{"id":"https://openalex.org/W2729863764","doi":"https://doi.org/10.1145/3071178.3071345","title":"Optimizing nucleic acid sequences for a molecular data recorder","display_name":"Optimizing nucleic acid sequences for a molecular data recorder","publication_year":2017,"publication_date":"2017-06-30","ids":{"openalex":"https://openalex.org/W2729863764","doi":"https://doi.org/10.1145/3071178.3071345","mag":"2729863764"},"language":"en","primary_location":{"id":"doi:10.1145/3071178.3071345","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3071178.3071345","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=3071345&type=pdf","source":{"id":"https://openalex.org/S4363608932","display_name":"Proceedings of the Genetic and Evolutionary Computation Conference","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Genetic and Evolutionary Computation Conference","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"http://dl.acm.org/ft_gateway.cfm?id=3071345&type=pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007258084","display_name":"Jerzy Kozyra","orcid":null},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jerzy Kozyra","raw_affiliation_strings":["Newcastle University, Newcastle-upon-Tyne, UK"],"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle-upon-Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055847229","display_name":"Harold Fellermann","orcid":"https://orcid.org/0000-0001-5861-1945"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Harold Fellermann","raw_affiliation_strings":["Newcastle University, Newcastle-upon-Tyne, UK"],"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle-upon-Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006728245","display_name":"Ben Shirt\u2010Ediss","orcid":"https://orcid.org/0000-0002-8853-0182"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ben Shirt-Ediss","raw_affiliation_strings":["Newcastle University, Newcastle-upon-Tyne, UK"],"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle-upon-Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038437306","display_name":"Annunziata Lopiccolo","orcid":"https://orcid.org/0000-0002-2145-6088"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Annunziata Lopiccolo","raw_affiliation_strings":["Newcastle University, Newcastle-upon-Tyne, UK"],"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle-upon-Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043620976","display_name":"Natalio Krasnogor","orcid":"https://orcid.org/0000-0002-2651-4320"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Natalio Krasnogor","raw_affiliation_strings":["Newcastle University, Newcastle-upon-Tyne"],"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle-upon-Tyne","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5007258084"],"corresponding_institution_ids":["https://openalex.org/I84884186"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.07862903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1145","last_page":"1152"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9994999766349792,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.6558314561843872},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6259868741035461},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5684572458267212},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5645031929016113},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5390289425849915},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.5203480124473572},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4750147759914398},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.45443907380104065},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4503919780254364},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.4297109842300415},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40901240706443787},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.35007065534591675},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22079381346702576},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1670404076576233},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15899613499641418},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13427966833114624},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12539446353912354}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6558314561843872},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6259868741035461},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5684572458267212},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5645031929016113},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5390289425849915},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.5203480124473572},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4750147759914398},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.45443907380104065},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4503919780254364},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.4297109842300415},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40901240706443787},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.35007065534591675},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22079381346702576},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1670404076576233},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15899613499641418},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13427966833114624},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12539446353912354},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3071178.3071345","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3071178.3071345","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=3071345&type=pdf","source":{"id":"https://openalex.org/S4363608932","display_name":"Proceedings of the Genetic and Evolutionary Computation Conference","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Genetic and Evolutionary Computation Conference","raw_type":"proceedings-article"},{"id":"pmh:oai:eprint.ncl.ac.uk:240069","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402485","display_name":"Newcastle University ePrints (Newcastle Univesity)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84884186","host_organization_name":"Newcastle University","host_organization_lineage":["https://openalex.org/I84884186"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1145/3071178.3071345","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3071178.3071345","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=3071345&type=pdf","source":{"id":"https://openalex.org/S4363608932","display_name":"Proceedings of the Genetic and Evolutionary Computation Conference","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Genetic and Evolutionary Computation Conference","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5140230474","display_name":null,"funder_award_id":"EP/J004111/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8035887905","display_name":null,"funder_award_id":"EP/N031962/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2729863764.pdf","grobid_xml":"https://content.openalex.org/works/W2729863764.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1567090568","https://openalex.org/W1596194860","https://openalex.org/W1617520624","https://openalex.org/W1964928696","https://openalex.org/W1975679096","https://openalex.org/W1985357096","https://openalex.org/W1989020100","https://openalex.org/W1990476699","https://openalex.org/W1991472095","https://openalex.org/W2003422946","https://openalex.org/W2004945910","https://openalex.org/W2023747155","https://openalex.org/W2041857964","https://openalex.org/W2063594852","https://openalex.org/W2075031385","https://openalex.org/W2086561953","https://openalex.org/W2099530721","https://openalex.org/W2125615424","https://openalex.org/W2126961173","https://openalex.org/W2143766500","https://openalex.org/W2148339059","https://openalex.org/W2150081162","https://openalex.org/W2163413204","https://openalex.org/W2171830519","https://openalex.org/W2186876778","https://openalex.org/W2504860691","https://openalex.org/W2588186673","https://openalex.org/W2605776352","https://openalex.org/W2622036660","https://openalex.org/W2911618051","https://openalex.org/W4298272808"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W1971444612","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2942366970","https://openalex.org/W1543504406","https://openalex.org/W2807634898","https://openalex.org/W633173308","https://openalex.org/W2035653613"],"abstract_inverted_index":{"We":[0,178],"recently":[1],"reported":[2],"the":[3,46,49,62,83,135,156],"design":[4,66],"for":[5,107],"a":[6,39,70,126,131,187],"DNA":[7,40,144],"nano-device":[8],"that":[9,28,82,129,146,174,180],"can":[10,183],"record":[11],"and":[12,52,97,111],"store":[13],"molecular":[14],"signals.":[15],"Here":[16],"we":[17,77,124,153],"present":[18],"an":[19,171],"evolutionary":[20],"algorithm":[21,128,139],"tailored":[22],"to":[23,103,115,142],"optimising":[24],"nucleic":[25],"acid":[26],"sequences":[27,85,145],"predictively":[29],"fold":[30,86],"into":[31,56,69,90],"our":[32,37,166],"desired":[33,54,91,109],"target":[34,92],"structures.":[35],"In":[36],"approach,":[38],"device":[41],"is":[42,67],"first":[43],"specified":[44],"abstractly:":[45],"topology":[47],"of":[48,72,134,170,190],"individual":[50],"strands":[51],"their":[53],"foldings":[55],"multi-strand":[57],"complexes":[58],"are":[59],"described":[60],"at":[61],"domain-level.":[63],"Initially,":[64],"this":[65,161,181],"decomposed":[68],"set":[71],"pairwise":[73],"strand":[74,192],"interactions.":[75],"Then,":[76],"optimize":[78],"candidate":[79],"domains,":[80],"such":[81],"resulting":[84],"with":[87,117],"high":[88,105],"accuracy":[89],"structures":[93],"both":[94],"(a)":[95],"individually":[96],"(b)":[98],"jointly,":[99],"but":[100],"also":[101],"(c)":[102],"show":[104],"affinity":[106,114],"binding":[108],"partners":[110],"simultaneously":[112],"low":[113],"bind":[116],"any":[118],"undesired":[119],"partner.":[120],"As":[121],"optimization":[122],"heuristic":[123],"use":[125],"genetic":[127],"employs":[130],"linear":[132],"combination":[133],"above":[136],"scores.":[137],"Our":[138],"was":[140],"able":[141],"generate":[143],"satisfy":[147],"all":[148],"given":[149],"criteria.":[150],"Even":[151],"though":[152],"cannot":[154],"establish":[155],"theoretically":[157],"achievable":[158],"optima":[159],"(as":[160],"would":[162],"require":[163],"exhaustive":[164],"search),":[165],"solutions":[167],"score":[168],"90%":[169],"upper":[172],"bound":[173],"ignores":[175],"conflicting":[176],"objectives.":[177],"envision":[179],"approach":[182],"be":[184],"generalized":[185],"towards":[186],"broad":[188],"class":[189],"toehold-mediated":[191],"displacement":[193],"systems.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
