Author: Kenneth Lyon; Luis U. Aguilera; Tatsuya Morisaki; Brian Munsky; Timothy J. Stasevich
Title: Live-cell single RNA imaging reveals bursts of translational frameshifting Document date: 2018_11_24
ID: 4fm1skgh_147
Snippet: Simulations were started at t = -10,000 seconds to approximate steady state at t = 0 using the Gillespie algorithm (Gillespie, 1976) . Ribosome densities were found by collecting position statistics for multiple simulations. Simulated ribosome numbers and positions and multi-frame tag probe locations were combined to estimate translation site intensities. Harringtonine assays were simulated by preventing the initiation reaction at the time of tre.....
Document: Simulations were started at t = -10,000 seconds to approximate steady state at t = 0 using the Gillespie algorithm (Gillespie, 1976) . Ribosome densities were found by collecting position statistics for multiple simulations. Simulated ribosome numbers and positions and multi-frame tag probe locations were combined to estimate translation site intensities. Harringtonine assays were simulated by preventing the initiation reaction at the time of treatment. Parameter estimation was performed using genetic algorithms and a multiple-objective cost function that considers the frameshifting efficiency, the number of ribosomes per RNA and the Harringtonine assays. A detailed description of the computational methods and codes is given in the 'Computational Details' section below.
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