A Ribosome Flow Model for Analyzing Translation Elongation: (Extended Abstract)

Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We describe the first genome wide analysis of translation based on a model aimed at capturing the physical and dynamical aspects of this process. The Ribosomal Flow Model (RFM) is a computationally efficient approximation of the Totally Asymmetric Exclusion Process (TASEP) model (e.g. see [1]). The RFM is sensitive to the order of codons in the coding sequence, the tRNA pool of the organism, interactions between ribosomes and their size (see Figure [1]). The RFM predicts fundamental outcomes of the translation process, including translation rates, protein abundance and ribosomal densities [2] and the relation between all these variables, better than alternative (’non-physical’) approaches (e.g. see [3,4]). In addition, we show that the RFM model can be used for accurate inference of initiation rates, the effect of codon order on protein abundance and the cost of translation. All these variables could not be inferred by previous predictors.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings
EditorsVineet Bafna, S. Cenk Sahinalp
Pages358-360
Number of pages3
DOIs
StatePublished - 2011
Event15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011 - Vancouver, BC, Canada
Duration: 28 Mar 201131 Mar 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6577 LNBI

Conference

Conference15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011
Country/TerritoryCanada
CityVancouver, BC
Period28/03/1131/03/11

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • General Computer Science

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