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Trends Plant Sci 8, 42\u201349 (2003).","journal-title":"Trends Plant Sci"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1104\/pp.105.062943","article-title":"Expression of Arabidopsis MIRNA genes","volume":"138","author":"Xie Z","year":"2005","unstructured":"Z Xie, et al., Expression of Arabidopsis MIRNA genes. Plant Physiol 138, 2145\u20132154 (2005).","journal-title":"Plant Physiol"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nchembio.1120","article-title":"Peptidomic discovery of short open reading frame-encoded peptides in human cells","volume":"9","author":"Slavoff SA","year":"2013","unstructured":"SA Slavoff, et al., Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9, 59\u201364 (2013).","journal-title":"Nat Chem Biol"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.tplants.2009.05.004","article-title":"Getting the message across: Cytoplasmic ribonucleoprotein complexes","volume":"14","author":"Bailey-Serres J","year":"2009","unstructured":"J Bailey-Serres, R Sorenson, P Juntawong, Getting the message across: Cytoplasmic ribonucleoprotein complexes. Trends Plant Sci 14, 443\u2013453 (2009).","journal-title":"Trends Plant Sci"},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature10534","article-title":"Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants","volume":"479","author":"Gibbs DJ","year":"2011","unstructured":"DJ Gibbs, et al., Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature 479, 415\u2013418 (2011).","journal-title":"Nature"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1016\/j.cell.2013.04.005","article-title":"MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis","volume":"153","author":"Li S","year":"2013","unstructured":"S Li, et al., MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153, 562\u2013574 (2013).","journal-title":"Cell"},{"key":"e_1_3_4_57_2","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1126\/science.1215704","article-title":"Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish","volume":"336","author":"Bazzini AA","year":"2012","unstructured":"AA Bazzini, MT Lee, AJ Giraldez, Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233\u2013237 (2012).","journal-title":"Science"},{"key":"e_1_3_4_58_2","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/978-1-60327-563-7_6","article-title":"Isolation of plant polysomal mRNA by differential centrifugation and ribosome immunopurification methods","volume":"553","author":"Mustroph A","year":"2009","unstructured":"A Mustroph, P Juntawong, J Bailey-Serres, Isolation of plant polysomal mRNA by differential centrifugation and ribosome immunopurification methods. Methods Mol Biol 553, 109\u2013126 (2009).","journal-title":"Methods Mol Biol"},{"key":"e_1_3_4_59_2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/S0076-6879(10)70006-9","article-title":"Genome-wide translational profiling by ribosome footprinting","volume":"470","author":"Ingolia NT","year":"2010","unstructured":"NT Ingolia, Genome-wide translational profiling by ribosome footprinting. 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