{"id":"https://openalex.org/W2149920627","doi":"https://doi.org/10.1371/journal.pcbi.0010021","title":"The RNA Silencing Pathway: The Bits and Pieces That Matter","display_name":"The RNA Silencing Pathway: The Bits and Pieces That Matter","publication_year":2005,"publication_date":"2005-07-28","ids":{"openalex":"https://openalex.org/W2149920627","doi":"https://doi.org/10.1371/journal.pcbi.0010021","mag":"2149920627","pmid":"https://pubmed.ncbi.nlm.nih.gov/16110335"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0010021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010021&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010021&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031808836","display_name":"Marian Groenenboom","orcid":null},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Marian A. C Groenenboom","raw_affiliation_strings":["Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands. m.a.c.groenenboom@bio.uu.nl","Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands. m.a.c.groenenboom@bio.uu.nl","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048414290","display_name":"Athanasius F. M. Mar\u00e9e","orcid":"https://orcid.org/0000-0003-2689-2484"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Athanasius F. M Mar\u00e9e","raw_affiliation_strings":["Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060013591","display_name":"Paulien Hogeweg","orcid":"https://orcid.org/0000-0003-3392-9839"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Paulien Hogeweg","raw_affiliation_strings":["Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5031808836"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6428,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.82805474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"1","issue":"2","first_page":"e21","last_page":"e21"},"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":0.9976999759674072,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9973999857902527,"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/rna-silencing","display_name":"RNA silencing","score":0.8028243780136108},{"id":"https://openalex.org/keywords/gene-silencing","display_name":"Gene silencing","score":0.7814174890518188},{"id":"https://openalex.org/keywords/rna-induced-silencing-complex","display_name":"RNA-induced silencing complex","score":0.7658573389053345},{"id":"https://openalex.org/keywords/trans-acting-sirna","display_name":"Trans-acting siRNA","score":0.7523032426834106},{"id":"https://openalex.org/keywords/rna-induced-transcriptional-silencing","display_name":"RNA-induced transcriptional silencing","score":0.6706525087356567},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.6621661186218262},{"id":"https://openalex.org/keywords/argonaute","display_name":"Argonaute","score":0.6423336267471313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5507753491401672},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5463736653327942},{"id":"https://openalex.org/keywords/rnase-p","display_name":"RNase P","score":0.5340057611465454},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.487148255109787},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4866805672645569},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4459435045719147},{"id":"https://openalex.org/keywords/piwi-interacting-rna","display_name":"Piwi-interacting RNA","score":0.4145326614379883},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3714483380317688},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14362561702728271}],"concepts":[{"id":"https://openalex.org/C2191507","wikidata":"https://www.wikidata.org/wiki/Q7277185","display_name":"RNA silencing","level":5,"score":0.8028243780136108},{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.7814174890518188},{"id":"https://openalex.org/C155330019","wikidata":"https://www.wikidata.org/wiki/Q21106117","display_name":"RNA-induced silencing complex","level":5,"score":0.7658573389053345},{"id":"https://openalex.org/C60723119","wikidata":"https://www.wikidata.org/wiki/Q7833577","display_name":"Trans-acting siRNA","level":5,"score":0.7523032426834106},{"id":"https://openalex.org/C172827444","wikidata":"https://www.wikidata.org/wiki/Q7277128","display_name":"RNA-induced transcriptional silencing","level":5,"score":0.6706525087356567},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.6621661186218262},{"id":"https://openalex.org/C201853390","wikidata":"https://www.wikidata.org/wiki/Q413236","display_name":"Argonaute","level":5,"score":0.6423336267471313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5507753491401672},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5463736653327942},{"id":"https://openalex.org/C10879258","wikidata":"https://www.wikidata.org/wiki/Q76826611","display_name":"RNase P","level":4,"score":0.5340057611465454},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.487148255109787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4866805672645569},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4459435045719147},{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.4145326614379883},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3714483380317688},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14362561702728271}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.0010021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010021&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:16110335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16110335","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.281.7643","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.281.7643","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/0a/c7/PLoS_Comput_Biol_2005_Jul_29_1(2)_e21.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.566.3055","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.566.3055","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www-binf.bio.uu.nl/stan/Pdf/Groenenboom_pcb05.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:12580b8c43584fa5b5981cd5ba50faad","is_oa":true,"landing_page_url":"https://doaj.org/article/12580b8c43584fa5b5981cd5ba50faad","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 1, Iss 2, Pp 155-165 (2005)","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:3008c56ef22b43cc98b26820f0175976","is_oa":true,"landing_page_url":"https://doaj.org/article/3008c56ef22b43cc98b26820f0175976","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 1, Iss 2, p e21 (2005)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:78001","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1185647","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"},{"id":"pmh:oai:https://orca.cardiff.ac.uk:119494","is_oa":false,"landing_page_url":"https://orca.cardiff.ac.uk/id/eprint/119494/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401195","display_name":"ORCA Online Research @Cardiff (Cardiff University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79510175","host_organization_name":"Cardiff University","host_organization_lineage":["https://openalex.org/I79510175"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0010021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010021&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149920627.pdf","grobid_xml":"https://content.openalex.org/works/W2149920627.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W341255601","https://openalex.org/W1567381189","https://openalex.org/W1589945560","https://openalex.org/W1602141296","https://openalex.org/W1647075334","https://openalex.org/W1729061915","https://openalex.org/W1963933516","https://openalex.org/W1967916752","https://openalex.org/W1972937465","https://openalex.org/W1988467918","https://openalex.org/W1991334252","https://openalex.org/W1992170226","https://openalex.org/W1992501118","https://openalex.org/W1997614771","https://openalex.org/W2004879680","https://openalex.org/W2009207290","https://openalex.org/W2010596106","https://openalex.org/W2011480379","https://openalex.org/W2016589137","https://openalex.org/W2018442829","https://openalex.org/W2022900230","https://openalex.org/W2026139002","https://openalex.org/W2034831897","https://openalex.org/W2036155471","https://openalex.org/W2050347642","https://openalex.org/W2070016382","https://openalex.org/W2077601414","https://openalex.org/W2077808289","https://openalex.org/W2095509700","https://openalex.org/W2107330252","https://openalex.org/W2108407529","https://openalex.org/W2109458502","https://openalex.org/W2114582526","https://openalex.org/W2120778382","https://openalex.org/W2121133384","https://openalex.org/W2127497651","https://openalex.org/W2127843746","https://openalex.org/W2135165188","https://openalex.org/W2136447541","https://openalex.org/W2137483650","https://openalex.org/W2138835651","https://openalex.org/W2139956963","https://openalex.org/W2141845832","https://openalex.org/W2154166273","https://openalex.org/W2158627784","https://openalex.org/W2161074631","https://openalex.org/W2166777442","https://openalex.org/W2166866388","https://openalex.org/W2166903671","https://openalex.org/W2167018286","https://openalex.org/W2171445973","https://openalex.org/W2400987909","https://openalex.org/W4229984123","https://openalex.org/W4251060592"],"related_works":["https://openalex.org/W2613401058","https://openalex.org/W1970681892","https://openalex.org/W1982264400","https://openalex.org/W2151284271","https://openalex.org/W2188681444","https://openalex.org/W1985027300","https://openalex.org/W1983871012","https://openalex.org/W2012211631","https://openalex.org/W2080767008","https://openalex.org/W2111139432"],"abstract_inverted_index":{"Cellular":[0],"pathways":[1],"are":[2,24,37],"generally":[3],"proposed":[4,13],"on":[5],"the":[6,21,43,47,68,71,83],"basis":[7],"of":[8,32,46,49,70,91,113,128],"available":[9],"experimental":[10],"knowledge.":[11],"The":[12,52],"pathways,":[14],"however,":[15],"may":[16],"be":[17],"inadequate":[18],"to":[19,26,39,67,82,100],"describe":[20],"phenomena":[22],"they":[23],"supposed":[25],"explain.":[27],"For":[28],"instance,":[29],"by":[30,56],"means":[31],"concise":[33],"mathematical":[34],"models":[35],"we":[36],"able":[38],"reveal":[40],"shortcomings":[41],"in":[42],"current":[44],"description":[45],"pathway":[48,54],"RNA":[50,93,99],"silencing.":[51],"silencing":[53,114],"operates":[55],"cleaving":[57],"siRNAs":[58,61],"from":[59],"dsRNA.":[60],"can":[62],"associate":[63],"with":[64],"RISC,":[65],"leading":[66],"degradation":[69],"target":[72],"mRNA.":[73],"We":[74],"propose":[75],"and":[76,95,122,126],"analyze":[77],"a":[78,85,107],"few":[79],"small":[80],"extensions":[81,104],"pathway:":[84],"siRNA":[86],"degrading":[87],"RNase,":[88],"primed":[89],"amplification":[90],"aberrant":[92,98],"pieces,":[94],"cooperation":[96],"between":[97,136],"trigger":[101],"amplification.":[102],"These":[103],"allow":[105],"for":[106,110,133],"consistent":[108],"explanation":[109],"various":[111],"types":[112],"phenomena,":[115],"such":[116],"as":[117,130,132],"virus":[118],"induced":[119,124],"silencing,":[120,125],"transgene":[121],"transposon":[123],"avoidance":[127],"self-reactivity,":[129],"well":[131],"differences":[134],"found":[135],"species":[137],"groups.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}