{"id":"https://openalex.org/W2083398732","doi":"https://doi.org/10.1142/s0219720013410047","title":"INFLUENCE OF mRNA FEATURES ON siRNA INTERFERENCE EFFICACY","display_name":"INFLUENCE OF mRNA FEATURES ON siRNA INTERFERENCE EFFICACY","publication_year":2012,"publication_date":"2012-12-31","ids":{"openalex":"https://openalex.org/W2083398732","doi":"https://doi.org/10.1142/s0219720013410047","mag":"2083398732","pmid":"https://pubmed.ncbi.nlm.nih.gov/23796181"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720013410047","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013410047","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5101708144","display_name":"Yuanning Liu","orcid":"https://orcid.org/0000-0003-2643-0976"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"YUANNING LIU","raw_affiliation_strings":["School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056123975","display_name":"Yaping Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"YAPING CHANG","raw_affiliation_strings":["School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060215226","display_name":"Chao Zhang","orcid":"https://orcid.org/0000-0001-8019-7998"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"CHAO ZHANG","raw_affiliation_strings":["Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007511595","display_name":"Qingkai Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"QINGKAI WEI","raw_affiliation_strings":["College of Automotive Engineering, Jilin University, Changchun 130012, P. R. China"],"affiliations":[{"raw_affiliation_string":"College of Automotive Engineering, Jilin University, Changchun 130012, P. R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100649322","display_name":"Jingbo Chen","orcid":"https://orcid.org/0000-0001-8113-7823"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"JINGBO CHEN","raw_affiliation_strings":["School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun 130012, P. R. China","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun, 130012, P.R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100648348","display_name":"Huiling Chen","orcid":"https://orcid.org/0000-0002-7714-9693"},"institutions":[{"id":"https://openalex.org/I146620803","display_name":"Wenzhou University","ror":"https://ror.org/020hxh324","country_code":"CN","type":"education","lineage":["https://openalex.org/I146620803"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"HUILING CHEN","raw_affiliation_strings":["College of Physics and Electronic Information, Wenzhou University, Wenzhou, 325035, P. R. China"],"affiliations":[{"raw_affiliation_string":"College of Physics and Electronic Information, Wenzhou University, Wenzhou, 325035, P. R. China","institution_ids":["https://openalex.org/I146620803"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DONG XU","raw_affiliation_strings":["Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101708144"],"corresponding_institution_ids":["https://openalex.org/I194450716"],"apc_list":null,"apc_paid":null,"fwci":0.5253,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.65144132,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"11","issue":"03","first_page":"1341004","last_page":"1341004"},"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":0.9990000128746033,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.80307936668396},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.7930049896240234},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.7272611856460571},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.6184057593345642},{"id":"https://openalex.org/keywords/trans-acting-sirna","display_name":"Trans-acting siRNA","score":0.5435206890106201},{"id":"https://openalex.org/keywords/interference","display_name":"Interference (communication)","score":0.5395327210426331},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5147397518157959},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5130385160446167},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.455860435962677},{"id":"https://openalex.org/keywords/rna-silencing","display_name":"RNA silencing","score":0.43499985337257385},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.396220326423645},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.35833245515823364},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3117429316043854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.25450751185417175},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22251248359680176},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.1334349513053894}],"concepts":[{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.80307936668396},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.7930049896240234},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.7272611856460571},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.6184057593345642},{"id":"https://openalex.org/C60723119","wikidata":"https://www.wikidata.org/wiki/Q7833577","display_name":"Trans-acting siRNA","level":5,"score":0.5435206890106201},{"id":"https://openalex.org/C32022120","wikidata":"https://www.wikidata.org/wiki/Q797225","display_name":"Interference (communication)","level":3,"score":0.5395327210426331},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5147397518157959},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5130385160446167},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.455860435962677},{"id":"https://openalex.org/C2191507","wikidata":"https://www.wikidata.org/wiki/Q7277185","display_name":"RNA silencing","level":5,"score":0.43499985337257385},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.396220326423645},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.35833245515823364},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3117429316043854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.25450751185417175},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22251248359680176},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.1334349513053894},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720013410047","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013410047","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:23796181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23796181","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.7099999785423279}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1509715834","https://openalex.org/W1520518044","https://openalex.org/W1975806245","https://openalex.org/W1986687961","https://openalex.org/W2033471072","https://openalex.org/W2060022712","https://openalex.org/W2064629375","https://openalex.org/W2097261962","https://openalex.org/W2099915551","https://openalex.org/W2103792213","https://openalex.org/W2106082032","https://openalex.org/W2128302979","https://openalex.org/W2134653938","https://openalex.org/W2141573080","https://openalex.org/W2149538815","https://openalex.org/W2160923685","https://openalex.org/W2165366948","https://openalex.org/W2166802510","https://openalex.org/W2167198781","https://openalex.org/W2170918433"],"related_works":["https://openalex.org/W3140432620","https://openalex.org/W1978057048","https://openalex.org/W2132697617","https://openalex.org/W2047147668","https://openalex.org/W2417470032","https://openalex.org/W2408799732","https://openalex.org/W1985127633","https://openalex.org/W1649999227","https://openalex.org/W2361323882","https://openalex.org/W1540115331"],"abstract_inverted_index":{"Design":[0],"of":[1,8,98,107,120,170],"small":[2],"interference":[3,18],"RNA":[4,17],"(siRNA)":[5],"is":[6],"one":[7,47],"the":[9,16,108,118],"most":[10],"important":[11],"steps":[12],"in":[13,172,176,208],"effectively":[14],"applying":[15],"(RNAi)":[19],"technology.":[20],"The":[21,202],"current":[22],"siRNA":[23,36,109,140,150,153,159,182,193,199],"design":[24,28,200],"often":[25,31],"produces":[26],"inconsistent":[27],"results,":[29],"which":[30],"fail":[32],"to":[33,113,132,148,178],"reliably":[34],"select":[35],"with":[37],"clear":[38],"silencing":[39,135],"effects.":[40],"We":[41,142],"propose":[42],"that":[43,188],"when":[44,180],"designing":[45],"siRNA,":[46],"should":[48],"consider":[49],"mRNA":[50,73,99,121,155,190],"global":[51,74,102,122],"features":[52,75,123,129,183,196],"and":[53,71,76,93,103,124,136,157,191,214],"near":[54,125,158,192],"siRNA-binding":[55,126],"site":[56,127,161,195],"local":[57,78,104,128],"features.":[58,79,162],"By":[59],"a":[60,138,144,167],"linear":[61],"regression":[62],"study,":[63],"we":[64],"discovered":[65],"strong":[66],"correlations":[67],"between":[68,212],"inhibitory":[69,115],"efficacy":[70,151,211],"both":[72,101],"neighboring":[77],"This":[80],"paper":[81],"shows":[82],"that,":[83],"on":[84],"average,":[85],"less":[86],"GC":[87],"content,":[88],"fewer":[89],"stem":[90],"secondary":[91,96],"structures,":[92],"more":[94],"loop":[95],"structures":[97],"at":[100],"flanking":[105],"regions":[106],"binding":[110,160,194,210],"sites":[111],"lead":[112],"stronger":[114],"efficacy.":[116],"Thus,":[117],"use":[119,143],"are":[130],"essential":[131],"successful":[133],"gene":[134],"hence,":[137],"better":[139],"design.":[141],"random":[145],"forest":[146],"model":[147],"predict":[149],"using":[152,181],"features,":[154,156],"Our":[163,185],"prediction":[164],"method":[165],"achieved":[166],"correlation":[168],"coefficient":[169],"0.7":[171],"10-fold":[173],"cross":[174],"validation":[175],"contrast":[177],"0.63":[179],"only.":[184],"study":[186],"demonstrates":[187],"considering":[189],"helps":[197],"improve":[198],"accuracy.":[201],"findings":[203],"may":[204],"also":[205],"be":[206],"helpful":[207],"understanding":[209],"microRNA":[213],"mRNA.":[215]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}