Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach

The RNA Polymerase Flow Model of Gene Transcription

(2014) Shlomit Edri et al.   IEEE Transactions on Biomedical Circuits and Systems

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

Entrainment to Periodic Initiation and Transition Rates in a Computational Model for Gene Translation

(2014) Michael Margaliot et al.   PLoS One

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

(2014) Shelly Mahlab et al.   PLoS Computational Biology

A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

(2014) Zohar Bloom-Ackermann et al.   PLoS Genetics

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model

(2013) Yoram Zarai et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Ribosome flow model with positive feedback

(2013) M. Margaliot et al.   Journal of the Royal Society Interface

Effect of ribosome shielding on mRNA stability

(2013) Carlus Deneke et al.   PHYSICAL BIOLOGY

Building better drugs: developing and regulating engineered therapeutic proteins

(2013) Chava Kimchi-Sarfaty et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

(2013) Julien Racle et al.   PLoS Computational Biology

New Universal Rules of Eukaryotic Translation Initiation Fidelity

(2013) Hadas Zur et al.   PLoS Computational Biology

On the Steady-State Distribution in the Homogeneous Ribosome Flow Model

(2012) Michael Margaliot et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Stability Analysis of the Ribosome Flow Model

(2012) Michael Margaliot et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach

(2012) Alexandra Dana et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Effects of codon sequence on the dynamics of genetic networks

(2012) Ilya Potapov et al.   JOURNAL OF THEORETICAL BIOLOGY

Tying up loose ends: ribosome recycling in eukaryotes and archaea

(2012) Elina Nürenberg et al.   TRENDS IN BIOCHEMICAL SCIENCES

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

(2012) Alexandra Dana et al.   PLoS Computational Biology

A novel and versatile computational tool to model translation

(2011) D. Chu et al.   BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

(2011) R. K. P. Zia et al.   JOURNAL OF STATISTICAL PHYSICS

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

(2011) Shlomi Reuveni et al.   PLoS Computational Biology

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

Genetic Engineering for Modern Agriculture: Challenges and Perspectives

(2010) Ron Mittler et al.   Annual Review of Plant Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

(2010) Wanjun Gu et al.   PLoS Computational Biology

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

(2009) Mark Welch et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Solubility enhancement of aggregation-prone heterologous proteins by fusion expression using stress-responsive Escherichia coli protein, RpoS

(2008) Jin-Seung Park et al.   BMC BIOTECHNOLOGY

Estimating Translational Selection in Eukaryotic Genomes

(2008) M. dos Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION