{"id":"https://openalex.org/W4225541717","doi":"https://doi.org/10.1073/pnas.2116269118","title":"LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2","display_name":"LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4225541717","doi":"https://doi.org/10.1073/pnas.2116269118","pmid":"https://pubmed.ncbi.nlm.nih.gov/34887342"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.2116269118","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2116269118","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1073/pnas.2116269118","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101703838","display_name":"Sizhen Li","orcid":"https://orcid.org/0000-0001-7807-5748"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sizhen Li","raw_affiliation_strings":["School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;"],"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420092","display_name":"He Zhang","orcid":"https://orcid.org/0000-0001-5877-2167"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"He Zhang","raw_affiliation_strings":["Baidu Research, Sunnyvale, CA 94089;","School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;"],"affiliations":[{"raw_affiliation_string":"Baidu Research, Sunnyvale, CA 94089;","institution_ids":[]},{"raw_affiliation_string":"School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425266","display_name":"Liang Zhang","orcid":"https://orcid.org/0000-0003-1146-7848"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Zhang","raw_affiliation_strings":["Baidu Research, Sunnyvale, CA 94089;","School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;"],"affiliations":[{"raw_affiliation_string":"Baidu Research, Sunnyvale, CA 94089;","institution_ids":[]},{"raw_affiliation_string":"School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101568681","display_name":"Kaibo Liu","orcid":"https://orcid.org/0000-0002-9053-8810"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kaibo Liu","raw_affiliation_strings":["Baidu Research, Sunnyvale, CA 94089;","School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;"],"affiliations":[{"raw_affiliation_string":"Baidu Research, Sunnyvale, CA 94089;","institution_ids":[]},{"raw_affiliation_string":"School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052636953","display_name":"Boxiang Liu","orcid":"https://orcid.org/0000-0002-2595-4463"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Boxiang Liu","raw_affiliation_strings":["Baidu Research, Sunnyvale, CA 94089;"],"affiliations":[{"raw_affiliation_string":"Baidu Research, Sunnyvale, CA 94089;","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002272329","display_name":"David H. Mathews","orcid":"https://orcid.org/0000-0002-2907-6557"},"institutions":[{"id":"https://openalex.org/I28792581","display_name":"University of Rochester Medical Center","ror":"https://ror.org/00trqv719","country_code":"US","type":"funder","lineage":["https://openalex.org/I28792581","https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David H. Mathews","raw_affiliation_strings":["Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642;","Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642;","Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY 14642"],"affiliations":[{"raw_affiliation_string":"Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642;","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642;","institution_ids":["https://openalex.org/I28792581"]},{"raw_affiliation_string":"Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY 14642","institution_ids":["https://openalex.org/I28792581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006404928","display_name":"Liang Huang","orcid":"https://orcid.org/0000-0001-6444-7045"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liang Huang","raw_affiliation_strings":["Baidu Research, Sunnyvale, CA 94089;","School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;"],"affiliations":[{"raw_affiliation_string":"Baidu Research, Sunnyvale, CA 94089;","institution_ids":[]},{"raw_affiliation_string":"School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97331;","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5002272329","https://openalex.org/A5006404928"],"corresponding_institution_ids":["https://openalex.org/I131249849","https://openalex.org/I28792581"],"apc_list":null,"apc_paid":null,"fwci":1.6231,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.84341282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"118","issue":"52","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":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":0.9993000030517578,"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":0.9980000257492065,"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","display_name":"RNA","score":0.7298880815505981},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6483572125434875},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6368576288223267},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.5948604345321655},{"id":"https://openalex.org/keywords/coronavirus","display_name":"Coronavirus","score":0.5471041798591614},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.5183752179145813},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5022943019866943},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.459434449672699},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4459567070007324},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.4165884852409363},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.36484387516975403},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36398816108703613},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3407004475593567},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33985477685928345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3065882921218872},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13955172896385193},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.07536351680755615}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7298880815505981},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6483572125434875},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6368576288223267},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.5948604345321655},{"id":"https://openalex.org/C2777648638","wikidata":"https://www.wikidata.org/wiki/Q57751738","display_name":"Coronavirus","level":5,"score":0.5471041798591614},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.5183752179145813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5022943019866943},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.459434449672699},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4459567070007324},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.4165884852409363},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.36484387516975403},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36398816108703613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3407004475593567},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33985477685928345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3065882921218872},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13955172896385193},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.07536351680755615},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000073640","descriptor_name":"Betacoronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1073/pnas.2116269118","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2116269118","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmid:34887342","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34887342","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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8719904","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8719904","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1073/pnas.2116269118","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2116269118","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8299999833106995,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G4633775321","display_name":null,"funder_award_id":"R01 