{"id":"https://openalex.org/W4399114806","doi":"https://doi.org/10.1186/s13015-025-00278-6","title":"RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs","display_name":"RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs","publication_year":2025,"publication_date":"2025-10-24","ids":{"openalex":"https://openalex.org/W4399114806","doi":"https://doi.org/10.1186/s13015-025-00278-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41137157"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-025-00278-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00278-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00278-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00278-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091932207","display_name":"Th\u00e9o Boury","orcid":"https://orcid.org/0009-0004-0553-4789"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210154111","display_name":"Universit\u00e9 Gustave Eiffel","ror":"https://ror.org/03x42jk29","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210154111"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Th\u00e9o Boury","raw_affiliation_strings":["Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France","LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)","LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)"],"raw_orcid":"https://orcid.org/0009-0004-0553-4789","affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]},{"raw_affiliation_string":"LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)","institution_ids":["https://openalex.org/I4210152518","https://openalex.org/I4210154111"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Samuel Gardelle","orcid":"https://orcid.org/0009-0003-6766-2383"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210154111","display_name":"Universit\u00e9 Gustave Eiffel","ror":"https://ror.org/03x42jk29","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210154111"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Samuel Gardelle","raw_affiliation_strings":["Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France","LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)"],"raw_orcid":"https://orcid.org/0009-0003-6766-2383","affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)","institution_ids":["https://openalex.org/I4210152518","https://openalex.org/I4210154111"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017247640","display_name":"Laurent Bulteau","orcid":"https://orcid.org/0000-0003-1645-9345"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210154111","display_name":"Universit\u00e9 Gustave Eiffel","ror":"https://ror.org/03x42jk29","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210154111"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurent Bulteau","raw_affiliation_strings":["Laboratoire d'Informatique Gaspard Monge (LIGM CNRS UMR 8049), Universit\u00e9 Gustave Eiffel, 5 Boulevard Descartes - Champs sur Marne, 77454, Marne La Vall\u00e9e, France. laurent.bulteau@univ-eiffel.fr","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)"],"raw_orcid":"https://orcid.org/0000-0003-1645-9345","affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique Gaspard Monge (LIGM CNRS UMR 8049), Universit\u00e9 Gustave Eiffel, 5 Boulevard Descartes - Champs sur Marne, 77454, Marne La Vall\u00e9e, France. laurent.bulteau@univ-eiffel.fr","institution_ids":["https://openalex.org/I4210152518","https://openalex.org/I1294671590","https://openalex.org/I4210154111"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Ponty","raw_affiliation_strings":["Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France. yann.ponty@lix.polytechnique.fr"],"raw_orcid":"https://orcid.org/0000-0002-7615-3930","affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique de l'Ecole Polytechnique (LIX CNRS UMR 7161), Institut Polytechnique de Paris, 1 Rue Honor\u00e9 d'Estienne d'Orves, 91120, Palaiseau, France. yann.ponty@lix.polytechnique.fr","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":1.1519,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.74568549,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"20","issue":"1","first_page":"20","last_page":"20"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9987999796867371,"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/folding","display_name":"Folding (DSP implementation)","score":0.630707323551178},{"id":"https://openalex.org/keywords/inverse","display_name":"Inverse","score":0.6207188367843628},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.5341628789901733},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5327109694480896},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.5288670659065247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47099512815475464},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.4433344602584839},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3526410162448883},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2575015127658844},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1546722948551178},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.14435049891471863},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13591060042381287},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.12128034234046936},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.1083049476146698},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.09551557898521423},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08994519710540771}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.630707323551178},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.6207188367843628},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.5341628789901733},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5327109694480896},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.5288670659065247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47099512815475464},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.4433344602584839},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3526410162448883},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2575015127658844},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1546722948551178},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.14435049891471863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13591060042381287},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.12128034234046936},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1083049476146698},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.09551557898521423},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08994519710540771},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":9,"locations":[{"id":"doi:10.1186/s13015-025-00278-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00278-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00278-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:41137157","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41137157","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:HAL:hal-04589901v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04589901","pdf_url":"https://hal.science/hal-04589901/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://hal.science/hal-04589901","raw_type":"info:eu-repo/semantics/preprint"},{"id":"pmh:oai:HAL:hal-04761629v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04761629","pdf_url":"https://hal.science/hal-04761629/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2024","raw_type":"Preprints, Working Papers, ..."