{"id":"https://openalex.org/W2785639765","doi":"https://doi.org/10.1109/ssci.2017.8285345","title":"Using matching substructures as an optimization objective for RNA design","display_name":"Using matching substructures as an optimization objective for RNA design","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2785639765","doi":"https://doi.org/10.1109/ssci.2017.8285345","mag":"2785639765"},"language":"en","primary_location":{"id":"doi:10.1109/ssci.2017.8285345","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssci.2017.8285345","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE Symposium Series on Computational Intelligence (SSCI)","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/A5004050862","display_name":"D.J. Hampson","orcid":"https://orcid.org/0000-0002-7729-0427"},"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":"David J. D. Hampson","raw_affiliation_strings":["Applied Research Lab, Trinity Western University, Langley, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Applied Research Lab, Trinity Western University, Langley, British Columbia, 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/I24370400","display_name":"Trinity Western University","ror":"https://ror.org/01j2kd606","country_code":"CA","type":"education","lineage":["https://openalex.org/I24370400"]},{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Herbert H. Tsang","raw_affiliation_strings":["Applied Research Lab, Trinity Western University, Langley, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Applied Research Lab, Trinity Western University, Langley, British Columbia, 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/A5004050862"],"corresponding_institution_ids":["https://openalex.org/I125749732","https://openalex.org/I24370400"],"apc_list":null,"apc_paid":null,"fwci":0.5317,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65805613,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"220","issue":null,"first_page":"1","last_page":"7"},"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":0.9905999898910522,"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":0.9829000234603882,"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/computer-science","display_name":"Computer science","score":0.6407315731048584},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5825613141059875},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5734334588050842},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.5138843059539795},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.48861414194107056},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47362276911735535},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4281969666481018},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.42653176188468933},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33190953731536865},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17713996767997742},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16008180379867554},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1392112374305725},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08756905794143677}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6407315731048584},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5825613141059875},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5734334588050842},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.5138843059539795},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.48861414194107056},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47362276911735535},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4281969666481018},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.42653176188468933},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33190953731536865},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17713996767997742},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16008180379867554},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1392112374305725},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08756905794143677},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ssci.2017.8285345","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssci.2017.8285345","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE Symposium Series on Computational Intelligence (SSCI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306203","display_name":"M.J. Murdock Charitable Trust","ror":"https://ror.org/02hxgd925"},{"id":"https://openalex.org/F4320313012","display_name":"Trinity Western University","ror":"https://ror.org/01j2kd606"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1934768785","https://openalex.org/W1969390039","https://openalex.org/W1989020100","https://openalex.org/W2012593394","https://openalex.org/W2020999234","https://openalex.org/W2024060531","https://openalex.org/W2122944508","https://openalex.org/W2126244322","https://openalex.org/W2135373808","https://openalex.org/W2136346399","https://openalex.org/W2146716393","https://openalex.org/W2148419405","https://openalex.org/W2158381555","https://openalex.org/W2253782003","https://openalex.org/W2276634778","https://openalex.org/W2331703335","https://openalex.org/W2558663629","https://openalex.org/W2588568083","https://openalex.org/W2588767476","https://openalex.org/W6653277019"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175"],"abstract_inverted_index":{"RNA":[0,20,22,43,99],"design":[1,44,112,150],"is":[2,13,64,79],"a":[3,35,50,58,72,80,103,108,116,138],"problem":[4,63,94],"that":[5,34,54,163,186],"has":[6],"been":[7],"shown":[8],"to":[9,91,111,135,149,173],"be":[10],"NP-Hard.":[11],"It":[12],"best":[14],"described":[15],"as":[16,137],"the":[17,25,29,46,69,126,168,175,195],"inverse":[18],"of":[19,27,37,48,52,71,82,119,128,140,179,200],"folding.":[21],"folding":[23],"describes":[24,45],"process":[26,47],"calculating":[28],"most":[30],"likely":[31],"secondary":[32,60,142],"structure":[33],"strand":[36,51],"nucleotides":[38,53],"will":[39,55],"fold":[40,56],"into.":[41],"Inversely,":[42],"designing":[49],"into":[57],"given":[59],"structure.":[61],"The":[62],"made":[65],"more":[66],"difficult":[67],"by":[68],"presence":[70],"second":[73],"objective,":[74],"structural":[75,83,177],"stability.":[76,84],"Free":[77],"energy":[78],"measure":[81],"In":[85,121],"previous":[86],"research,":[87],"we":[88,124],"have":[89],"attempted":[90],"solve":[92],"this":[93,122],"using":[95],"SIMARD":[96,101,136,187],"(Simulated":[97],"Annealing":[98],"Design).":[100],"employs":[102],"simulated":[104],"annealing":[105],"framework":[106],"alongside":[107],"preselection":[109],"strategy":[110],"high-quality":[113],"sequences":[114,151,166],"in":[115,198],"reasonable":[117],"amount":[118],"time.":[120],"paper,":[123],"introduce":[125],"integration":[127],"BEAR":[129,169],"(Brand":[130],"nEw":[131],"Alphabet":[132],"for":[133,144],"RNAs)":[134],"way":[139],"notating":[141],"structures":[143],"quality":[145],"evaluation.":[146],"We":[147,161,183],"attempt":[148],"with":[152,167],"four":[153],"different":[154],"experimental":[155],"configurations":[156],"across":[157],"two":[158],"data":[159],"sets.":[160],"find":[162,185],"representing":[164],"our":[165,180],"grammar":[170],"allows":[171],"us":[172],"improve":[174],"average":[176],"similarity":[178],"generated":[181],"sequences.":[182],"also":[184],"outperforms":[188],"six":[189],"other":[190],"algorithms":[191],"when":[192],"running":[193],"on":[194],"Eterna100":[196],"benchmark":[197],"terms":[199],"successfully":[201],"designed":[202],"structures.":[203]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
