On the Ribosomal Density that Maximizes Protein Translation Rate

The complexity of the translation ability of circRNAs

(2016) Javier T. Granados-Riveron et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

A model for competition for ribosomes in the cell

(2016) Alon Raveh et al.   Journal of the Royal Society Interface

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Ribosome Flow Model on a Ring

(2015) Alon Raveh et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Greedy scheduling of cellular self-replication leads to optimal doubling times with a log-Frechet distribution

(2015) Rami Pugatch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

(2015) Zohar Zafrir et al.   RNA

Sensitivity of mRNA Translation

(2015) Gilad Poker et al.   Scientific Reports

Rolling Circle Translation of Circular RNA in Living Human Cells

(2015) Naoko Abe et al.   Scientific Reports

An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation

(2014) Arvind R. Subramaniam et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

The RNA Polymerase Flow Model of Gene Transcription

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

Ribosome recycling induces optimal translation rate at low ribosomal availability

(2014) E. Marshall et al.   Journal of the Royal Society Interface

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

(2014) G. Poker et al.   Journal of the Royal Society Interface

Multiple roles of the coding sequence 5′ end in gene expression regulation

(2014) Tamir Tuller 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

Quantifying the Effect of Ribosomal Density on mRNA Stability

(2014) Shlomit Edri et al.   PLoS One

Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt

(2014) Mounir Georges AbouHaidar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The significance of translation regulation in the stress response

(2013) Flora Picard et al.   BMC GENOMICS

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

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Building better drugs: developing and regulating engineered therapeutic proteins

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

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

(2013) Julien Racle et al.   PLoS Computational Biology

A computational framework for the design of optimal protein synthesis

(2012) Julien Racle et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A novel and versatile computational tool to model translation

(2011) D. Chu et al.   BIOINFORMATICS

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

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

Transcriptome-wide discovery of circular RNAs in Archaea

(2011) Miri Danan et al.   NUCLEIC ACIDS RESEARCH

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

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk

(2010) Christin E. Burd et al.   PLoS Genetics

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

(2009) Maria Piques et al.   Molecular Systems Biology

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

(2009) Gong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL