Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli

Gene Architectures that Minimize Cost of Gene Expression

(2017) Idan Frumkin et al.   MOLECULAR CELL

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

(2016) Melissa K. Takahashi et al.   RNA

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

(2016) Eric D. Kelsic et al.   Cell Systems

Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production

(2015) Congqiang Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

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

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

(2015) Yiliang Ding et al.   Nature Protocols

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

(2015) Cristian Del Campo et al.   PLoS Genetics

Messenger RNA Degradation in Bacterial Cells

(2014) Monica P. Hui et al.   Annual Review of Genetics

D-Tailor: automated analysis and design of DNA sequences

(2014) Joao C. Guimaraes et al.   BIOINFORMATICS

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

(2014) Gene-Wei Li et al.   CELL

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

The Effects of Codon Context on In Vivo Translation Speed

(2014) Fabienne F. V. Chevance et al.   PLoS Genetics

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Positive Charge Loading at Protein Termini Is Due to Membrane Protein Topology, Not a Translational Ramp

(2013) Catherine A. Charneski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Quantitative estimation of activity and quality for collections of functional genetic elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

Measurement and modeling of intrinsic transcription terminators

(2013) Guillaume Cambray et al.   NUCLEIC ACIDS RESEARCH

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

(2013) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation

(2013) Mélodie Duval et al.   PLOS BIOLOGY

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

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

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

CBDB: The codon bias database

(2012) Adam Hilterbrand et al.   BMC BIOINFORMATICS

Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs

(2012) Balint Csorgo et al.   Microbial Cell Factories

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

(2012) Joe C. Liang et al.   NUCLEIC ACIDS RESEARCH

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

(2011) Eugene Oh et al.   CELL

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

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

(2011) Tamir Tuller et al.   GENOME BIOLOGY

BglBrick vectors and datasheets: A synthetic biology platform for gene expression

(2011) Taek Lee et al.   Journal of Biological Engineering

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

(2010) Malin Allert et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

An Enhanced System for Unnatural Amino Acid Mutagenesis in E. coli

(2009) Travis S. Young et al.   JOURNAL OF MOLECULAR BIOLOGY

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization

(2008) Namiko Mitarai et al.   JOURNAL OF MOLECULAR BIOLOGY

Requirements for translation re-initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3

(2008) Jae-Ho Yoo et al.   MOLECULAR MICROBIOLOGY

Practical applications of design of experiments in the field of engineering: a bibliographical review

(2008) Laura Ilzarbe et al.   QUALITY AND RELIABILITY ENGINEERING INTERNATIONAL