{"id":"https://openalex.org/W1533190684","doi":"https://doi.org/10.1109/csb.2003.1227360","title":"OptiRNAi, a Web-based program to select siRNA sequences","display_name":"OptiRNAi, a Web-based program to select siRNA sequences","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W1533190684","doi":"https://doi.org/10.1109/csb.2003.1227360","mag":"1533190684"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227360","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227360","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","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/A5062280572","display_name":"Wenwu Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wenwu Cui","raw_affiliation_strings":["Department of Biological Science, University of Delaware, Newark, Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Science, University of Delaware, Newark, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102145571","display_name":"Jianchang Ning","orcid":null},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianchang Ning","raw_affiliation_strings":["Delaware Biotechnology Institute, University of Delaware, Newark, Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute, University of Delaware, Newark, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945","https://openalex.org/I1312106833"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048642675","display_name":"Ulhas P. Naik","orcid":"https://orcid.org/0000-0001-7556-444X"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"U.P. Naik","raw_affiliation_strings":["Department of Biological Science, University of Delaware, Newark, Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Science, University of Delaware, Newark, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010301642","display_name":"Melinda K. Duncan","orcid":"https://orcid.org/0000-0003-1570-322X"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M.K. Duncan","raw_affiliation_strings":["Department of Biological Science, University of Delaware, Newark, Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Science, University of Delaware, Newark, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062280572"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":0.1169,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.44981993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"433","last_page":"434"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","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/T10725","display_name":"RNA Interference and Gene Delivery","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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9993000030517578,"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/T10613","display_name":"Virus-based gene therapy research","score":0.9861999750137329,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.891125500202179},{"id":"https://openalex.org/keywords/gene-knockdown","display_name":"Gene knockdown","score":0.6853001117706299},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.6580175757408142},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5574312806129456},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5390858054161072},{"id":"https://openalex.org/keywords/interference","display_name":"Interference (communication)","score":0.4529312252998352},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4427633285522461},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4291055500507355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37919002771377563},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.34434831142425537},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2640528678894043},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.173444002866745}],"concepts":[{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.891125500202179},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.6853001117706299},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.6580175757408142},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5574312806129456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5390858054161072},{"id":"https://openalex.org/C32022120","wikidata":"https://www.wikidata.org/wiki/Q797225","display_name":"Interference (communication)","level":3,"score":0.4529312252998352},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4427633285522461},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4291055500507355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37919002771377563},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.34434831142425537},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2640528678894043},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.173444002866745},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2003.1227360","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227360","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","score":0.6299999952316284,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1647075334","https://openalex.org/W1975822917","https://openalex.org/W2017642141","https://openalex.org/W2077489356","https://openalex.org/W2093008096","https://openalex.org/W2115678473","https://openalex.org/W2117648777","https://openalex.org/W2128212057","https://openalex.org/W2152993806","https://openalex.org/W4211039187"],"related_works":["https://openalex.org/W4391126805","https://openalex.org/W2093213574","https://openalex.org/W2076785949","https://openalex.org/W2167306613","https://openalex.org/W1963563485","https://openalex.org/W2129321041","https://openalex.org/W1974857950","https://openalex.org/W2048380765","https://openalex.org/W2024030923","https://openalex.org/W2047147668"],"abstract_inverted_index":{"RNA":[0,44],"interference":[1],"(RNAi)":[2],"is":[3,46,158],"a":[4,78,103,109,159],"recently":[5],"developed":[6,76],"reverse":[7],"genetic":[8],"tool":[9,162],"to":[10,31,48,88],"knockdown":[11],"expression":[12],"of":[13,20,26,34,97,105,124,132,138],"specific":[14,32],"genes":[15],"in":[16,128],"eukaryotes.":[17],"Successful":[18],"implementation":[19],"this":[21],"technology":[22],"requires":[23],"the":[24,35,68,83,98,115,118,122,125,129,136,145,148],"design":[25,165],"double":[27],"stranded":[28],"RNAs":[29],"identical":[30],"regions":[33],"target":[36,50,126,137],"gene.":[37],"However,":[38],"not":[39],"every":[40],"possible":[41],"small":[42],"interfering":[43],"(siRNA)":[45],"able":[47],"reduce":[49],"gene":[51],"expression.":[52],"Recently,":[53],"Elbashir":[54,84],"et":[55,85],"al":[56,86],"has":[57],"established":[58],"empirical":[59,119],"criteria":[60,87,167],"for":[61,71,92,135,153,163],"siRNA":[62,93,107],"sequence":[63,116,127],"selection":[64],"that":[65,111,168],"significantly":[66],"improved":[67],"success":[69],"rate":[70],"RNAi":[72,154,164],"attempts.":[73],"We":[74],"have":[75],"OptiRNAi,":[77],"computational":[79],"tool,":[80],"which":[81],"uses":[82],"predict":[89],"appropriate":[90],"sequences":[91],"production.":[94],"The":[95],"output":[96],"program":[99],"provides":[100],"researchers":[101],"with":[102],"number":[104],"potential":[106],"targets,":[108],"score":[110],"reflects":[112],"how":[113],"well":[114],"fulfills":[117],"criteria,":[120],"and":[121],"location":[123],"input.":[130],"Specificity":[131],"these":[133],"siRNAs":[134],"interest":[139],"can":[140],"then":[141],"be":[142],"assessed":[143],"by":[144],"investigator":[146],"using":[147,166],"embedded":[149],"Blast":[150],"server":[151],"optimized":[152],"design.":[155],"Thus,":[156],"OptiRNAi":[157],"labor":[160],"saving":[161],"are":[169],"more":[170],"stringent":[171],"than":[172],"other":[173],"available":[174],"tools.":[175]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
