{"id":"https://openalex.org/W2159268893","doi":"https://doi.org/10.1093/bioinformatics/btn442","title":"<i>siDRM</i>: an effective and generally applicable online siRNA design tool","display_name":"<i>siDRM</i>: an effective and generally applicable online siRNA design tool","publication_year":2008,"publication_date":"2008-08-20","ids":{"openalex":"https://openalex.org/W2159268893","doi":"https://doi.org/10.1093/bioinformatics/btn442","mag":"2159268893","pmid":"https://pubmed.ncbi.nlm.nih.gov/18718944"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/20/2405/49051902/bioinformatics_24_20_2405.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/20/2405/49051902/bioinformatics_24_20_2405.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066838536","display_name":"Wuming Gong","orcid":"https://orcid.org/0000-0002-3147-4028"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wuming Gong","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101105277","display_name":"Yongliang Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongliang Ren","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077384845","display_name":"Haiyan Zhou","orcid":"https://orcid.org/0000-0003-1569-532X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haiyan Zhou","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103072026","display_name":"Yejun Wang","orcid":"https://orcid.org/0000-0003-4030-0027"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yejun Wang","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074324847","display_name":"Shuli Kang","orcid":"https://orcid.org/0000-0002-5000-657X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuli Kang","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051142815","display_name":"Tongbin Li","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tongbin Li","raw_affiliation_strings":["Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5066838536"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5129,"has_fulltext":false,"cited_by_count":53,"citation_normalized_percentile":{"value":0.8218682,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"24","issue":"20","first_page":"2405","last_page":"2406"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9998000264167786,"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":0.9998000264167786,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9943000078201294,"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":0.7185201048851013},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.6235615611076355},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37443456053733826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13147512078285217},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1281716525554657},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.12582716345787048}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7185201048851013},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.6235615611076355},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37443456053733826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13147512078285217},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1281716525554657},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.12582716345787048},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","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:10.1093/bioinformatics/btn442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/20/2405/49051902/bioinformatics_24_20_2405.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18718944","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18718944","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/20/2405/49051902/bioinformatics_24_20_2405.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159268893.pdf","grobid_xml":"https://content.openalex.org/works/W2159268893.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1978552532","https://openalex.org/W1996164865","https://openalex.org/W2003507585","https://openalex.org/W2004981153","https://openalex.org/W2029827106","https://openalex.org/W2043828851","https://openalex.org/W2059369194","https://openalex.org/W2107235611","https://openalex.org/W2109609799","https://openalex.org/W2110471348","https://openalex.org/W2119293746","https://openalex.org/W2138386457","https://openalex.org/W2141157874","https://openalex.org/W2144510218","https://openalex.org/W2151432781","https://openalex.org/W2156061695","https://openalex.org/W2157078151","https://openalex.org/W2165586566","https://openalex.org/W2170781554","https://openalex.org/W6680330254"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2153033713","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Small":[0],"interfering":[1],"RNAs":[2],"(siRNAs)":[3],"have":[4,44],"become":[5],"an":[6,46,120],"indispensable":[7],"tool":[8],"for":[9],"the":[10,30,50,67],"investigation":[11],"of":[12],"gene":[13],"functions.":[14],"Most":[15],"existing":[16,128],"siRNA":[17,32,76,129],"design":[18,77,130],"tools":[19,38,131],"were":[20],"trained":[21],"on":[22,56],"datasets":[23],"assembled":[24],"from":[25,63],"confined":[26],"origins,":[27],"incompatible":[28],"with":[29],"diverse":[31,60],"laboratory":[33],"practice":[34],"to":[35,92,98],"which":[36],"these":[37],"will":[39],"ultimately":[40],"be":[41],"applied.":[42],"We":[43],"performed":[45],"updated":[47],"analysis":[48],"using":[49,119],"disjunctive":[51],"rule":[52,69,85,89],"merging":[53],"(DRM)":[54],"approach":[55],"a":[57,73,82],"large":[58],"and":[59,65,87,94,110],"dataset":[61,122],"compiled":[62],"siRecords,":[64,93],"implemented":[66],"resulting":[68],"sets":[70,86],"in":[71,113,132],"siDRM,":[72],"new":[74],"online":[75],"tool.":[78],"siDRM":[79,125],"also":[80],"implements":[81],"few":[83],"high-sensitivity":[84],"fast":[88],"sets,":[90],"links":[91],"uses":[95],"several":[96],"filters":[97],"check":[99],"unwanted":[100],"detrimental":[101],"effects,":[102],"including":[103],"innate":[104],"immune":[105],"responses,":[106],"cell":[107],"toxic":[108],"effects":[109],"off-target":[111],"activities":[112],"selecting":[114],"siRNAs.":[115,135],"A":[116],"performance":[117],"comparison":[118],"independent":[121],"indicated":[123],"that":[124],"outperforms":[126],"19":[127],"identifying":[133],"effective":[134]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":6}],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2016-06-24T00:00:00"}