},{"id":"pmh:oai:HAL:hal-04773768v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04773768","pdf_url":"https://hal.science/hal-04773768/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SEQBIM 2024 - Journ\u00e9es du groupe de travail S\u00e9quences en Bioinformatique, Nov 2024, Rennes, France","raw_type":"Conference papers"},{"id":"pmh:oai:drops-oai.dagstuhl.de:20663","is_oa":true,"landing_page_url":"https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.19","pdf_url":"https://drops.dagstuhl.de/storage/00lipics/lipics-vol312-wabi2024/LIPIcs.WABI.2024.19/LIPIcs.WABI.2024.19.pdf","source":{"id":"https://openalex.org/S4377196569","display_name":"DROPS (Schloss Dagstuhl \u2013 Leibniz Center for Informatics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799853480","host_organization_name":"Schloss Dagstuhl \u2013 Leibniz Center for Informatics","host_organization_lineage":["https://openalex.org/I2799853480"],"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":null,"raw_type":"publishedVersion"},{"id":"pmh:oai:doaj.org/article:8e38a5c641424df186461e0c8d76aa9d","is_oa":true,"landing_page_url":"https://doaj.org/article/8e38a5c641424df186461e0c8d76aa9d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 20, Iss 1, Pp 1-25 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11360831","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12553252","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"doi:10.4230/lipics.wabi.2024.19","is_oa":true,"landing_page_url":"https://doi.org/10.4230/lipics.wabi.2024.19","pdf_url":null,"source":{"id":"https://openalex.org/S7407052059","display_name":"Dagstuhl Research Online Publication Server","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":""}],"best_oa_location":{"id":"doi:10.1186/s13015-025-00278-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00278-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00278-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6017754060","display_name":null,"funder_award_id":"ANR-19-CE30-0021","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399114806.pdf","grobid_xml":"https://content.openalex.org/works/W4399114806.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2610782116","https://openalex.org/W4317939968","https://openalex.org/W2024970374","https://openalex.org/W2549419714","https://openalex.org/W1980269403","https://openalex.org/W4390144857","https://openalex.org/W4281647907","https://openalex.org/W2058985883","https://openalex.org/W2638372604","https://openalex.org/W1979242040"],"abstract_inverted_index":{"Abstract":[0],"Inverse":[1],"folding":[2,56,66,166],"is":[3,57,116,153,232],"a":[4,15,21,50,74,122,129,137,144,154,161,180,211,239],"classic":[5],"instance":[6],"of":[7,33,49,54,77,97,132,139,160,176,221,260],"negative":[8],"RNA":[9],"design":[10],"which":[11],"consists":[12],"in":[13,40,70,188,249],"finding":[14],"sequence":[16,184,212],"that":[17,64,82,217],"uniquely":[18],"folds":[19],"into":[20],"target":[22],"secondary":[23,174],"structure":[24,81,175,219],"with":[25],"respect":[26],"to":[27,120,163],"energy":[28],"minimization.":[29],"A":[30],"breakthrough":[31],"result":[32],"Bonnet":[34],"et":[35,149],"al.":[36],"shows":[37],"that,":[38,170],"even":[39,253],"simple":[41],"base":[42,106,230],"pairs-based":[43],"(BP)":[44],"models,":[45],"the":[46,158,164,258],"decision":[47],"version":[48,53],"mildly":[51],"constrained":[52],"inverse":[55,65,165],"NP-hard.":[58],"In":[59],"this":[60],"work,":[61],"we":[62,215],"show":[63,169,216],"can":[67,185,245],"be":[68,186,247,254],"solved":[69],"linear":[71,114,250],"time":[72,189],"for":[73,128,157,171],"large":[75,130],"collection":[76],"targets,":[78],"including":[79],"every":[80],"contains":[83],"no":[84,88,117],"isolated":[85,89],"BP":[86],"and":[87,252],"stack":[90],"(or,":[91],"equivalently,":[92],"when":[93],"all":[94],"helices":[95],"consist":[96],"$$3^{+}$$":[98,222],"<mml:math":[99,193,223],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[100,194,224],"<mml:msup>":[101,202,225],"<mml:mn>3</mml:mn>":[102,226],"<mml:mo>+</mml:mo>":[103,227],"</mml:msup>":[104,205,228],"</mml:math>":[105,208,229],"pairs).":[107],"For":[108],"structures":[109],"featuring":[110],"shorter":[111],"helices,":[112],"our":[113],"algorithm":[115],"longer":[118],"guaranteed":[119],"produce":[121],"solution,":[123],"but":[124],"still":[125],"does":[126],"so":[127],"proportion":[131],"instances.":[133],"Our":[134],"approach":[135],"introduces":[136],"notion":[138],"modulo":[140,181],"m":[141,182],"-separability,":[142],"generalizing":[143],"property":[145],"pioneered":[146],"by":[147],"Hales":[148],"al":[150],".":[151],"Separability":[152],"sufficient":[155],"condition":[156],"existence":[159],"solution":[162],"problem.":[167],"We":[168],"any":[172,218],"input":[173],"length":[177],"n":[178],",":[179],"-separated":[183],"produced":[187,248],"$$\\mathcal":[190],"{O}(n\\,m\\,":[191],"2^m)$$":[192],"<mml:mrow>":[195],"<mml:mi>O</mml:mi>":[196],"<mml:mo>(</mml:mo>":[197],"<mml:mi>n</mml:mi>":[198],"<mml:mspace/>":[199,201],"<mml:mi>m</mml:mi>":[200,204],"<mml:mn>2</mml:mn>":[203],"<mml:mo>)</mml:mo>":[206],"</mml:mrow>":[207],"anytime":[209],"such":[210],"exists.":[213],"Meanwhile,":[214],"consisting":[220],"pairs":[231],"either":[233],"trivially":[234],"non-designable,":[235],"or":[236],"always":[237],"admits":[238],"modulo-2":[240,261],"separated":[241],"solution.":[242],"Solution":[243],"sequences":[244],"thus":[246],"time,":[251],"uniformly":[255],"generated":[256],"within":[257],"set":[259],"separable":[262],"sequences.":[263]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
