{"id":"https://openalex.org/W1977815530","doi":"https://doi.org/10.1145/2506583.2506623","title":"Flexible RNA design under structure and sequence constraints using formal languages","display_name":"Flexible RNA design under structure and sequence constraints using formal languages","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W1977815530","doi":"https://doi.org/10.1145/2506583.2506623","mag":"1977815530"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506623","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1305.3830","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006208781","display_name":"Yu Zhou","orcid":"https://orcid.org/0000-0002-2102-9377"},"institutions":[{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Yu Zhou","raw_affiliation_strings":["LRI, Univ. Paris-Sud, Orsay F-91405, France"],"affiliations":[{"raw_affiliation_string":"LRI, Univ. Paris-Sud, Orsay F-91405, France","institution_ids":["https://openalex.org/I102197404","https://openalex.org/I4210144804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"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/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Ponty","raw_affiliation_strings":["LIX, Ecole Polytechnique and AMIB, INRIA Saclay, Palaiseau F-91128, France","LIX, Ecole Polytechnique and AMIB, INRIA Saclay, Palaiseau F-91128, France#TAB#"],"affiliations":[{"raw_affiliation_string":"LIX, Ecole Polytechnique and AMIB, INRIA Saclay, Palaiseau F-91128, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]},{"raw_affiliation_string":"LIX, Ecole Polytechnique and AMIB, INRIA Saclay, Palaiseau F-91128, France#TAB#","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027495509","display_name":"St\u00e9phane Vialette","orcid":"https://orcid.org/0000-0003-2308-6970"},"institutions":[{"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phane Vialette","raw_affiliation_strings":["LIGM, Univ. Paris-Est, Marne-la-Vall\u00e9e F-77454, France"],"affiliations":[{"raw_affiliation_string":"LIGM, Univ. Paris-Est, Marne-la-Vall\u00e9e F-77454, France","institution_ids":["https://openalex.org/I4210152518"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000881484","display_name":"J\u00e9r\u00f4me Waldisp\u00fchl","orcid":"https://orcid.org/0000-0002-2561-7117"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Waldispuhl","raw_affiliation_strings":["McGill University, Montreal, Quebec H3A 2B2, Canada","McGill University, Montreal, Quebec H3A 2B2, Canada#TAB#"],"affiliations":[{"raw_affiliation_string":"McGill University, Montreal, Quebec H3A 2B2, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"McGill University, Montreal, Quebec H3A 2B2, Canada#TAB#","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100652543","display_name":"Yi Zhang","orcid":"https://orcid.org/0000-0003-1035-6134"},"institutions":[{"id":"https://openalex.org/I4210106882","display_name":"Wuhan Institute of Virology","ror":"https://ror.org/01jxjav08","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106882"]},{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhang","raw_affiliation_strings":["State Key Laboratory of Virology, Wuhan University, and ABLife Inc, Wuhan, Hubei 430072, China","State Key Laboratory of Virology, Wuhan University, and ABLife Inc, Wuhan, Hubei 430072, China#TAB#"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Virology, Wuhan University, and ABLife Inc, Wuhan, Hubei 430072, China","institution_ids":["https://openalex.org/I37461747","https://openalex.org/I4210106882"]},{"raw_affiliation_string":"State Key Laboratory of Virology, Wuhan University, and ABLife Inc, Wuhan, Hubei 430072, China#TAB#","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011363744","display_name":"Alain Denise","orcid":"https://orcid.org/0000-0003-4484-4996"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en informatique et en automatique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"id":"https://openalex.org/I4210126360","display_name":"Inria Saclay - \u00cele de France","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alain Denise","raw_affiliation_strings":["LRI and IGM, Univ. Paris-Sud, Orsay F-91405 and AMIB, INRIA Saclay, France","LRI and IGM, Univ. Paris-Sud, Orsay F-91405 and AMIB, INRIA Saclay, France#TAB#"],"affiliations":[{"raw_affiliation_string":"LRI and IGM, Univ. Paris-Sud, Orsay F-91405 and AMIB, INRIA Saclay, France","institution_ids":["https://openalex.org/I4210126360","https://openalex.org/I277688954","https://openalex.org/I102197404","https://openalex.org/I4210144804"]},{"raw_affiliation_string":"LRI and IGM, Univ. Paris-Sud, Orsay F-91405 and AMIB, INRIA