GM132185","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4976625600","display_name":null,"funder_award_id":"IIS-1817231","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W166206240","https://openalex.org/W894213101","https://openalex.org/W1542426682","https://openalex.org/W1559908984","https://openalex.org/W1965077482","https://openalex.org/W1966500795","https://openalex.org/W1980410097","https://openalex.org/W1984006325","https://openalex.org/W1984675364","https://openalex.org/W1987680287","https://openalex.org/W1988512789","https://openalex.org/W2011368877","https://openalex.org/W2013989449","https://openalex.org/W2018216725","https://openalex.org/W2019590688","https://openalex.org/W2024412145","https://openalex.org/W2051188149","https://openalex.org/W2082847215","https://openalex.org/W2086561953","https://openalex.org/W2087021327","https://openalex.org/W2095145214","https://openalex.org/W2098271534","https://openalex.org/W2098571862","https://openalex.org/W2111272410","https://openalex.org/W2114094654","https://openalex.org/W2119340328","https://openalex.org/W2119377644","https://openalex.org/W2124861326","https://openalex.org/W2133279153","https://openalex.org/W2134861301","https://openalex.org/W2137076005","https://openalex.org/W2140872496","https://openalex.org/W2141152740","https://openalex.org/W2141351700","https://openalex.org/W2142056356","https://openalex.org/W2153140501","https://openalex.org/W2159548583","https://openalex.org/W2160378127","https://openalex.org/W2165824239","https://openalex.org/W2166745309","https://openalex.org/W2168420558","https://openalex.org/W2169185001","https://openalex.org/W2170157200","https://openalex.org/W2170342148","https://openalex.org/W2300188811","https://openalex.org/W2408839459","https://openalex.org/W2472632604","https://openalex.org/W2587970647","https://openalex.org/W2733628661","https://openalex.org/W2759571676","https://openalex.org/W2763042654","https://openalex.org/W2790566782","https://openalex.org/W2897202882","https://openalex.org/W3003217347","https://openalex.org/W3004499272","https://openalex.org/W3005389897","https://openalex.org/W3024057275","https://openalex.org/W3034555852","https://openalex.org/W3036482641","https://openalex.org/W3043664941","https://openalex.org/W3087412117","https://openalex.org/W3091134219","https://openalex.org/W3091406140","https://openalex.org/W3095990266","https://openalex.org/W3098049011","https://openalex.org/W3116296722","https://openalex.org/W3116376362","https://openalex.org/W3127145950","https://openalex.org/W3134749134","https://openalex.org/W3158350126","https://openalex.org/W4245668478","https://openalex.org/W6600991755"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W2581348958","https://openalex.org/W2264054990","https://openalex.org/W2581888268","https://openalex.org/W2902683473","https://openalex.org/W1989561030","https://openalex.org/W2088051090"],"abstract_inverted_index":{"The":[0],"constant":[1],"emergence":[2],"of":[3,9,141],"COVID-19":[4],"variants":[5],"reduces":[6],"the":[7,41,71,170,249],"effectiveness":[8],"existing":[10,82],"vaccines":[11],"and":[12,38,51,63,143,175,197,207,220,237,241,251],"test":[13],"kits.":[14],"Therefore,":[15],"it":[16],"is":[17,153,224],"critical":[18],"to":[19,43,89,155,233],"identify":[20],"conserved":[21,46,195,198],"structures":[22,87,196],"in":[23,110,148,247],"severe":[24],"acute":[25],"respiratory":[26],"syndrome":[27],"coronavirus":[28],"2":[29],"(SARS-CoV-2)":[30],"genomes":[31,73],"as":[32,92,94,201],"potential":[33,202],"targets":[34,203],"for":[35,67,120,159,204],"variant-proof":[36],"diagnostics":[37],"therapeutics.":[39],"However,":[40],"algorithms":[42],"predict":[44],"these":[45],"structures,":[47,161],"which":[48,69,102],"simultaneously":[49],"fold":[50],"align":[52],"multiple":[53],"RNA":[54,77,111,122,235],"homologs,":[55],"scale":[56],"at":[57],"best":[58],"cubically":[59],"with":[60,98,127,186],"sequence":[61,128],"length":[62],"are":[64,108],"thus":[65],"infeasible":[66],"coronaviruses,":[68],"possess":[70],"longest":[72],"(\u223c30,000":[74],"nt)":[75],"among":[76],"viruses.":[78],"As":[79],"a":[80,139,187,225,244],"result,":[81],"efforts":[83],"on":[84,135,138],"modeling":[85],"SARS-CoV-2":[86,142],"resort":[88],"single-sequence":[90],"folding":[91,96,121],"well":[93],"local":[95,160],"methods":[97],"short":[99],"window":[100],"sizes,":[101],"inevitably":[103],"neglect":[104],"long-range":[105],"interactions":[106],"that":[107,124,183,228],"crucial":[109],"functions.":[112],"Here":[113],"we":[114],"present":[115],"LinearTurboFold,":[116],"an":[117],"efficient":[118,206],"algorithm":[119],"homologs":[123],"scales":[125],"linearly":[126],"length,":[129],"enabling":[130],"unprecedented":[131],"global":[132],"structural":[133],"analysis":[134],"SARS-CoV-2.":[136],"Surprisingly,":[137],"group":[140],"SARS-related":[144],"genomes,":[145],"LinearTurboFold's":[146],"purely":[147,188],"silico":[149],"prediction":[150],"not":[151],"only":[152],"close":[154],"experimentally":[156],"guided":[157],"models":[158],"but":[162],"also":[163,230],"goes":[164],"far":[165],"beyond":[166],"them":[167],"by":[168],"capturing":[169],"end-to-end":[171],"pairs":[172],"between":[173],"5'":[174],"3'":[176],"untranslated":[177],"regions":[178,200],"(UTRs)":[179],"(\u223c29,800":[180],"nt":[181],"apart)":[182],"match":[184],"perfectly":[185],"experimental":[189],"work.":[190],"Furthermore,":[191],"LinearTurboFold":[192,223],"identifies":[193],"undiscovered":[194],"accessible":[199],"designing":[205],"mutation-insensitive":[208],"small-molecule":[209],"drugs,":[210],"antisense":[211],"oligonucleotides,":[212],"small":[213],"interfering":[214],"RNAs":[215],"(siRNAs),":[216],"CRISPR-Cas13":[217],"guide":[218],"RNAs,":[219],"RT-PCR":[221],"primers.":[222],"general":[226],"technique":[227],"can":[229],"be":[231,243],"applied":[232],"other":[234],"viruses":[236],"full-length":[238],"genome":[239],"studies":[240],"will":[242],"useful":[245],"tool":[246],"fighting":[248],"current":[250],"future":[252],"pandemics.":[253]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}