Entrainment to periodic initiation and transition rates in a computational model for gene translation

M Margaliot, ED Sontag, T Tuller - PloS one, 2014 - journals.plos.org
Periodic oscillations play an important role in many biomedical systems. Proper functioning
of biological systems that respond to periodic signals requires the ability to synchronize with …

An algorithmic framework for genome-wide modeling and analysis of translation networks

A Mehra, V Hatzimanikatis - Biophysical Journal, 2006 - cell.com
The sequencing of genomes of several organisms and advances in high throughput
technologies for transcriptome and proteome analysis has allowed detailed mechanistic …

Analysis of translation elongation dynamics in the context of an Escherichia coli cell

JP Vieira, J Racle, V Hatzimanikatis - Biophysical journal, 2016 - cell.com
Understanding the mechanisms behind translation and its rate-limiting steps is crucial for
both the development of drug targets and improvement of heterologous protein production …

Stability analysis of the ribosome flow model

M Margaliot, T Tuller - IEEE/ACM Transactions on …, 2012 - ieeexplore.ieee.org
Gene translation is a central process in all living organisms. Developing a better
understanding of this complex process may have ramifications to almost every biomedical …

The key parameters that govern translation efficiency

DD Erdmann-Pham, KD Duc, YS Song - Cell systems, 2020 - cell.com
Translation of mRNA into protein is a fundamental yet complex biological process with
multiple factors that can potentially affect its efficiency. Here, we study a stochastic model …

On the steady-state distribution in the homogeneous ribosome flow model

M Margaliot, T Tuller - IEEE/ACM Transactions on …, 2012 - ieeexplore.ieee.org
A central biological process in all living organisms is gene translation. Developing a deeper
understanding of this complex process may have ramifications to almost every biomedical …

Stochastic sequence-level model of coupled transcription and translation in prokaryotes

J Mäkelä, J Lloyd-Price, O Yli-Harja, AS Ribeiro - BMC bioinformatics, 2011 - Springer
Background In prokaryotes, transcription and translation are dynamically coupled, as the
latter starts before the former is complete. Also, from one transcript, several translation …

A stochastic model for simulating ribosome kinetics in vivo

EC Dykeman - PLoS computational biology, 2020 - journals.plos.org
Computational modelling of in vivo protein synthesis is highly complicated, as it requires the
simulation of ribosomal movement over the entire transcriptome, as well as consideration of …

Explicit expression for the steady-state translation rate in the infinite-dimensional homogeneous ribosome flow model

Y Zarai, M Margaliot, T Tuller - IEEE/ACM Transactions on …, 2013 - ieeexplore.ieee.org
Gene translation is a central stage in the intracellular process of protein synthesis. Gene
translation proceeds in three major stages: initiation, elongation, and termination. During the …

The RNA polymerase flow model of gene transcription

S Edri, E Gazit, E Cohen, T Tuller - IEEE Transactions on …, 2014 - ieeexplore.ieee.org
Gene expression is a fundamental cellular process by which proteins are synthesized based
on the information coded in the genes. The two major steps of this process are the …