{"id":"https://openalex.org/W3135161193","doi":"https://doi.org/10.1093/bioinformatics/btab165","title":"Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning","display_name":"Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning","publication_year":2021,"publication_date":"2021-03-08","ids":{"openalex":"https://openalex.org/W3135161193","doi":"https://doi.org/10.1093/bioinformatics/btab165","mag":"3135161193","pmid":"https://pubmed.ncbi.nlm.nih.gov/33704363"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab165","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab165","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jaswinder Singh","orcid":"https://orcid.org/0000-0003-4974-5188"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jaswinder Singh","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046089538","display_name":"Kuldip K. Paliwal","orcid":"https://orcid.org/0000-0002-3553-3662"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kuldip Paliwal","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067213513","display_name":"Tongchuan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Tongchuan Zhang","raw_affiliation_strings":["Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jaspreet Singh","orcid":"https://orcid.org/0000-0002-0478-5533"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jaspreet Singh","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia and","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048999222","display_name":"Thomas Litfin","orcid":"https://orcid.org/0000-0002-4863-3865"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas Litfin","raw_affiliation_strings":["Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032724151","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0002-9958-5699"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University , Southport, QLD, 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I11701301"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.0184,"has_fulltext":false,"cited_by_count":113,"citation_normalized_percentile":{"value":0.97534301,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"37","issue":"17","first_page":"2589","last_page":"2600"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/base-pair","display_name":"Base pair","score":0.6883653402328491},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.6620283126831055},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6590344905853271},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6150413155555725},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.611386239528656},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5628012418746948},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5308968424797058},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.48431363701820374},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.48205527663230896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47477126121520996},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.45699048042297363},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.4554036557674408},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4534284770488739},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36833202838897705},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3484686613082886},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.24372732639312744},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22981342673301697},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11904612183570862},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08782467246055603}],"concepts":[{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6883653402328491},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.6620283126831055},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6590344905853271},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6150413155555725},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.611386239528656},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5628012418746948},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5308968424797058},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.48431363701820374},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.48205527663230896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47477126121520996},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.45699048042297363},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.4554036557674408},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4534284770488739},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36833202838897705},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3484686613082886},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.24372732639312744},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22981342673301697},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11904612183570862},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08782467246055603},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab165","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab165","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33704363","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33704363","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/403138","is_oa":false,"landing_page_url":"http://hdl.handle.net/10072/403138","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1114770080","display_name":null,"funder_award_id":"DP180102060","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G5321982477","display_name":null,"funder_award_id":"Titan V GPU","funder_id":"https://openalex.org/F4320309480","funder_display_name":"Nvidia"},{"id":"https://openalex.org/G5657866599","display_name":null,"funder_award_id":"DP210101875","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320315813","display_name":"Queensland Cyber Infrastructure Foundation","ror":"https://ror.org/03sd43014"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W654652841","https://openalex.org/W1522301498","https://openalex.org/W1581231885","https://openalex.org/W1603840783","https://openalex.org/W1672171675","https://openalex.org/W1686007471","https://openalex.org/W1944024379","https://openalex.org/W1988512789","https://openalex.org/W1988884185","https://openalex.org/W1994958501","https://openalex.org/W2013425283","https://openalex.org/W2064675550","https://openalex.org/W2086561953","https://openalex.org/W2095145214","https://openalex.org/W2095705004","https://openalex.org/W2096525273","https://openalex.org/W2098571862","https://openalex.org/W2102017611","https://openalex.org/W2114977400","https://openalex.org/W2131462431","https://openalex.org/W2131774270","https://openalex.org/W2134489577","https://openalex.org/W2139541234","https://openalex.org/W2141152740","https://openalex.org/W2141351700","https://openalex.org/W2142038007","https://openalex.org/W2143407915","https://openalex.org/W2158267024","https://openalex.org/W2158714788","https://openalex.org/W2170747616","https://openalex.org/W2176412452","https://openalex.org/W2196304378","https://openalex.org/W2302255633","https://openalex.org/W2342307854","https://openalex.org/W2520200494","https://openalex.org/W2544136853","https://openalex.org/W2548501546","https://openalex.org/W2612940361","https://openalex.org/W2759571676","https://openalex.org/W2766234835","https://openalex.org/W2766848373","https://openalex.org/W2767701940","https://openalex.org/W2796092158","https://openalex.org/W2807745747","https://openalex.org/W2808896479","https://openalex.org/W2808950571","https://openalex.org/W2883782161","https://openalex.org/W2895077357","https://openalex.org/W2896704238","https://openalex.org/W2936498246","https://openalex.org/W2949867299","https://openalex.org/W2951298881","https://openalex.org/W2953085814","https://openalex.org/W2954102902","https://openalex.org/W2963285578","https://openalex.org/W2963840672","https://openalex.org/W2964121744","https://openalex.org/W2969527868","https://openalex.org/W2990528340","https://openalex.org/W2992343969","https://openalex.org/W2998627042","https://openalex.org/W3005909538","https://openalex.org/W3043664941","https://openalex.org/W3047090055","https://openalex.org/W3047826661","https://openalex.org/W3049756659","https://openalex.org/W3093994104","https://openalex.org/W3095895146","https://openalex.org/W3100820581","https://openalex.org/W3126773939","https://openalex.org/W3199799076","https://openalex.org/W3212533323","https://openalex.org/W4231042054","https://openalex.org/W4243601081","https://openalex.org/W6631190155","https://openalex.org/W6637288986","https://openalex.org/W6674330103","https://openalex.org/W6685562342","https://openalex.org/W6696085341","https://openalex.org/W6771520483","https://openalex.org/W6780226713","https://openalex.org/W6781590543","https://openalex.org/W6781813153","https://openalex.org/W7075630220"],"related_works":["https://openalex.org/W3047450301","https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W1978187259","https://openalex.org/W4318218930","https://openalex.org/W2057388609","https://openalex.org/W2159621058","https://openalex.org/W2412575231"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":29},{"year":2024,"cited_by_count":29},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":7}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
