{"id":"https://openalex.org/W4245380199","doi":"https://doi.org/10.1109/cbms.2004.1311737","title":"3Si: a computer program for the optimal design of short interfering RNA (siRNA) for gene silencing","display_name":"3Si: a computer program for the optimal design of short interfering RNA (siRNA) for gene silencing","publication_year":2004,"publication_date":"2004-10-04","ids":{"openalex":"https://openalex.org/W4245380199","doi":"https://doi.org/10.1109/cbms.2004.1311737"},"language":"en","primary_location":{"id":"doi:10.1109/cbms.2004.1311737","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2004.1311737","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 17th IEEE Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"},"type":"conference-paper","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/A5100652326","display_name":"Weiping Chen","orcid":"https://orcid.org/0000-0002-0459-0605"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"WeiPing Chen","raw_affiliation_strings":["National Eye Institute, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Eye Institute, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100946624","display_name":"Wei Zha","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wei Zha","raw_affiliation_strings":["Cable and Wireless, Reston, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cable and Wireless, Reston, VA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103042084","display_name":"Terry A. Cox","orcid":"https://orcid.org/0000-0002-8681-5811"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Terry Cox","raw_affiliation_strings":["National Eye Institute, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Eye Institute, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xiujun Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiujun Zhao","raw_affiliation_strings":["National Eye Institute, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Eye Institute, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024894704","display_name":"P. Russell","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Russell","raw_affiliation_strings":["National Eye Institute, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Eye Institute, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210139686"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7365,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.81092616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"17","issue":null,"first_page":"335","last_page":"342"},"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":0.9995999932289124,"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":0.989799976348877,"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/gene-silencing","display_name":"Gene silencing","score":0.9399691224098206},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.7282971143722534},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.6767678260803223},{"id":"https://openalex.org/keywords/trans-acting-sirna","display_name":"Trans-acting siRNA","score":0.5878444314002991},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.516769289970398},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4887566566467285},{"id":"https://openalex.org/keywords/rna-induced-silencing-complex","display_name":"RNA-induced silencing complex","score":0.4712688624858856},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46728333830833435},{"id":"https://openalex.org/keywords/rna-silencing","display_name":"RNA silencing","score":0.4571629762649536},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35933825373649597},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.35677117109298706}],"concepts":[{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.9399691224098206},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.7282971143722534},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.6767678260803223},{"id":"https://openalex.org/C60723119","wikidata":"https://www.wikidata.org/wiki/Q7833577","display_name":"Trans-acting siRNA","level":5,"score":0.5878444314002991},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.516769289970398},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4887566566467285},{"id":"https://openalex.org/C155330019","wikidata":"https://www.wikidata.org/wiki/Q21106117","display_name":"RNA-induced silencing complex","level":5,"score":0.4712688624858856},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46728333830833435},{"id":"https://openalex.org/C2191507","wikidata":"https://www.wikidata.org/wiki/Q7277185","display_name":"RNA silencing","level":5,"score":0.4571629762649536},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35933825373649597},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.35677117109298706}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cbms.2004.1311737","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2004.1311737","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 17th IEEE Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.6200000047683716,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1509830195","https://openalex.org/W1611419331","https://openalex.org/W1916491745","https://openalex.org/W1996163490","https://openalex.org/W2004981153","https://openalex.org/W2012188597","https://openalex.org/W2012547585","https://openalex.org/W2019387053","https://openalex.org/W2023246459","https://openalex.org/W2034709592","https://openalex.org/W2045452812","https://openalex.org/W2050066317","https://openalex.org/W2054757478","https://openalex.org/W2072543946","https://openalex.org/W2082213106","https://openalex.org/W2085307948","https://openalex.org/W2096018896","https://openalex.org/W2114106114","https://openalex.org/W2114110579","https://openalex.org/W2116009187","https://openalex.org/W2125710038","https://openalex.org/W2128212057","https://openalex.org/W2136361016","https://openalex.org/W2139802966","https://openalex.org/W2141157874","https://openalex.org/W2153140501","https://openalex.org/W2154166273","https://openalex.org/W2166989126","https://openalex.org/W4236503414","https://openalex.org/W4253820701"],"related_works":["https://openalex.org/W2039740951","https://openalex.org/W2129401531","https://openalex.org/W2072680951","https://openalex.org/W633773340","https://openalex.org/W2160381063","https://openalex.org/W1982264400","https://openalex.org/W2411312501","https://openalex.org/W2111383435","https://openalex.org/W1930224804","https://openalex.org/W606763619"],"abstract_inverted_index":{"siRNA":[0,58,92,112,124,130,139],"is":[1,10,26,75,223],"a":[2,37,80,98,101,146,195,224],"powerful":[3],"technique":[4],"for":[5,23,68,111,137,211],"gene":[6,20,42,55,120,229],"silencing.":[7,93,113],"However,":[8],"it":[9],"still":[11],"not":[12,189],"clear":[13],"how":[14],"to":[15,106,201,235],"accurately":[16],"determine":[17],"an":[18],"effective":[19],"targeting":[21],"region":[22,82,86],"siRNA.":[24,46,181,213],"It":[25],"also":[27],"controversial":[28],"if":[29],"the":[30,41,45,48,51,77,84,89,95,108,123,141,151,159,167,170,174,179,204,207,218],"targeted":[31,219],"mRNA":[32,220],"secondary":[33,52,157,221],"structure":[34,53,222],"would":[35],"have":[36],"significant":[38,135,226],"impact":[39],"on":[40],"silencing":[43,56,121,230],"by":[44,57,122],"Understanding":[47],"relationship":[49],"between":[50,119],"and":[54,67,100,125,154,169,231],"could":[59],"help":[60],"in":[61,228],"high":[62],"throughput":[63],"function-based":[64],"genetic":[65],"screens":[66],"development":[69],"of":[70,79,91,166,173,178,198,206],"therapeutic":[71],"tools.":[72],"Our":[73,214],"hypothesis":[74],"that":[76,149,186,217],"selection":[78],"single-stranded":[81,109,143],"as":[83,194],"target":[85,152],"should":[87,188,232],"increase":[88],"efficiency":[90],"For":[94],"first":[96,175],"time,":[97],"formula":[99],"computer":[102],"program":[103],"were":[104],"developed":[105],"select":[107],"regions":[110],"We":[114],"statistically":[115,225],"analyzed":[116],"quantitative":[117],"relationships":[118],"ten":[126],"parameters":[127,136],"from":[128],"published":[129],"sequences.":[131],"The":[132,182],"four":[133,176],"nonlinear":[134,183],"designing":[138,212],"are":[140],"RNA":[142],"index":[144],"(SSi),":[145],"new":[147],"parameter":[148],"identifies":[150],"position":[153],"its":[155],"related":[156],"structures,":[158],"GC":[160,196],"content,":[161],"/spl":[162],"Delta/G":[163],"free":[164],"energy":[165],"siRNA,":[168],"5'GC":[171],"content":[172,197],"bases":[177],"antisense":[180],"complexity":[184],"suggested":[185],"one":[187],"use":[190],"simple":[191],"criteria":[192],"such":[193],"around":[199],"30":[200],"50%":[202],"or":[203],"absence":[205],"sequence":[208],"pattern":[209],"GGG":[210],"results":[215],"indicate":[216],"determinant":[227],"be":[233],"used":[234],"optimize":[236],"RNAi":[237],"technology.":[238]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}