{"id":"https://openalex.org/W2973044881","doi":"https://doi.org/10.1145/3307339.3342163","title":"Exponentially Few RNA Structures are Designable","display_name":"Exponentially Few RNA Structures are Designable","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2973044881","doi":"https://doi.org/10.1145/3307339.3342163","mag":"2973044881"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3342163","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342163","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://inria.hal.science/hal-02141853","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025033338","display_name":"Hua-Ting Yao","orcid":"https://orcid.org/0000-0002-1720-5737"},"institutions":[{"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":"Hua-Ting Yao","raw_affiliation_strings":["Ecole Polytechnique, Palaiseau, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique, Palaiseau, France","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063811688","display_name":"C\u00e9dric Chauve","orcid":"https://orcid.org/0000-0001-9837-1878"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"C\u00e9dric Chauve","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC, Canada","SFU - Department of Mathematics [Burnaby] (Simon Fraser University, 8888 University Drive, \r\nBurnaby, British Columbia V5A 1S6 - Canada)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"SFU - Department of Mathematics [Burnaby] (Simon Fraser University, 8888 University Drive, \r\nBurnaby, British Columbia V5A 1S6 - Canada)","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105346792","display_name":"Mireille R\u00e9gnier","orcid":"https://orcid.org/0000-0001-9566-0105"},"institutions":[{"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":"Mireille Regnier","raw_affiliation_strings":["Ecole Polytechnique, Palaiseau, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique, Palaiseau, France","institution_ids":["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/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":["Ecole Polytechnique, Palaiseau, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique, Palaiseau, France","institution_ids":["https://openalex.org/I142476485"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.08458066,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"289","last_page":"298"},"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":0.996399998664856,"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":0.9962999820709229,"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/exponential-growth","display_name":"Exponential growth","score":0.708499014377594},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6600555181503296},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6449801325798035},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5668975114822388},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.49802422523498535},{"id":"https://openalex.org/keywords/exponential-function","display_name":"Exponential function","score":0.49164801836013794},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4885905683040619},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.46407583355903625},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.35009604692459106},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34917354583740234},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3484920263290405},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32792532444000244},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.24906376004219055},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.21230027079582214},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19324281811714172},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12683910131454468},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10123604536056519},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.0884351134300232},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08511477708816528}],"concepts":[{"id":"https://openalex.org/C75235859","wikidata":"https://www.wikidata.org/wiki/Q582659","display_name":"Exponential growth","level":2,"score":0.708499014377594},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6600555181503296},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6449801325798035},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5668975114822388},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.49802422523498535},{"id":"https://openalex.org/C151376022","wikidata":"https://www.wikidata.org/wiki/Q168698","display_name":"Exponential function","level":2,"score":0.49164801836013794},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4885905683040619},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.46407583355903625},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.35009604692459106},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34917354583740234},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3484920263290405},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32792532444000244},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.24906376004219055},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.21230027079582214},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19324281811714172},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12683910131454468},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10123604536056519},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0884351134300232},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08511477708816528},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3307339.3342163","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342163","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-02141853v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-02141853","pdf_url":null,"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://acm-bcb.org/","raw_type":"Conference papers"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-02141853v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-02141853","pdf_url":null,"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://acm-bcb.org/","raw_type":"Conference papers"},"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1826494656","https://openalex.org/W1860906034","https://openalex.org/W1969390039","https://openalex.org/W2003189478","https://openalex.org/W2009818318","https://openalex.org/W2018919817","https://openalex.org/W2025746238","https://openalex.org/W2025763720","https://openalex.org/W2099895168","https://openalex.org/W2111342151","https://openalex.org/W2122944508","https://openalex.org/W2125615424","https://openalex.org/W2139541234","https://openalex.org/W2140505514","https://openalex.org/W2143386289","https://openalex.org/W2147828873","https://openalex.org/W2148339059","https://openalex.org/W2152678443","https://openalex.org/W2187781745","https://openalex.org/W2498333024","https://openalex.org/W2529169893","https://openalex.org/W2611488297","https://openalex.org/W2940260877","https://openalex.org/W4249015934"],"related_works":["https://openalex.org/W3047450301","https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W4394883359","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W2919479895","https://openalex.org/W2131054067","https://openalex.org/W1602624896","https://openalex.org/W3196523453"],"abstract_inverted_index":{"The":[0],"problem":[1],"of":[2,22,26,99,108,117,135,153],"RNA":[3,8,27,33,69],"design":[4,28,121],"attempts":[5],"to":[6,43,48,88,132,146],"construct":[7],"sequences":[9],"that":[10,30,61,96],"perform":[11],"a":[12,37,49],"predefined":[13,38],"biological":[14],"function,":[15],"identified":[16],"by":[17],"several":[18,59],"additional":[19],"constraints.":[20],"One":[21],"the":[23,31,74,97,106,109,133,151],"foremost":[24],"objective":[25],"is":[29,86],"designed":[32],"sequence":[34,70],"should":[35],"adopt":[36],"target":[39,75,110],"secondary":[40,63,101,111],"structure":[41,76],"preferentially":[42],"any":[44],"alternative":[45,89],"structure,":[46,112],"according":[47],"given":[50],"metrics":[51],"and":[52,120,143],"folding":[53,85],"model.":[54],"It":[55],"was":[56],"observed":[57],"in":[58,129],"works":[60],"some":[62,79],"structures":[64,102],"are":[65],"undesignable,":[66],"i.e.":[67],"no":[68],"can":[71,139],"fold":[72],"into":[73],"while":[77],"satisfying":[78],"criterion":[80],"measuring":[81],"how":[82],"preferential":[83],"this":[84,92],"compared":[87],"conformations.":[90],"In":[91],"paper,":[93],"we":[94],"show":[95],"proportion":[98],"designable":[100,154],"decreases":[103],"exponentially":[104],"with":[105],"size":[107],"for":[113],"various":[114],"popular":[115],"combinations":[116],"energy":[118],"models":[119],"objectives.":[122],"This":[123],"exponential":[124],"decay":[125],"is,":[126],"at":[127],"least":[128],"part,":[130],"due":[131],"existence":[134],"undesignable":[136],"motifs,":[137],"which":[138],"be":[140],"generically":[141],"constructed,":[142],"jointly":[144],"analyzed":[145],"yield":[147],"asymptotic":[148],"upper-bounds":[149],"on":[150],"number":[152],"structures.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}