{"id":"https://openalex.org/W2897838249","doi":"https://doi.org/10.1093/database/bay109","title":"siAbasic: a comprehensive database for potent siRNA-6\u00d8 sequences without off-target effects","display_name":"siAbasic: a comprehensive database for potent siRNA-6\u00d8 sequences without off-target effects","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2897838249","doi":"https://doi.org/10.1093/database/bay109","mag":"2897838249","pmid":"https://pubmed.ncbi.nlm.nih.gov/30321353"},"language":"en","primary_location":{"id":"doi:10.1093/database/bay109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay109","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay109/27329194/bay109.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay109/27329194/bay109.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027425249","display_name":"Jongyeun Park","orcid":"https://orcid.org/0000-0001-7394-5361"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jongyeun Park","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049035981","display_name":"Seung Hyun Ahn","orcid":"https://orcid.org/0000-0002-8409-4096"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seung Hyun Ahn","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111364392","display_name":"Kwang Moon Cho","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kwang Moon Cho","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012059957","display_name":"Dowoon Gu","orcid":"https://orcid.org/0000-0002-8551-7863"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Dowoon Gu","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112188661","display_name":"Eun-Sook Jang","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Eun-Sook Jang","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea","EncodeGEN Co. Ltd., Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]},{"raw_affiliation_string":"EncodeGEN Co. Ltd., Seoul, Korea","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078973583","display_name":"Sung Wook","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Sung Wook Chi","raw_affiliation_strings":["Department of Life Sciences, Korea University, Seoul, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Korea University, Seoul, Korea","institution_ids":["https://openalex.org/I197347611"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5078973583"],"corresponding_institution_ids":["https://openalex.org/I197347611"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.3677,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60578991,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"2018","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"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":0.5841103792190552},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.46186381578445435},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3893411159515381},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35635411739349365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18519023060798645}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5841103792190552},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.46186381578445435},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3893411159515381},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35635411739349365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18519023060798645}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bay109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay109","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay109/27329194/bay109.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:30321353","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30321353","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:5145146","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6183071","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bay109","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay109","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay109/27329194/bay109.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321373","display_name":"Korea University","ror":"https://ror.org/047dqcg40"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2897838249.pdf","grobid_xml":"https://content.openalex.org/works/W2897838249.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W2027954222","https://openalex.org/W2047277267","https://openalex.org/W2052312685","https://openalex.org/W2059273126","https://openalex.org/W2071596792","https://openalex.org/W2078187809","https://openalex.org/W2086561953","https://openalex.org/W2104806799","https://openalex.org/W2110083155","https://openalex.org/W2110586067","https://openalex.org/W2115873803","https://openalex.org/W2117977572","https://openalex.org/W2128212057","https://openalex.org/W2143313350","https://openalex.org/W2149538815","https://openalex.org/W2157287222","https://openalex.org/W2160923685","https://openalex.org/W2165065179","https://openalex.org/W2165366948","https://openalex.org/W2166802510","https://openalex.org/W2167754184","https://openalex.org/W2265699209","https://openalex.org/W2418467353","https://openalex.org/W2462467792","https://openalex.org/W2470357604","https://openalex.org/W2577903052","https://openalex.org/W2626938836","https://openalex.org/W2754456924","https://openalex.org/W6718700107","https://openalex.org/W6732537500","https://openalex.org/W6739672105","https://openalex.org/W6744191731"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Small":[0],"interfering":[1],"RNA":[2,93],"(siRNA)":[3],"is":[4],"widely":[5],"used":[6],"to":[7,38,66,193],"specifically":[8],"silence":[9],"target":[10,90],"gene":[11],"expression,":[12],"but":[13],"its":[14,58,71],"microRNA":[15],"(miRNA)-like":[16],"function":[17],"inevitably":[18],"suppresses":[19],"hundreds":[20],"of":[21,26,44,60,75,84,92,98,114,124,140,168,174,186,196],"off-targets.":[22],"Recently,":[23],"complete":[24],"elimination":[25],"the":[27,39,68,82,89,111,122,166],"off-target":[28,201],"repression":[29],"has":[30],"been":[31],"achieved":[32],"by":[33],"introducing":[34],"an":[35],"abasic":[36],"nucleotide":[37,150,153],"pivot":[40],"(position":[41],"6;":[42],"siRNA-6\u00d8),":[43],"which":[45],"impaired":[46],"base":[47],"pairing":[48],"destabilizes":[49],"transitional":[50,85,115],"nucleation":[51,86,116],"(positions":[52,117],"2-6).":[53],"However,":[54],"siRNA-6\u00d8":[55,120,170,197],"varied":[56],"in":[57,119],"conservation":[59],"on-target":[61,72,128],"activity":[62,129],"(\u223c80-100%),":[63],"demanding":[64],"bioinformatics":[65],"discover":[67],"principles":[69],"underlying":[70],"efficiency.":[73],"Analyses":[74],"miRNA-target":[76],"interactions":[77],"(Ago":[78],"HITS-CLIP)":[79],"showed":[80,109],"that":[81,110,164],"stability":[83,125],"correlated":[87],"with":[88,144],"affinity":[91],"interference.":[94],"Furthermore,":[95],"interrogated":[96],"analyses":[97],"siRNA":[99],"screening":[100],"efficiency,":[101],"experimental":[102,204],"data":[103],"and":[104,155,176,205],"broadly":[105],"conserved":[106],"miRNA":[107],"sequences":[108,171,198],"free":[112],"energy":[113],"2-5)":[118],"required":[121],"range":[123],"for":[126,172,203],"effective":[127],"(-6":[130],"\u2264":[131,133],"\u0394G[2:5]":[132],"-3.5":[134],"kcal":[135],"mol-1).":[136],"Taking":[137],"into":[138],"consideration":[139],"these":[141],"features":[142],"together":[143],"locations,":[145],"guanine-cytosine":[146],"content":[147],"(GC":[148],"content),":[149],"stretches,":[151],"single":[152],"polymorphisms":[154],"repetitive":[156],"elements,":[157],"we":[158,182],"implemented":[159],"a":[160],"database":[161],"named":[162],"'siAbasic'":[163],"provided":[165],"list":[167],"potent":[169],"most":[173],"human":[175],"mouse":[177],"genes":[178],"(\u2265":[179],"\u223c95%),":[180],"wherein":[181],"experimentally":[183],"validated":[184],"some":[185],"their":[187],"therapeutic":[188],"potency.":[189],"siAbasic":[190],"will":[191],"aid":[192],"ensure":[194],"potency":[195],"without":[199],"concerning":[200],"effects":[202],"clinical":[206],"purposes.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
