{"id":"https://openalex.org/W2147427953","doi":"https://doi.org/10.1162/106454600568294","title":"RNA Shape Space Topology","display_name":"RNA Shape Space Topology","publication_year":2000,"publication_date":"2000-01-01","ids":{"openalex":"https://openalex.org/W2147427953","doi":"https://doi.org/10.1162/106454600568294","mag":"2147427953","pmid":"https://pubmed.ncbi.nlm.nih.gov/10943663"},"language":"en","primary_location":{"id":"doi:10.1162/106454600568294","is_oa":false,"landing_page_url":"https://doi.org/10.1162/106454600568294","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718","https://openalex.org/P4310316440"],"host_organization_lineage_names":["The MIT Press","Massachusetts Institute of Technology"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050727753","display_name":"Jan Cupal","orcid":null},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Jan Cupal","raw_affiliation_strings":["Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035634179","display_name":"Stephan Kopp","orcid":null},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["AT","US"],"is_corresponding":false,"raw_author_name":"Stephan Kopp","raw_affiliation_strings":["Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","Los Alamos National Laboratory, TSA/DO-SA Los Alamos, NM 87545-1663, USA Mailstop: TA-0, SM-1237, MS M997"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Los Alamos National Laboratory, TSA/DO-SA Los Alamos, NM 87545-1663, USA Mailstop: TA-0, SM-1237, MS M997","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]}],"countries":["AT","US"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","The Santa Fe Institute 1399 Hyde Park Road, Santa Fe, NM 87501, USA","The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"The Santa Fe Institute 1399 Hyde Park Road, Santa Fe, NM 87501, USA","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA","institution_ids":["https://openalex.org/I1308548392"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8311,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.72555527,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"6","issue":"1","first_page":"3","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9940000176429749,"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/topology","display_name":"Topology (electrical circuits)","score":0.6859327554702759},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.5755032300949097},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5456947684288025},{"id":"https://openalex.org/keywords/zero-dimensional-space","display_name":"Zero-dimensional space","score":0.5240921378135681},{"id":"https://openalex.org/keywords/general-topology","display_name":"General topology","score":0.5069206357002258},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.39648503065109253},{"id":"https://openalex.org/keywords/topological-space","display_name":"Topological space","score":0.38008663058280945},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3319556713104248},{"id":"https://openalex.org/keywords/topological-vector-space","display_name":"Topological vector space","score":0.26383641362190247},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.22420534491539001},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11000281572341919}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6859327554702759},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.5755032300949097},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5456947684288025},{"id":"https://openalex.org/C140936041","wikidata":"https://www.wikidata.org/wiki/Q1801244","display_name":"Zero-dimensional space","level":4,"score":0.5240921378135681},{"id":"https://openalex.org/C129089157","wikidata":"https://www.wikidata.org/wiki/Q621550","display_name":"General topology","level":3,"score":0.5069206357002258},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.39648503065109253},{"id":"https://openalex.org/C81332173","wikidata":"https://www.wikidata.org/wiki/Q179899","display_name":"Topological space","level":2,"score":0.38008663058280945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3319556713104248},{"id":"https://openalex.org/C47776270","wikidata":"https://www.wikidata.org/wiki/Q1455249","display_name":"Topological vector space","level":3,"score":0.26383641362190247},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.22420534491539001},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11000281572341919},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1162/106454600568294","is_oa":false,"landing_page_url":"https://doi.org/10.1162/106454600568294","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718","https://openalex.org/P4310316440"],"host_organization_lineage_names":["The MIT Press","Massachusetts Institute of Technology"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},{"id":"pmid:10943663","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10943663","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":"Artificial life","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.17.3268","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.17.3268","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.tbi.univie.ac.at/papers/Abstracts/99-03-022.ps.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.35.9567","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.9567","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.santafe.edu/sfi/publications/Working-Papers/99-03-022.ps.gz","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W107021117","https://openalex.org/W1543796220","https://openalex.org/W1551334274","https://openalex.org/W1552834166","https://openalex.org/W1569069879","https://openalex.org/W1574322829","https://openalex.org/W1968961038","https://openalex.org/W1971013467","https://openalex.org/W1971399377","https://openalex.org/W1971974598","https://openalex.org/W1973220360","https://openalex.org/W1974272811","https://openalex.org/W1976215910","https://openalex.org/W1977940795","https://openalex.org/W1995403172","https://openalex.org/W2003016191","https://openalex.org/W2011397566","https://openalex.org/W2017313617","https://openalex.org/W2022730625","https://openalex.org/W2032388273","https://openalex.org/W2044595289","https://openalex.org/W2044982349","https://openalex.org/W2046289407","https://openalex.org/W2046585679","https://openalex.org/W2049092030","https://openalex.org/W2059557910","https://openalex.org/W2061158331","https://openalex.org/W2061384718","https://openalex.org/W2070100044","https://openalex.org/W2072459054","https://openalex.org/W2075121996","https://openalex.org/W2076963640","https://openalex.org/W2080574919","https://openalex.org/W2093397547","https://openalex.org/W2113368761","https://openalex.org/W2205082498","https://openalex.org/W2321457778","https://openalex.org/W3098195359","https://openalex.org/W3123454693","https://openalex.org/W3124837637","https://openalex.org/W4229809574","https://openalex.org/W4234667141","https://openalex.org/W4241340146","https://openalex.org/W4243468655","https://openalex.org/W4244253496","https://openalex.org/W4253350674"],"related_works":["https://openalex.org/W2381544357","https://openalex.org/W2593417979","https://openalex.org/W4376620846","https://openalex.org/W2354885222","https://openalex.org/W3112765868","https://openalex.org/W2796588032","https://openalex.org/W2104793728","https://openalex.org/W3042449214","https://openalex.org/W2348145403","https://openalex.org/W1568599732"],"abstract_inverted_index":{"The":[0,60],"distinction":[1],"between":[2],"continuous":[3,79],"and":[4,81],"discontinuous":[5],"transitions":[6],"is":[7,18,41,50,67],"a":[8,19,24,33,38],"long-standing":[9],"problem":[10],"in":[11,88],"the":[12,28,44,57],"theory":[13],"of":[14,30,63],"evolution.":[15],"Because":[16],"continuity":[17],"topological":[20,35],"property,":[21],"we":[22],"present":[23],"formalism":[25],"that":[26,40,75],"treats":[27],"space":[29,62],"phenotypes":[31],"as":[32],"(finite)":[34],"space,":[36],"with":[37,46],"topology":[39],"derived":[42],"from":[43,52],"probabilities":[45],"which":[47],"one":[48],"phenotype":[49,89],"accessible":[51],"another":[53],"through":[54],"changes":[55],"at":[56],"genotypic":[58],"level.":[59],"shape":[61],"RNA":[64],"secondary":[65],"structures":[66],"used":[68],"to":[69],"illustrate":[70],"this":[71],"approach.":[72],"We":[73],"show":[74],"evolutionary":[76],"trajectories":[77],"are":[78],"if":[80,83],"only":[82],"they":[84],"follow":[85],"connected":[86],"paths":[87],"space.":[90]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
