{"id":"https://openalex.org/W1998215345","doi":"https://doi.org/10.1038/nbt1155","title":"Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes","display_name":"Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes","publication_year":2005,"publication_date":"2005-10-23","ids":{"openalex":"https://openalex.org/W1998215345","doi":"https://doi.org/10.1038/nbt1155","mag":"1998215345","pmid":"https://pubmed.ncbi.nlm.nih.gov/16244657"},"language":"en","primary_location":{"id":"doi:10.1038/nbt1155","doi":"https://doi.org/10.1038/nbt1155","is_oa":false,"landing_page_url":"https://doi.org/10.1038/nbt1155","pdf_url":null,"source":{"id":"https://openalex.org/S106963461","display_name":"Nature Biotechnology","issn_l":"0733-222X","issn":["0733-222X","1087-0156","1546-1696","2331-3684"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Biotechnology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5008605394","display_name":"Prof. Robert Penchovsky, Dr. rer. nat.","orcid":"https://orcid.org/0000-0001-9502-3421","observed_orcids":["https://orcid.org/0000-0001-9502-3421"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Penchovsky","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520-8103, USA","Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520-8103, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058375820","display_name":"Ronald R. Breaker","orcid":"https://orcid.org/0000-0002-2165-536X","observed_orcids":["https://orcid.org/0000-0002-2165-536X"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ronald R Breaker","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, 06520-8103, Connecticut, USA","Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, 06520-8103, Connecticut, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5058375820"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":12690,"currency":"USD","value_usd":12690},"apc_paid":null,"fwci":5.4009,"has_fulltext":false,"cited_by_count":212,"citation_normalized_percentile":{"value":0.97316286,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"23","issue":"11","first_page":"1424","last_page":"1433"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9901999831199646,"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":0.9901999831199646,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.003700000001117587,"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/T12029","display_name":"DNA and Biological Computing","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/allosteric-ribozymes","display_name":"allosteric ribozymes","score":0.984000027179718},{"id":"https://openalex.org/keywords/riboswitches","display_name":"riboswitches","score":0.7820000052452087},{"id":"https://openalex.org/keywords/rna-engineering","display_name":"RNA engineering","score":0.828000009059906},{"id":"https://openalex.org/keywords/boolean-circuits","display_name":"Boolean circuits","score":0.6499999761581421},{"id":"https://openalex.org/keywords/rna-switches","display_name":"RNA switches","score":0.4020000100135803},{"id":"https://openalex.org/keywords/ligand-specificity","display_name":"ligand specificity","score":0.7730000019073486},{"id":"https://openalex.org/keywords/self-cleavage","display_name":"self-cleavage","score":0.7919999957084656},{"id":"https://openalex.org/keywords/nucleic-acid-detection","display_name":"nucleic acid detection","score":0.9240000247955322}],"concepts":[{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.9547784328460693},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.9030835628509521},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.7092223167419434},{"id":"https://openalex.org/C1342335","wikidata":"https://www.wikidata.org/wiki/Q6545871","display_name":"Ligase ribozyme","level":5,"score":0.6169389486312866},{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.6043550968170166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.567391037940979},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.5318652391433716},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5212136507034302},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4326026439666748},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.41232702136039734},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3896395266056061},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3261362612247467},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21902772784233093},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.21433934569358826},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.18664097785949707},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.17691686749458313},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15941360592842102},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15093794465065002}],"mesh":[{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D012547","descriptor_name":"Schistosoma","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1038/nbt1155","doi":"https://doi.org/10.1038/nbt1155","is_oa":false,"landing_page_url":"https://doi.org/10.1038/nbt1155","pdf_url":null,"source":{"id":"https://openalex.org/S106963461","display_name":"Nature Biotechnology","issn_l":"0733-222X","issn":["0733-222X","1087-0156","1546-1696","2331-3684"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Biotechnology","raw_type":"journal-article"},{"id":"pmid:16244657","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16244657","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,"listed_in":[],"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":"Nature biotechnology","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1039129229","display_name":null,"funder_award_id":"N01 HV-28186","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2538371663","display_name":"NHLBI PROTEOMICS INITIATIVE","funder_award_id":"n01hv28186-13-0-0","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1562297375","https://openalex.org/W1574590441","https://openalex.org/W1581075644","https://openalex.org/W1950531847","https://openalex.org/W1971951387","https://openalex.org/W1972708527","https://openalex.org/W1984675364","https://openalex.org/W1986107627","https://openalex.org/W1986232581","https://openalex.org/W1987841739","https://openalex.org/W1989297603","https://openalex.org/W2000973947","https://openalex.org/W2001138936","https://openalex.org/W2007909703","https://openalex.org/W2009528855","https://openalex.org/W2009818318","https://openalex.org/W2010304578","https://openalex.org/W2012486340","https://openalex.org/W2012879790","https://openalex.org/W2015960673","https://openalex.org/W2020283561","https://openalex.org/W2021594503","https://openalex.org/W2030621944","https://openalex.org/W2031512086","https://openalex.org/W2033597631","https://openalex.org/W2034361830","https://openalex.org/W2034372974","https://openalex.org/W2046509103","https://openalex.org/W2047206115","https://openalex.org/W2049105226","https://openalex.org/W2052812744","https://openalex.org/W2053361782","https://openalex.org/W2054428590","https://openalex.org/W2056789539","https://openalex.org/W2060995595","https://openalex.org/W2062218409","https://openalex.org/W2062540870","https://openalex.org/W2064350910","https://openalex.org/W2064809769","https://openalex.org/W2065225159","https://openalex.org/W2069253276","https://openalex.org/W2072363537","https://openalex.org/W2075734969","https://openalex.org/W2080251448","https://openalex.org/W2080544129","https://openalex.org/W2086298020","https://openalex.org/W2092016699","https://openalex.org/W2092541496","https://openalex.org/W2092734987","https://openalex.org/W2096883982","https://openalex.org/W2103250001","https://openalex.org/W2114892973","https://openalex.org/W2130978693","https://openalex.org/W2133777805","https://openalex.org/W2134097743","https://openalex.org/W2134672977","https://openalex.org/W2142157992","https://openalex.org/W2149096104","https://openalex.org/W2151957804","https://openalex.org/W2155752821","https://openalex.org/W2158654777","https://openalex.org/W2162920755","https://openalex.org/W2169436912"],"related_works":["https://openalex.org/W7168036781","https://openalex.org/W2134273382","https://openalex.org/W7160630860","https://openalex.org/W15068435","https://openalex.org/W2330277270","https://openalex.org/W4223425825","https://openalex.org/W2075734969","https://openalex.org/W2034080548","https://openalex.org/W2092541496","https://openalex.org/W4385330568"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":17},{"year":2012,"cited_by_count":10}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2016-06-24T00:00:00"}