{"id":"https://openalex.org/W4390946662","doi":"https://doi.org/10.1093/bioinformatics/btae022","title":"Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework","display_name":"Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework","publication_year":2024,"publication_date":"2024-01-12","ids":{"openalex":"https://openalex.org/W4390946662","doi":"https://doi.org/10.1093/bioinformatics/btae022","pmid":"https://pubmed.ncbi.nlm.nih.gov/38230755"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae022/56168003/btae022.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae022/56168003/btae022.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027608007","display_name":"Gabriel Loyer","orcid":null},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Gabriel Loyer","raw_affiliation_strings":["Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montr\u00e9al, QC H2X 3Y7, Canada","Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montr\u00e9al, QC H2X 3Y7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montr\u00e9al, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]},{"raw_affiliation_string":"Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montr\u00e9al, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089144463","display_name":"Vladimir Reinharz","orcid":"https://orcid.org/0000-0001-8481-1094"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Vladimir Reinharz","raw_affiliation_strings":["Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montr\u00e9al, QC H2X 3Y7, Canada","Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montr\u00e9al, QC H2X 3Y7, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montr\u00e9al, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]},{"raw_affiliation_string":"Department of Computer Science, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montr\u00e9al, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027608007"],"corresponding_institution_ids":["https://openalex.org/I159129438"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6028,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.81831698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"40","issue":"2","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/T11482","display_name":"RNA modifications and cancer","score":0.9973999857902527,"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":0.9973000288009644,"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/integer-programming","display_name":"Integer programming","score":0.6370353698730469},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6094310879707336},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5844008922576904},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5325053930282593},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.45427072048187256},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43392831087112427},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41078445315361023},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37242764234542847},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2675710916519165},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2239251434803009},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1872066855430603},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07216799259185791}],"concepts":[{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.6370353698730469},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6094310879707336},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5844008922576904},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5325053930282593},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.45427072048187256},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43392831087112427},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41078445315361023},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37242764234542847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2675710916519165},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2239251434803009},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1872066855430603},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07216799259185791}],"mesh":[{"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":"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":"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":"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae022/56168003/btae022.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38230755","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38230755","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:pubmedcentral.nih.gov:10868335","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10868335","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10868335/pdf/btae022.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae022/56168003/btae022.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3028888727","display_name":null,"funder_award_id":"RGPIN-2020-0","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3525686075","display_name":null,"funder_award_id":"RGPIN-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6485536667","display_name":null,"funder_award_id":"RGPIN-2020-05","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G7645049029","display_name":null,"funder_award_id":"RGPIN-2020-05795","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8105784103","display_name":null,"funder_award_id":"RGPIN-202","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334618","display_name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","ror":"https://ror.org/02eqrsj93"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390946662.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1988884185","https://openalex.org/W2023013439","https://openalex.org/W2070136856","https://openalex.org/W2076756368","https://openalex.org/W2086561953","https://openalex.org/W2098571862","https://openalex.org/W2101497394","https://openalex.org/W2106478835","https://openalex.org/W2111272410","https://openalex.org/W2123241418","https://openalex.org/W2130479394","https://openalex.org/W2131462431","https://openalex.org/W2132129663","https://openalex.org/W2134489577","https://openalex.org/W2136556521","https://openalex.org/W2143407915","https://openalex.org/W2148599336","https://openalex.org/W2150404344","https://openalex.org/W2159117141","https://openalex.org/W2162935469","https://openalex.org/W2170030776","https://openalex.org/W2402481807","https://openalex.org/W2554065905","https://openalex.org/W2614469195","https://openalex.org/W2783814264","https://openalex.org/W2795053763","https://openalex.org/W2799306311","https://openalex.org/W2799989945","https://openalex.org/W2807635396","https://openalex.org/W2954102902","https://openalex.org/W2990528340","https://openalex.org/W2999081115","https://openalex.org/W3017832738","https://openalex.org/W3022554208","https://openalex.org/W3034567160","https://openalex.org/W3084513853","https://openalex.org/W3100348855","https://openalex.org/W3126773939","https://openalex.org/W3164771453","https://openalex.org/W3204096889","https://openalex.org/W4283447041","https://openalex.org/W4366990642"],"related_works":["https://openalex.org/W2147993839","https://openalex.org/W1840103016","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2109912052","https://openalex.org/W1711527768","https://openalex.org/W4385457841","https://openalex.org/W2581348958","https://openalex.org/W4367048159","https://openalex.org/W962838231"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"of":[3],"the":[4],"framework":[5],"is":[6],"available":[7],"at":[8,15],"https://gitlab.info.uqam.ca/cbe/RNAMoIP":[9],"and":[10],"an":[11],"interactive":[12],"web":[13],"server":[14],"https://rnamoip.cbe.uqam.ca/.":[16]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
