Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium

Visualizing translation dynamics at atomic detail inside a bacterial cell

(2022) Liang Xue et al.   NATURE

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

(2021) Ekaterina Samatova et al.   Frontiers in Microbiology

Translational adaptation of human viruses to the tissues they infect

(2021) Xavier Hernandez-Alias et al.   Cell Reports

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae

(2021) Kotchaphorn Mangkalaphiban et al.   PLoS Genetics

Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed

(2021) Xueliang Lyu et al.   NUCLEIC ACIDS RESEARCH

Introduction of an AU-rich Element into the 5’ UTR of mRNAs Enhances Protein Expression in Escherichia coli by S1 Protein and Hfq Protein

(2021) Hyang-Mi Lee et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103

(2021) Xuejing Fan et al.   Frontiers in Microbiology

The impact of leadered and leaderless gene structures on translation efficiency, transcript stability, and predicted transcription rates in Mycobacterium smegmatis

(2020) Tien G. Nguyen et al.   JOURNAL OF BACTERIOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing

(2020) Kazuki Saito et al.   eLife

Impact of C‐terminal amino acid composition on protein expression in bacteria

(2020) Marc Weber et al.   Molecular Systems Biology

Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

(2020) Diego Rivera Gelsinger et al.   NUCLEIC ACIDS RESEARCH

Translational regulation of environmental adaptation in bacteria

(2020) Rodney Tollerson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep-sequencing library preparation

(2020) Ji Wang et al.   RNA Biology

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

Inferring efficiency of translation initiation and elongation from ribosome profiling

(2020) Juraj Szavits-Nossan et al.   NUCLEIC ACIDS RESEARCH

Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor

(2020) Nana Ding et al.   NUCLEIC ACIDS RESEARCH

Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae

(2020) Raul Burgos et al.   Molecular Systems Biology

Unraveling the hidden universe of small proteins in bacterial genomes

(2019) Samuel Miravet‐Verde et al.   Molecular Systems Biology

Absolute quantification of translational regulation and burden using combined sequencing approaches

(2019) Thomas E Gorochowski et al.   Molecular Systems Biology

A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

(2019) Fuad Mohammad et al.   eLife

SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes

(2019) Ariadna Montero-Blay et al.   DNA RESEARCH

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

(2019) Andrea Riba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5′ structure element

(2019) Cédric Romilly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

(2019) Eva Yus et al.   Cell Systems

Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria

(2019) William D Baez et al.   NUCLEIC ACIDS RESEARCH

Translational coupling via termination-reinitiation in archaea and bacteria

(2019) Madeleine Huber et al.   Nature Communications

On the role of mRNA secondary structure in bacterial translation

(2019) Claude Chiaruttini et al.   Wiley Interdisciplinary Reviews-RNA

A short translational ramp determines the efficiency of protein synthesis

(2019) Manasvi Verma et al.   Nature Communications

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translational Control in Virus-Infected Cells

(2018) Noam Stern-Ginossar et al.   Cold Spring Harbor Perspectives in Biology

Translational Control in Cancer

(2018) Nathaniel Robichaud et al.   Cold Spring Harbor Perspectives in Biology

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

(2018) Khanh Dao Duc et al.   PLoS Genetics

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

(2018) Guillaume Cambray et al.   NATURE BIOTECHNOLOGY

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

(2018) Fabio Lauria et al.   PLoS Computational Biology

Comparison of Internal Standard Approaches for SRM Analysis of Alpha-Synuclein in Cerebrospinal Fluid

(2017) Patrick Oeckl et al.   JOURNAL OF PROTEOME RESEARCH

Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands

(2017) Adam J Hockenberry et al.   MOLECULAR BIOLOGY AND EVOLUTION

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Coevolution of the translational machinery optimizes initiation with unusual initiator tRNAs and initiation codons in mycoplasmas

(2017) Shreya Ahana Ayyub et al.   RNA Biology

A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants

(2017) Eva Yus et al.   Nature Communications

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

(2017) Tasos Gogakos et al.   Cell Reports

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

(2017) Petri-Jaan Lahtvee et al.   Cell Systems

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

(2016) Renana Sabi et al.   BIOINFORMATICS

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

(2016) Alon Diament et al.   Biology Direct

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

(2016) Joana Pinto Vieira et al.   BIOPHYSICAL JOURNAL

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

(2016) Marc Sturm et al.   BMC BIOINFORMATICS

Initiator tRNA genes template the 3′ CCA end at high frequencies in bacteria

(2016) David H. Ardell et al.   BMC GENOMICS

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

(2016) Caitlin E. Gamble et al.   CELL

Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling

(2016) Kenji Nakahigashi et al.   DNA RESEARCH

Absolute quantitative measurement of transcriptional kinetic parametersin vivo

(2016) Sukanya Iyer et al.   NUCLEIC ACIDS RESEARCH

A ribosome profiling study of mRNA cleavage by the endonuclease RelE

(2016) Jae-Yeon Hwang et al.   NUCLEIC ACIDS RESEARCH

Quantitative assessment of ribosome drop-off inE. coli

(2016) Celine Sin 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

Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center

(2016) James Marks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

(2016) Patrick B. F. O’Connor et al.   Nature Communications

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

(2016) Ivan Junier et al.   Cell Systems

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

(2016) Xiongfeng Dai et al.   Nature Microbiology

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

Distribution and diversity of ribosome binding sites in prokaryotic genomes

(2015) Damilola Omotajo et al.   BMC GENOMICS

Ribosome profiling reveals an important role for translational control in circadian gene expression

(2015) Christopher Jang et al.   GENOME RESEARCH

Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli

(2015) H. Chen et al.   Molecular Systems Biology

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

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

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

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

(2015) Alexey A. Gritsenko et al.   PLoS Computational Biology

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo

(2015) Kenji Nakahigashi et al.   BMC GENOMICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

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

(2014) Gene-Wei Li et al.   CELL

Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

(2014) Renana Sabi et al.   DNA RESEARCH

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

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

Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes

(2014) Henri Grosjean et al.   PLoS Genetics

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae

(2013) Tobias Maier et al.   Molecular BioSystems

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

Nascent peptides that block protein synthesis in bacteria

(2013) C. J. Woolstenhulme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying Translational Coupling in E. coli Synthetic Operons Using RBS Modulation and Fluorescent Reporters

(2013) Ayelet Levin-Karp et al.   ACS Synthetic 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

tRNA genes rapidly change in evolution to meet novel translational demands

(2013) Avihu H Yona et al.   eLife

General LC-MS/MS Method Approach to Quantify Therapeutic Monoclonal Antibodies Using a Common Whole Antibody Internal Standard with Application to Preclinical Studies

(2012) Hongyan Li et al.   ANALYTICAL CHEMISTRY

A Role for tRNA Modifications in Genome Structure and Codon Usage

(2012) Eva Maria Novoa et al.   CELL

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

(2012) Somenath Bakshi et al.   MOLECULAR MICROBIOLOGY

Transcription start site associated RNAs in bacteria

(2012) Eva Yus et al.   Molecular Systems Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The architecture of eukaryotic translation

(2012) Dominique Chu et al.   NUCLEIC ACIDS RESEARCH

Comparison of mRNA features affecting translation initiation and reinitiation

(2012) Ilya A. Osterman et al.   NUCLEIC ACIDS RESEARCH

Ribosomal protein S1 unwinds double-stranded RNA in multiple steps

(2012) X. Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unconventional initiator tRNAs sustain Escherichia coli

(2012) L. Samhita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ViennaRNA Package 2.0

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

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli

(2011) Oliver Vesper 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

The diversity of protein turnover and abundance under nitrogen-limited steady-state conditions in Saccharomyces cerevisiae

(2011) Andreas O. Helbig et al.   Molecular BioSystems

Quantification of mRNA and protein and integration with protein turnover in a bacterium

(2011) T. Maier et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

mRNA pseudoknot structures can act as ribosomal roadblocks

(2011) Jesper Tholstrup et al.   NUCLEIC ACIDS RESEARCH

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

(2011) P. O'Donoghue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of absolute peptide quantitation strategies using selected reaction monitoring

(2011) James Campbell et al.   PROTEOMICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Role for Codon Order in Translation Dynamics

(2010) Gina Cannarozzi et al.   CELL

Proximity of the Start Codon to a Leaderless mRNA's 5' Terminus Is a Strong Positive Determinant of Ribosome Binding and Expression in Escherichia coli

(2010) K. M. Krishnan et al.   JOURNAL OF BACTERIOLOGY

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Dynamic evolution of translation initiation mechanisms in prokaryotes

(2010) S. Nakagawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comprehensive, Quantitative, and Genome-Wide Model of Translation

(2010) Marlena Siwiak et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling

(2009) B. Seidelt et al.   SCIENCE

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

(2009) E. Yus et al.   SCIENCE

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE