{"id":"https://openalex.org/W4293519391","doi":"https://doi.org/10.1109/cibcb55180.2022.9863040","title":"Length-Based Substructure Mutation Policies for Improved RNA Design in Simulated Annealing","display_name":"Length-Based Substructure Mutation Policies for Improved RNA Design in Simulated Annealing","publication_year":2022,"publication_date":"2022-08-15","ids":{"openalex":"https://openalex.org/W4293519391","doi":"https://doi.org/10.1109/cibcb55180.2022.9863040"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb55180.2022.9863040","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb55180.2022.9863040","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5031452464","display_name":"Ryan McBride","orcid":"https://orcid.org/0000-0001-8616-1910"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I24370400","display_name":"Trinity Western University","ror":"https://ror.org/01j2kd606","country_code":"CA","type":"education","lineage":["https://openalex.org/I24370400"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Ryan McBride","raw_affiliation_strings":["Trinity Western University,Applied Research Lab,Langley,Canada","Applied Research Lab, Trinity Western University, Langley, Canada"],"affiliations":[{"raw_affiliation_string":"Trinity Western University,Applied Research Lab,Langley,Canada","institution_ids":["https://openalex.org/I24370400","https://openalex.org/I125749732"]},{"raw_affiliation_string":"Applied Research Lab, Trinity Western University, Langley, Canada","institution_ids":["https://openalex.org/I24370400","https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049705327","display_name":"Herbert H. Tsang","orcid":"https://orcid.org/0000-0001-8928-7375"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I24370400","display_name":"Trinity Western University","ror":"https://ror.org/01j2kd606","country_code":"CA","type":"education","lineage":["https://openalex.org/I24370400"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Herbert H. Tsang","raw_affiliation_strings":["Trinity Western University,Applied Research Lab,Langley,Canada","Applied Research Lab, Trinity Western University, Langley, Canada"],"affiliations":[{"raw_affiliation_string":"Trinity Western University,Applied Research Lab,Langley,Canada","institution_ids":["https://openalex.org/I24370400","https://openalex.org/I125749732"]},{"raw_affiliation_string":"Applied Research Lab, Trinity Western University, Langley, Canada","institution_ids":["https://openalex.org/I24370400","https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031452464"],"corresponding_institution_ids":["https://openalex.org/I125749732","https://openalex.org/I24370400"],"apc_list":null,"apc_paid":null,"fwci":0.0858,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42474165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"abs 2111 4504","issue":null,"first_page":"1","last_page":"9"},"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":0.995199978351593,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9872000217437744,"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/substructure","display_name":"Substructure","score":0.8837557435035706},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.7376542091369629},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.6944413185119629},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5172472596168518},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5078747868537903},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44378238916397095},{"id":"https://openalex.org/keywords/mutation-testing","display_name":"Mutation testing","score":0.4406812787055969},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4218118488788605},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.3916524648666382},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33112335205078125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30197200179100037},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26371046900749207},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1250695288181305}],"concepts":[{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.8837557435035706},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7376542091369629},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.6944413185119629},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5172472596168518},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5078747868537903},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44378238916397095},{"id":"https://openalex.org/C163565370","wikidata":"https://www.wikidata.org/wiki/Q4308623","display_name":"Mutation testing","level":4,"score":0.4406812787055969},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4218118488788605},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3916524648666382},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33112335205078125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30197200179100037},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26371046900749207},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1250695288181305},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb55180.2022.9863040","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb55180.2022.9863040","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313012","display_name":"Trinity Western University","ror":"https://ror.org/01j2kd606"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1508006319","https://openalex.org/W1593394816","https://openalex.org/W1989454102","https://openalex.org/W2020865862","https://openalex.org/W2055078783","https://openalex.org/W2061587202","https://openalex.org/W2089019240","https://openalex.org/W2103250001","https://openalex.org/W2106293441","https://openalex.org/W2158381555","https://openalex.org/W2163557777","https://openalex.org/W2164618041","https://openalex.org/W2276634778","https://openalex.org/W2785639765","https://openalex.org/W2809642602","https://openalex.org/W2914444921","https://openalex.org/W2944734652","https://openalex.org/W2954102902","https://openalex.org/W2999044305","https://openalex.org/W3004318991","https://openalex.org/W3007425848","https://openalex.org/W3083215873","https://openalex.org/W3189680464","https://openalex.org/W4226279290","https://openalex.org/W4248523071","https://openalex.org/W6635489133","https://openalex.org/W6803814732"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W2581348958","https://openalex.org/W2264054990","https://openalex.org/W2581888268","https://openalex.org/W2902683473","https://openalex.org/W1989561030","https://openalex.org/W2088051090"],"abstract_inverted_index":{"RNA":[0,10,31,63,127,145],"Design":[1,146],"is":[2,53],"a":[3,67,91,138],"crucial":[4],"bioinformatics":[5],"problem":[6,74],"to":[7,46,125,129,167],"tailor":[8],"specific":[9],"sequences":[11,24],"into":[12],"structures":[13],"that":[14,132],"guide":[15],"our":[16,78],"biology":[17],"and":[18,33,95,116],"medicine.":[19],"Because":[20],"these":[21,154],"computer":[22],"generated":[23],"are":[25,44,59,75,120],"often":[26],"statistically":[27],"different":[28],"from":[29],"observed":[30,62],"sequence":[32],"do":[34],"not":[35],"fold":[36],"as":[37],"intended":[38],"in":[39,66,123,160],"real":[40],"lab":[41],"conditions,":[42],"methods":[43,158],"developed":[45],"ensure":[47],"more":[48],"biological":[49],"consistency.":[50],"One":[51],"approach":[52],"substructure":[54,100,155],"restriction":[55],"where":[56],"any":[57,114],"solutions":[58,161],"composed":[60],"of":[61,98,109,137,153,164],"substructures":[64,87,119,131],"recorded":[65],"database.":[68],"However,":[69],"studies":[70],"on":[71,142],"this":[72],"restricted":[73],"limited:":[76],"while":[77],"Applied":[79],"Research":[80],"Lab's":[81],"Simulated":[82,174],"Annealing":[83,175],"solution":[84],"(SIMARD)":[85],"uses":[86],"it":[88],"only":[89],"considers":[90],"single":[92,96],"mutation":[93,157],"policy":[94],"method":[97],"generating":[99],"consistent":[101],"sequences.":[102],"We":[103],"therefore":[104],"propose":[105],"two":[106],"new":[107],"policies":[108],"mutation:":[110],"uniform,":[111],"randomly":[112,122],"modifying":[113],"structure,":[115],"length":[117,128],"proportional,":[118],"swapped":[121],"proportion":[124],"their":[126],"target":[130,169],"cover":[133],"the":[134,150,168],"most":[135],"bases":[136,165],"problem.":[139],"In":[140],"experiments":[141],"roughly":[143],"fifty":[144],"problems,":[147],"we":[148],"conclude":[149],"potential":[151],"value":[152],"based":[156],"resulting":[159],"potentially":[162],"hundreds":[163],"closer":[166],"folded":[170],"structure":[171],"than":[172],"previous":[173],"solutions.":[176]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
