Ribosome flow model with positive feedback

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

(2013) Luca Ciandrini 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

Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles

(2012) Philip Greulich et al.   PHYSICAL REVIEW E

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

(2012) Alexandra Dana et al.   PLoS Computational Biology

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov et al.   CELL

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

Finite Time Corrections in KPZ Growth Models

(2011) Patrik L. Ferrari et al.   JOURNAL OF STATISTICAL PHYSICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

A Role for Codon Order in Translation Dynamics

(2010) Gina Cannarozzi et al.   CELL

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Real-time tRNA transit on single translating ribosomes at codon resolution

(2010) Sotaro Uemura et al.   NATURE

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

Conditions for global stability of monotone tridiagonal systems with negative feedback

(2010) Liming Wang et al.   SYSTEMS & CONTROL LETTERS

Global Entrainment of Transcriptional Systems to Periodic Inputs

(2010) Giovanni Russo et al.   PLoS Computational Biology

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

(2010) Wanjun Gu et al.   PLoS Computational Biology

Traffic by multiple species of molecular motors

(2009) Yan Chai et al.   PHYSICAL REVIEW E

Trafficlike Collective Movement of Ants on Trails: Absence of a Jammed Phase

(2009) Alexander John et al.   PHYSICAL REVIEW LETTERS

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

Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

(2008) Arthur G Hunt et al.   BMC GENOMICS

Oscillations in I/O Monotone Systems Under Negative Feedback

(2008) David Angeli et al.   IEEE TRANSACTIONS ON AUTOMATIC CONTROL

Far-from-equilibrium transport with constrained resources

(2008) D A Adams et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology