https://openalex.org/W2142217851","https://openalex.org/W2158503240","https://openalex.org/W2177784250","https://openalex.org/W2335029242","https://openalex.org/W2339812959","https://openalex.org/W2415310056","https://openalex.org/W2512477880","https://openalex.org/W2611058586","https://openalex.org/W2769887238","https://openalex.org/W2771225301","https://openalex.org/W2780936345","https://openalex.org/W2801398392","https://openalex.org/W2808191239","https://openalex.org/W2886900083","https://openalex.org/W2890017579","https://openalex.org/W2906416051","https://openalex.org/W2910705748","https://openalex.org/W2921372942","https://openalex.org/W2944704300","https://openalex.org/W2951413354","https://openalex.org/W2967960129","https://openalex.org/W2972223935","https://openalex.org/W2991913838","https://openalex.org/W2994158303","https://openalex.org/W2997903277","https://openalex.org/W3006550325","https://openalex.org/W3011537067","https://openalex.org/W3035761298","https://openalex.org/W3037668068","https://openalex.org/W3084492347","https://openalex.org/W3091943457","https://openalex.org/W3108297111","https://openalex.org/W3125850677","https://openalex.org/W3131672097","https://openalex.org/W3133097471","https://openalex.org/W3134163647","https://openalex.org/W3160021293","https://openalex.org/W3164771453","https://openalex.org/W3200707343","https://openalex.org/W3207924272","https://openalex.org/W3212684988","https://openalex.org/W3213133098","https://openalex.org/W4200038759","https://openalex.org/W4214812055","https://openalex.org/W4214837029","https://openalex.org/W4220832915","https://openalex.org/W4221132793","https://openalex.org/W4282929726","https://openalex.org/W4292406516","https://openalex.org/W4303859523","https://openalex.org/W4308735427","https://openalex.org/W4310665480","https://openalex.org/W4316468754","https://openalex.org/W4363649728","https://openalex.org/W4378349624","https://openalex.org/W4387616670","https://openalex.org/W4388763601","https://openalex.org/W4389117601","https://openalex.org/W4390704327","https://openalex.org/W4391920714","https://openalex.org/W4392462890","https://openalex.org/W4399691497","https://openalex.org/W4400060796","https://openalex.org/W4400956650","https://openalex.org/W4403172808","https://openalex.org/W4405310560","https://openalex.org/W4405706573","https://openalex.org/W4407843114","https://openalex.org/W4408745432","https://openalex.org/W4409786620","https://openalex.org/W4412587213","https://openalex.org/W4413893116"],"related_works":[],"abstract_inverted_index":{"Machine":[0],"learning":[1],"is":[2,26],"a":[3,96,123],"powerful":[4],"approach":[5],"for":[6,11],"analysing":[7],"RNA":[8,54,150],"sequences,":[9],"particularly":[10],"understanding":[12],"the":[13,51,75,78,101,110],"function":[14],"and":[15,42,59,64,90,130,136,145],"regulation":[16],"of":[17,53,77,103,112,126],"noncoding":[18],"RNAs.":[19],"A":[20],"critical":[21],"step":[22],"in":[23,147],"this":[24,70,138],"process":[25],"feature":[27,55,85,104,114],"extraction,":[28],"which":[29],"transforms":[30],"biological":[31,45],"sequences":[32],"into":[33,88],"numerical":[34],"representations":[35],"that":[36],"allow":[37],"computational":[38],"models":[39],"to":[40,141],"capture":[41],"interpret":[43],"complex":[44],"patterns.":[46],"Despite":[47],"its":[48],"central":[49],"role,":[50],"field":[52,79],"extraction":[56,86],"remains":[57],"broad":[58],"fragmented,":[60],"with":[61],"limited":[62],"standardization":[63],"accessibility":[65],"hindering":[66],"consistent":[67],"application.":[68],"In":[69],"comprehensive":[71],"review,":[72],"we":[73],"address":[74],"fragmentation":[76],"by":[80],"systematically":[81],"organizing":[82],"over":[83],"25":[84],"strategies":[87],"sequence-":[89],"structure-based":[91],"approaches.":[92],"We":[93],"further":[94],"conduct":[95],"comparative":[97],"analysis":[98],"highlighting":[99],"how":[100],"choice":[102],"sets":[105],"impacts":[106],"model":[107],"performance,":[108],"reinforcing":[109],"importance":[111],"integrated":[113],"engineering.":[115],"To":[116],"facilitate":[117],"practical":[118],"adoption,":[119],"it":[120],"also":[121],"provides":[122],"curated":[124],"list":[125],"publicly":[127],"available":[128],"tools":[129],"software":[131],"packages.":[132],"By":[133],"consolidating":[134],"methodologies":[135],"resources,":[137],"work":[139],"seeks":[140],"improve":[142],"reproducibility,":[143],"scalability,":[144],"interpretability":[146],"machine":[148],"learning-driven":[149],"research.":[151]},"counts_by_year":[],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2026-01-01T00:00:00"}