{"id":"https://openalex.org/W3029756392","doi":"https://doi.org/10.1080/15476286.2020.1760534","title":"Predicting RNA SHAPE scores with deep learning","display_name":"Predicting RNA SHAPE scores with deep learning","publication_year":2020,"publication_date":"2020-05-31","ids":{"openalex":"https://openalex.org/W3029756392","doi":"https://doi.org/10.1080/15476286.2020.1760534","mag":"3029756392","pmid":"https://pubmed.ncbi.nlm.nih.gov/32476596","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7549691"},"language":"en","primary_location":{"id":"doi:10.1080/15476286.2020.1760534","doi":"https://doi.org/10.1080/15476286.2020.1760534","is_oa":false,"landing_page_url":"https://doi.org/10.1080/15476286.2020.1760534","pdf_url":null,"source":{"id":"https://openalex.org/S143072383","display_name":"RNA Biology","issn_l":"1547-6286","issn":["1547-6286","1555-8584"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RNA Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7549691/pdf/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058269509","display_name":"Noah Bliss","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah Bliss","raw_affiliation_strings":["RNA Biology Laboratory, National Cancer Institute , Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RNA Biology Laboratory, National Cancer Institute , Frederick, MD, USA","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108820718","display_name":"Eckart Bindewald","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eckart Bindewald","raw_affiliation_strings":["Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210130649"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010562576","display_name":"Bruce A. Shapiro","orcid":"https://orcid.org/0000-0002-4443-0788","observed_orcids":["https://orcid.org/0000-0002-4443-0788"]},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bruce A. Shapiro","raw_affiliation_strings":["RNA Biology Laboratory, National Cancer Institute , Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RNA Biology Laboratory, National Cancer Institute , Frederick, MD, USA","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010562576"],"corresponding_institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"],"apc_list":{"value":3175,"currency":"USD","value_usd":3175},"apc_paid":null,"fwci":0.2141,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.38363847,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"17","issue":"9","first_page":"1324","last_page":"1330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9970999956130981,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10044","display_name":"Protein Structure and Dynamics","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/T10604","display_name":"RNA Research and Splicing","score":0.00039999998989515007,"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/rna-secondary-structure-prediction","display_name":"RNA secondary structure prediction","score":0.8379999995231628},{"id":"https://openalex.org/keywords/shape-map","display_name":"SHAPE-MaP","score":0.8769999742507935},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.5960000157356262},{"id":"https://openalex.org/keywords/nucleotide-sequence","display_name":"nucleotide sequence","score":0.7369999885559082}],"concepts":[{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.777894139289856},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.777011513710022},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6341294050216675},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6310815215110779},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5922300219535828},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.577548623085022},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.541810154914856},{"id":"https://openalex.org/C207001950","wikidata":"https://www.wikidata.org/wiki/Q141124","display_name":"In vivo","level":2,"score":0.46380093693733215},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45986318588256836},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43416231870651245},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4298114776611328},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3652702569961548},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21505051851272583},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18697649240493774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16863355040550232},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1070123016834259},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018387","descriptor_name":"Codon, Initiator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1080/15476286.2020.1760534","doi":"https://doi.org/10.1080/15476286.2020.1760534","is_oa":false,"landing_page_url":"https://doi.org/10.1080/15476286.2020.1760534","pdf_url":null,"source":{"id":"https://openalex.org/S143072383","display_name":"RNA Biology","issn_l":"1547-6286","issn":["1547-6286","1555-8584"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RNA Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7549691","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7549691/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7549691/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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RNA Biol","raw_type":"Text"},{"id":"pmid:32476596","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32476596","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,"listed_in":[],"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":"RNA biology","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7549691","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7549691/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7549691/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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RNA Biol","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3503792436","display_name":null,"funder_award_id":"#HHSN261200800001E","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G386607036","display_name":null,"funder_award_id":"HHSN261200800001E)","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4585269469","display_name":null,"funder_award_id":"HHSN261200800001E","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G4988656331","display_name":null,"funder_award_id":"HHSN261200800001E.","funder_id":"https://openalex.org/F4320313762","funder_display_name":"Frederick National Laboratory for Cancer Research"},{"id":"https://openalex.org/G5888954722","display_name":null,"funder_award_id":"HHSN261200800001C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320313762","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3029756392.pdf","grobid_xml":"https://content.openalex.org/works/W3029756392.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1972533328","https://openalex.org/W1985278607","https://openalex.org/W2003993220","https://openalex.org/W2036412199","https://openalex.org/W2076091642","https://openalex.org/W2086561953","https://openalex.org/W2097117768","https://openalex.org/W2112796928","https://openalex.org/W2131841865","https://openalex.org/W2133203832","https://openalex.org/W2271840356","https://openalex.org/W2463016798","https://openalex.org/W2793097545","https://openalex.org/W2958013639","https://openalex.org/W2995939123","https://openalex.org/W4236965008"],"related_works":["https://openalex.org/W2624696515","https://openalex.org/W7212420088","https://openalex.org/W3176770387","https://openalex.org/W2071883352","https://openalex.org/W611505772","https://openalex.org/W3126773939","https://openalex.org/W2558432341","https://openalex.org/W3154280227","https://openalex.org/W2553954981","https://openalex.org/W2766137885"],"abstract_inverted_index":{"Secondary":[0],"structure":[1,28,82,132],"prediction":[2,83],"approaches":[3],"rely":[4],"typically":[5],"on":[6,16,30],"models":[7,48],"of":[8,24,55],"equilibrium":[9],"free":[10],"energies":[11],"that":[12,36,78,98,134],"are":[13],"themselves":[14],"based":[15,29],"in":[17,25,44,49,66,88,92],"vitro":[18],"physical":[19],"chemistry.":[20],"Recent":[21],"transcriptome-wide":[22],"experiments":[23,32],"vivo":[26,67,93],"RNA":[27,46,57,68,80,130],"SHAPE-MaP":[31],"provide":[33],"important":[34,118],"information":[35],"may":[37],"make":[38],"it":[39],"possible":[40],"to":[41,51,62,90],"extend":[42],"current":[43],"vitro-based":[45],"folding":[47,58,138],"order":[50,89],"improve":[52],"the":[53,63],"accuracy":[54],"computational":[56,125],"simulations":[59],"with":[60,107,124,129],"respect":[61],"experimentally":[64],"measured":[65],"secondary":[69,81,131],"structure.":[70],"Here":[71],"we":[72],"present":[73],"a":[74,102],"machine":[75],"learning":[76],"approach":[77,100],"utilizes":[79],"results":[84,123],"and":[85,127],"nucleotide":[86],"sequence":[87],"predict":[91],"SHAPE":[94,109],"scores.":[95],"We":[96],"show":[97],"this":[99],"has":[101],"higher":[103],"Pearson":[104],"correlation":[105],"coefficient":[106],"experimental":[108,122],"scores":[110],"than":[111],"thermodynamic":[112],"folding.":[113],"This":[114],"could":[115],"be":[116],"an":[117],"step":[119],"towards":[120],"augmenting":[121],"predictions":[126,133],"help":[128],"inherently":[135],"take":[136],"in-vivo":[137],"properties":[139],"into":[140],"account.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2020-06-05T00:00:00"}
