{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T18:57:21Z","timestamp":1762541841210},"reference-count":56,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2009,9,25]],"date-time":"2009-09-25T00:00:00Z","timestamp":1253836800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000516","type":"journal-article","created":{"date-parts":[[2009,9,25]],"date-time":"2009-09-25T08:12:27Z","timestamp":1253866347000},"page":"e1000516","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification"],"prefix":"10.1371","volume":"5","author":[{"given":"Stephen A.","family":"Stanhope","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Srikumar","family":"Sengupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johan","family":"den Boon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Ahlquist","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael A.","family":"Newton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2009,9,25]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"S25","DOI":"10.1038\/ng1793","article-title":"Viruses and microRNAs.","volume":"38","author":"B Cullen","year":"2006","journal-title":"Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.pbi.2004.11.008","article-title":"The developmental role of microRNA in plants.","volume":"8","author":"C Kidner","year":"2005","journal-title":"Curr Opin Plant Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"S31","DOI":"10.1038\/ng1791","article-title":"Functions of microRNAs and related small RNAs in plants.","volume":"38","author":"A Mallory","year":"2006","journal-title":"Nat Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/nrg1379","article-title":"MicroRNAs: Small RNAs with a Big Role in Gene Regulation.","volume":"5","author":"L He","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"4653","DOI":"10.1242\/dev.02073","article-title":"MicroRNA functions in animal development and human disease.","volume":"132","author":"I Alvarez-Garcia","year":"2005","journal-title":"Development"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"5911","DOI":"10.1016\/j.febslet.2005.07.070","article-title":"MicroRNA function in animal development.","volume":"579(26)","author":"E Wienholds","year":"2005","journal-title":"FEBS Lett"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/S1044-579X(03)00038-5","article-title":"MicroRNAs and cancer.","volume":"13","author":"M McManus","year":"2003","journal-title":"Semin Cancer Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"19075","DOI":"10.1073\/pnas.0509603102","article-title":"The role of microRNA genes in papillary thyroid carcinoma.","volume":"102(52)","author":"H He","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nature03552","article-title":"A microRNA polycistron as a potential human oncogene.","volume":"435(9)","author":"L He","year":"2005","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"5874","DOI":"10.1073\/pnas.0801130105","article-title":"MicroRNA 29c is Downregulated in Nasopharyngeal Carcinomas, Upregulating mRNAs Encoding Extracellular Matrix Proteins.","volume":"105(15)","author":"S Sengupta","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1016\/j.tibs.2003.08.005","article-title":"The microRNA world: small is mighty.","volume":"28(10)","author":"P Nelson","year":"2003","journal-title":"Trends Biochem Sci"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: Genomics, Biogenesis, Mechanism, and Function.","volume":"116","author":"D Bartel","year":"2004","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"3509","DOI":"10.1158\/0008-5472.CAN-05-0298","article-title":"MicroRNA Biogenesis and Cancer.","volume":"65(9)","author":"R Gregory","year":"2005","journal-title":"Cancer Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nrm1644","article-title":"MicroRNA Biogenesis: Coordinated Cropping and Dicing.","volume":"6","author":"V Kim","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.cell.2005.10.022","article-title":"Human RISC Couples MicroRNA Biogenesis and Posttranscriptional Gene Silencing.","volume":"123","author":"R Gregory","year":"2005","journal-title":"Cell"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/j.sbi.2005.05.006","article-title":"Post-transcriptional gene silencing by siRNAs and miRNAs.","volume":"15","author":"W Filipowicz","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1101\/gad.1284105","article-title":"Perspective: machines for RNAi.","volume":"19","author":"Y Tomari","year":"2005","journal-title":"Genes Dev"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nsmb918","article-title":"Purified Argonaute2 and an siRNA form recombinant human RISC.","volume":"12","author":"F Rivas","year":"2005","journal-title":"Nat Struct Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1126\/science.1102513","article-title":"Argonaute2 Is the Catalytic Engine of Mammalian RNAi.","volume":"305","author":"J Liu","year":"2004","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.cell.2008.03.015","article-title":"Sorting Out Small RNAs.","volume":"133(1)","author":"V Kim","year":"2008","journal-title":"Cell"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"11928","DOI":"10.1073\/pnas.0505461102","article-title":"Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs.","volume":"102(33)","author":"N Baumberger","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.molcel.2004.07.007","article-title":"Human Argonaute 2 Mediates RNA Cleavage Targeted by miRNAs and siRNAs.","volume":"15","author":"G Meister","year":"2004","journal-title":"Mol Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"4801","DOI":"10.1093\/nar\/gkl646","article-title":"Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells.","volume":"34(17)","author":"D Schmitter","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"14385","DOI":"10.1073\/pnas.0405913101","article-title":"Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity.","volume":"101(40)","author":"T Rand","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3813","DOI":"10.1093\/hmg\/ddi397","article-title":"Physiological identification of human transcripts translationally regulated by a specific microRNA.","volume":"14(24)","author":"M Nakamoto","year":"2005","journal-title":"Hum Mol Genet"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/ncb0608-630","article-title":"Small RNAs tell big stories in Whistler.","volume":"10(6)","author":"A Seila","year":"2008","journal-title":"Nat Cell Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S1359-6446(05)03399-4","article-title":"A computational view of microRNAs and their targets.","volume":"10(8)","author":"J Brown","year":"2005","journal-title":"Drug Discov Today"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1038\/ng1799","article-title":"Strategies to determine the biological function of microRNAs.","volume":"38","author":"J Krutzfeldt","year":"2006","journal-title":"Nat Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1038\/ng1798","article-title":"microRNA target predictions in animals.","volume":"38","author":"N Rajewsky","year":"2006","journal-title":"Nat Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/nmeth954","article-title":"A guide through present computational approaches for the identification of mammalian microRNA targets.","volume":"3(11)","author":"P Sethupathy","year":"2006","journal-title":"Nat Methods"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1089\/dna.2006.0549","article-title":"MicroRNA Detection and Target Prediction: Integration of Computational and Experimental Approaches.","volume":"26(5)","author":"K Chaudhuri","year":"2007","journal-title":"DNA Cell Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1089\/dna.2006.0566","article-title":"Algorithms for Mapping of mRNA Targets for MicroRNA.","volume":"26(4)","author":"I Ioshikhes","year":"2007","journal-title":"DNA Cell Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1089\/dna.2006.0551","article-title":"Principles and Limitations of Computational MicroRNA Gene and Target Finding.","volume":"26(5)","author":"M Lindow","year":"2007","journal-title":"DNA Cell Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.bbrc.2007.08.030","article-title":"MiRnomics \u2013 The bioinformatics of microRNA genes.","volume":"363","author":"Z Ghosh","year":"2007","journal-title":"Biochem Biophys Res Commun"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA Targets in Drosophila.","volume":"5(1)","author":"A Enright","year":"2003","journal-title":"Genome Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/ng1536","article-title":"Combinatorial microRNA target predictions.","volume":"37(5)","author":"A Krek","year":"2005","journal-title":"Nat Genet"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.molcel.2007.06.017","article-title":"MicroRNA Target Specificity in Mammals: Determinants beyond Seed Pairing.","volume":"27(1)","author":"A Grimson","year":"2007","journal-title":"Mol Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","article-title":"Prediction of Mammalian MicroRNA Targets.","volume":"115","author":"B Lewis","year":"2003","journal-title":"Cell"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","article-title":"Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets.","volume":"120","author":"B Lewis","year":"2005","journal-title":"Cell"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/ng2135","article-title":"The role of site accessibility in microRNA target recognition.","volume":"39","author":"M Kertesz","year":"2007","journal-title":"Nat Genet"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1093\/nar\/gkl068","article-title":"Systematic identification of microRNA functions by combining target prediction and expression profiling.","volume":"34(5)","author":"X Wang","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"7999","DOI":"10.1158\/0008-5472.CAN-05-4399","article-title":"Genome-Wide Expression Profiling Reveals EBV-Associated Inhibition of MHC Class I Expression in Nasopharyngeal Carcinoma.","volume":"66(16)","author":"S Sengupta","year":"2006","journal-title":"Cancer Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"MicroRNA expression profiles classify human cancers.","volume":"435(9)","author":"J Lu","year":"2005","journal-title":"Nature"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1261\/rna.2239606","article-title":"TarBase: A comprehensive database of experimentally supported animal microRNA targets.","volume":"12","author":"P Seupathy","year":"2006","journal-title":"RNA"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkh023","article-title":"The microRNA Registry.","volume":"32","author":"S Griffiths-Jones","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature.","volume":"34","author":"S Griffiths-Jones","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkm952","article-title":"miRBase: tools for microRNA genomics.","volume":"36","author":"S Griffiths-Jones","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1097\/01.LAB.0000067480.44925.10","article-title":"Alterations of Biologic Properties and Gene Expression in Nasopharyngeal Epithelial Cells by the Epstein-Barr Virus-Encoded Latent Membrane Protein 1.","volume":"83","author":"A Lo","year":"2003","journal-title":"Lab Invest"},{"key":"ref49","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-2917-7","article-title":"Model Selection and Inference: A Practical Information-Theoretic Approach","author":"K Burnham","year":"1998"},{"key":"ref50","first-page":"221","article-title":"An asymptotic theory for linear model selection.","volume":"7","author":"J Shao","year":"1997","journal-title":"Statist Sinica"},{"key":"ref51","article-title":"Linear Models in Statistics","author":"A Rencher","year":"2000"},{"key":"ref52","article-title":"Modern Applied Statistics with S, Fourth Ed","author":"W Venables","year":"2002"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1089\/cmb.2007.R002","article-title":"Bayesian Inference of MicroRNA Targets from Sequence and Expression Data.","volume":"14(5)","author":"J Huang","year":"2007","journal-title":"J Comput Biol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nmeth1130","article-title":"Using expression profiling data to identify human microRNA targets.","volume":"4(12)","author":"J Huang","year":"2007","journal-title":"Nat Methods"},{"key":"ref55","first-page":"52","article-title":"Comparing sequence and expression for predicting microRNA targets using GenMiR3.","author":"J Huang","year":"2008","journal-title":"Pac Symp Biocomput"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"6162","DOI":"10.1158\/0008-5472.CAN-08-0144","article-title":"Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.","volume":"68(15)","author":"S Ambs","year":"2008","journal-title":"Cancer Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000516","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T19:11:09Z","timestamp":1540235469000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000516"}},"subtitle":[],"editor":[{"given":"Weixiong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2009,9,25]]},"references-count":56,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2009,9,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000516","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,9,25]]}}}