Modelling and measuring intracellular competition for finite resources during gene expression

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

(2018) Yoram Zarai et al.   PLoS Computational Biology

Decoupling Resource-Coupled Gene Expression in Living Cells

(2017) Tatenda Shopera et al.   ACS Synthetic Biology

Resource Competition Shapes the Response of Genetic Circuits

(2017) Yili Qian et al.   ACS Synthetic Biology

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

(2017) Lucas D. Fernandes et al.   Scientific Reports

stAI calc : tRNA adaptation index calculator based on species-specific weights

(2016) Renana Sabi et al.   BIOINFORMATICS

Pathways to Specialized Ribosomes: The Brussels Lecture

(2016) Jonathan D. Dinman   JOURNAL OF MOLECULAR BIOLOGY

A model for competition for ribosomes in the cell

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

A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes

(2016) Thomas E. Gorochowski et al.   ACS Synthetic Biology

Structural insights into ribosome translocation

(2016) Clarence Ling et al.   Wiley Interdisciplinary Reviews-RNA

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

How do bacteria tune translation efficiency?

(2015) Gene-Wei Li   CURRENT OPINION IN MICROBIOLOGY

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Quantification of transcription factor-DNA binding affinity in a living cell

(2015) Sergey Belikov et al.   NUCLEIC ACIDS RESEARCH

Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law

(2015) M. Carbonell-Ballestero et al.   NUCLEIC ACIDS RESEARCH

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA–RNA interactions in gene regulation: the coding and noncoding players

(2015) Sonia Guil et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

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

(2014) Gene-Wei Li et al.   CELL

Geometry of the nucleus: a perspective on gene expression regulation

(2014) Maxime Woringer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Competition between target sites of regulators shapes post-transcriptional gene regulation

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

An Integrated Model of Transcription Factor Diffusion Shows the Importance of Intersegmental Transfer and Quaternary Protein Structure for Target Site Finding

(2014) Hugo G. Schmidt et al.   PLoS One

A Model for Sigma Factor Competition in Bacterial Cells

(2014) Marco Mauri et al.   PLoS Computational Biology

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

Translational Cross Talk in Gene Networks

(2013) William H. Mather et al.   BIOPHYSICAL JOURNAL

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy

(2013) Z. W. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells

(2012) Somenath Bakshi et al.   MOLECULAR MICROBIOLOGY

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship

(2012) Amy E. Pasquinelli   NATURE REVIEWS GENETICS

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

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

miRmap: Comprehensive prediction of microRNA target repression strength

(2012) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Philip Greulich et al.   PHYSICAL REVIEW E

Conservation of the relative tRNA composition in healthy and cancerous tissues

(2012) S. Mahlab et al.   RNA

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW

(2012) Tobias von der Haar   Computational and Structural Biotechnology Journal

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules

(2011) Alvaro Sanchez et al.   EMBO JOURNAL

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

The Dynamics of Supply and Demand in mRNA Translation

(2011) Chris A. Brackley 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

tRNA biology charges to the front

(2010) E. M. Phizicky et al.   GENES & DEVELOPMENT

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

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

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Feedback and fluctuations in a totally asymmetric simple exclusion process with finite resources

(2009) L Jonathan Cook et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

(2009) Iris Bahir et al.   Molecular Systems Biology

Absolute quantification of microRNAs by using a universal reference

(2009) U. Bissels et al.   RNA

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs

(2008) Fumihito Miura et al.   BMC GENOMICS

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

(2008) Tobias von der Haar   BMC Systems Biology

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Far-from-equilibrium transport with constrained resources

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

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

EcoCyc: A comprehensive view of Escherichia coli biology

(2008) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH