Translation efficiency is maintained at elevated temperature inEscherichia coli

Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences

(2017) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

(2017) David H Burkhardt et al.   eLife

Ribosome Profiling Reveals Genome-wide Cellular Translational Regulation upon Heat Stress in Escherichia coli

(2017) Yanqing Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Global profiling of SRP interaction with nascent polypeptides

(2016) Daniela Schibich et al.   NATURE

Discharging tRNAs: a tug of war between translation and detoxification inEscherichia coli

(2016) Irem Avcilar-Kucukgoze et al.   NUCLEIC ACIDS RESEARCH

Bacteria differently regulate mRNA abundance to specifically respond to various stresses

(2016) Alexander Bartholomäus et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

How do bacteria tune translation efficiency?

(2015) Gene-Wei Li   CURRENT OPINION IN MICROBIOLOGY

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

(2015) Thomas E. Gorochowski et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Cristian Del Campo et al.   PLoS Genetics

Heat-Shock Response Transcriptional Program Enables High-Yield and High-Quality Recombinant Protein Production in Escherichia coli

(2014) Xin Zhang et al.   ACS Chemical Biology

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

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

(2014) Joao C. Guimaraes 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 Coding and Noncoding Architecture of the Caulobacter crescentus Genome

(2014) Jared M. Schrader et al.   PLoS Genetics

Signal Recognition Particle: An Essential Protein-Targeting Machine

(2013) David Akopian et al.   Annual Review of Biochemistry

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

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

(2013) Silvi Rouskin et al.   NATURE

Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes

(2013) Annemarie H Becker et al.   Nature Protocols

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

Differential Translation Tunes Uneven Production of Operon-Encoded Proteins

(2013) Tessa E.F. Quax et al.   Cell Reports

Heat Shock Transcription Factor σ32 Co-opts the Signal Recognition Particle to Regulate Protein Homeostasis in E. coli

(2013) Bentley Lim et al.   PLOS BIOLOGY

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li et al.   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

FoldEco: A Model for Proteostasis in E. coli

(2012) Evan T. Powers et al.   Cell Reports

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

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

(2011) Eugene Oh et al.   CELL

Translation-Independent Localization of mRNA in E. coli

(2011) K. Nevo-Dinur et al.   SCIENCE

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA

(2010) Anna Maria Giuliodori et al.   MOLECULAR CELL

Identification of differential translation in genome wide studies

(2010) O. Larsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Native 3D Organization of Bacterial Polysomes

(2009) Florian Brandt et al.   CELL

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

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Protein abundance profiling of the Escherichia coli cytosol

(2008) Yasushi Ishihama et al.   BMC GENOMICS

Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the Escherichia coli Heat Shock Response

(2008) E. Guisbert et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS