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A Deterministic Mathematical Model for Bidirectional Excluded Flow with Langmuir Kinetics (preprint) <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/arxiv.org\/pdf\/1609.05676.pdf\" xlink:type=\"simple\">https:\/\/arxiv.org\/pdf\/1609.05676.pdf<\/ext-link>"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1042\/BC20070037","article-title":"Halting a cellular production line: responses to ribosomal pausing during translation","volume":"99","author":"JR Buchan","year":"2007","journal-title":"Biol. 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