{"id":"https://openalex.org/W4281749338","doi":"https://doi.org/10.1093/nar/gkac435","title":"Web-based platform for analysis of RNA folding from high throughput chemical probing data","display_name":"Web-based platform for analysis of RNA folding from high throughput chemical probing data","publication_year":2022,"publication_date":"2022-06-03","ids":{"openalex":"https://openalex.org/W4281749338","doi":"https://doi.org/10.1093/nar/gkac435","pmid":"https://pubmed.ncbi.nlm.nih.gov/35657086"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac435","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W266/44376882/gkac435.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/50/W1/W266/44376882/gkac435.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037300351","display_name":"Christopher P. Jurich","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher P Jurich","raw_affiliation_strings":["Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077412301","display_name":"Amir Brivanlou","orcid":"https://orcid.org/0009-0006-0058-8432"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amir Brivanlou","raw_affiliation_strings":["Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027703906","display_name":"Silvi Rouskin","orcid":"https://orcid.org/0000-0003-2042-6642"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Silvi Rouskin","raw_affiliation_strings":["Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035373472","display_name":"Joseph D. Yesselman","orcid":"https://orcid.org/0000-0001-8878-8119"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph D Yesselman","raw_affiliation_strings":["Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA"],"raw_orcid":"https://orcid.org/0000-0001-8878-8119","affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027703906","https://openalex.org/A5035373472"],"corresponding_institution_ids":["https://openalex.org/I114395901","https://openalex.org/I136199984"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.3917,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.53644811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"50","issue":"W1","first_page":"W266","last_page":"W271"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9983999729156494,"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/biology","display_name":"Biology","score":0.9052230715751648},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6094092726707458},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5275048017501831},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5043047666549683},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4846392273902893},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.338321328163147},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2099267542362213},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.16710886359214783}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9052230715751648},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6094092726707458},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5275048017501831},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5043047666549683},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4846392273902893},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.338321328163147},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2099267542362213},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16710886359214783},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":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":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":"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":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013463","descriptor_name":"Sulfuric Acid Esters","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkac435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac435","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W266/44376882/gkac435.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:35657086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35657086","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:digitalcommons.unl.edu:chemfacpub-1264","is_oa":true,"landing_page_url":"https://digitalcommons.unl.edu/chemfacpub/264","pdf_url":null,"source":{"id":"https://openalex.org/S4306513441","display_name":"Insecta mundi","issn_l":"0749-6737","issn":["0749-6737","1942-1354","1942-1362"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310316217","host_organization_name":"Center for Systematic Entomology","host_organization_lineage":["https://openalex.org/P4310316217"],"host_organization_lineage_names":["Center for Systematic Entomology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications -- Chemistry Department","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:9252807","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252807","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac435","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W266/44376882/gkac435.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6200000047683716}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281749338.pdf","grobid_xml":"https://content.openalex.org/works/W4281749338.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1551812998","https://openalex.org/W1970441908","https://openalex.org/W2003993220","https://openalex.org/W2129726167","https://openalex.org/W2170551349","https://openalex.org/W2233915997","https://openalex.org/W2340426779","https://openalex.org/W2554920439","https://openalex.org/W2796037415","https://openalex.org/W2949078846","https://openalex.org/W2969527868","https://openalex.org/W3022360544","https://openalex.org/W3159478241","https://openalex.org/W3161191932","https://openalex.org/W4205750016","https://openalex.org/W4214910897","https://openalex.org/W4289549951","https://openalex.org/W4295308923"],"related_works":["https://openalex.org/W2136583354","https://openalex.org/W2111238207","https://openalex.org/W2760721665","https://openalex.org/W2147993839","https://openalex.org/W330130819","https://openalex.org/W2288610023","https://openalex.org/W2112044895","https://openalex.org/W1840103016","https://openalex.org/W3121416282","https://openalex.org/W54859794"],"abstract_inverted_index":{"RNA":[0,27,165],"structures":[1,36,78],"play":[2],"critical":[3],"roles":[4],"in":[5,37,67,83,169],"regulating":[6],"gene":[7],"expression":[8],"across":[9],"all":[10],"domains":[11],"of":[12,34,59,79,101,141,152,164,172],"life":[13],"and":[14,48,61,64,81,91,99,127,167],"viruses.":[15],"Chemical":[16],"probing":[17,143],"methods":[18],"coupled":[19],"with":[20],"massively":[21],"parallel":[22],"sequencing":[23,147],"have":[24],"revolutionized":[25],"the":[26,32,56,68,76,97,102,124,139,170],"structure":[28,166],"field":[29],"by":[30,109],"enabling":[31],"assessment":[33],"many":[35],"their":[38],"native,":[39],"physiological":[40],"context.":[41],"Previously,":[42],"we":[43,131],"developed":[44],"Dimethyl-Sulfate-based":[45],"Mutational":[46],"Profiling":[47],"Sequencing":[49],"(DMS-MaPseq),":[50],"which":[51,86],"uses":[52],"DMS":[53],"to":[54,74,96],"label":[55],"Watson-Crick":[57],"face":[58],"open":[60],"accessible":[62],"adenine":[63],"cytosine":[65],"bases":[66],"RNA.":[69],"We":[70],"used":[71],"this":[72],"approach":[73],"determine":[75],"genome-wide":[77],"HIV-1":[80],"SARS-CoV-2":[82],"infected":[84],"cells,":[85],"permitted":[87],"uncovering":[88],"new":[89],"biology":[90],"identifying":[92],"therapeutic":[93],"targets.":[94],"Due":[95],"simplicity":[98],"ease":[100],"experimental":[103],"procedure,":[104],"DMS-MaPseq":[105,158],"has":[106],"been":[107],"adopted":[108],"labs":[110,120],"worldwide.":[111],"However,":[112],"bioinformatic":[113],"analysis":[114,140,159],"remains":[115],"a":[116,133,153],"substantial":[117],"hurdle":[118],"for":[119,157],"that":[121,137],"often":[122],"lack":[123],"necessary":[125],"infrastructure":[126],"computational":[128],"expertise.":[129],"Here":[130],"present":[132],"modern":[134],"web-based":[135,155],"interface":[136],"automates":[138],"chemical":[142],"profiles":[144],"from":[145],"raw":[146],"files":[148],"(http://rnadreem.org).":[149],"The":[150],"availability":[151],"simple":[154],"platform":[156],"will":[160],"dramatically":[161],"expand":[162],"studies":[163],"aid":[168],"design":[171],"structure-based":[173],"therapeutics.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}