Saclay, France#TAB#","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I102197404","https://openalex.org/I4210144804"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006208781"],"corresponding_institution_ids":["https://openalex.org/I102197404","https://openalex.org/I4210144804"],"apc_list":null,"apc_paid":null,"fwci":0.4492,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.64646789,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"229","last_page":"238"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9951000213623047,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9940000176429749,"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/sequence","display_name":"Sequence (biology)","score":0.7232010364532471},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6045304536819458},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4897301197052002},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4878261387348175},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4620015323162079},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4277384281158447},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39155498147010803},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2524178922176361},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14406895637512207},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10249888896942139}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7232010364532471},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6045304536819458},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4897301197052002},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4878261387348175},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4620015323162079},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4277384281158447},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39155498147010803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2524178922176361},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14406895637512207},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10249888896942139}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2506583.2506623","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1305.3830","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1305.3830","pdf_url":"https://arxiv.org/pdf/1305.3830","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"pmh:oai:HAL:hal-00823279v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-00823279","pdf_url":"https://inria.hal.science/hal-00823279/document","source":{"id":"https://openalex.org/S4406922461","display_name":"SPIRE - Sciences Po Institutional REpository","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States","raw_type":"Conference papers"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1305.3830","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1305.3830","pdf_url":"https://arxiv.org/pdf/1305.3830","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1511098027","https://openalex.org/W1543796220","https://openalex.org/W1969390039","https://openalex.org/W1989020100","https://openalex.org/W2005787143","https://openalex.org/W2021099440","https://openalex.org/W2025763720","https://openalex.org/W2053350156","https://openalex.org/W2054167614","https://openalex.org/W2063594852","https://openalex.org/W2070222482","https://openalex.org/W2071510967","https://openalex.org/W2090335524","https://openalex.org/W2099530721","https://openalex.org/W2099964107","https://openalex.org/W2109389103","https://openalex.org/W2109881896","https://openalex.org/W2111342151","https://openalex.org/W2117365957","https://openalex.org/W2122944508","https://openalex.org/W2125615424","https://openalex.org/W2135373808","https://openalex.org/W2140505514","https://openalex.org/W2143407915","https://openalex.org/W2150887741","https://openalex.org/W2152678443","https://openalex.org/W2157507882","https://openalex.org/W2164530723","https://openalex.org/W2914032487"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W1640318440","https://openalex.org/W2264054990","https://openalex.org/W2581888268","https://openalex.org/W2954917112","https://openalex.org/W2581348958","https://openalex.org/W4385457841"],"abstract_inverted_index":{"The":[0],"problem":[1],"of":[2,48],"RNA":[3],"secondary":[4,13],"structure":[5],"design":[6],"is":[7,25],"the":[8,46,59],"following:":[9],"given":[10,29],"a":[11,19,28,53],"target":[12],"structure,":[14],"one":[15],"aims":[16],"to":[17],"create":[18],"sequence":[20],"that":[21],"folds":[22],"into,":[23],"or":[24,56],"compatible":[26],"with,":[27],"structure.":[30],"In":[31],"several":[32],"practical":[33],"applications":[34],"in":[35,58],"biology,":[36],"additional":[37],"constraints":[38],"must":[39],"be":[40],"taken":[41],"into":[42],"account,":[43],"such":[44],"as":[45],"presence/absence":[47],"regulatory":[49],"motifs,":[50],"either":[51],"at":[52],"specific":[54],"location":[55],"anywhere":[57],"sequence.":[60]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
