A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

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

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

Polycysteine‐encoding leaderless short ORFs function as cysteine‐responsive attenuators of operonic gene expression in mycobacteria

(2020) Jill G. Canestrari et al.   MOLECULAR MICROBIOLOGY

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

Selective translation by alternative bacterial ribosomes

(2020) Yu-Xiang Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia

(2019) M. Carla Martini et al.   Frontiers in Microbiology

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

(2019) Fuad Mohammad et al.   eLife

Dynamics of the context-specific translation arrest by chloramphenicol and linezolid

(2019) Junhong Choi et al.   Nature Chemical Biology

Translational regulation in mycobacteria and its implications for pathogenicity

(2018) Elizabeth B Sawyer et al.   NUCLEIC ACIDS RESEARCH

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA

(2018) Satabdi Mishra et al.   Scientific Reports

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

(2017) Zhen Shi et al.   MOLECULAR CELL

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival

(2017) Teresa Cortes et al.   Scientific Reports

The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis

(2017) Diana A. Aguilar-Ayala et al.   Scientific Reports

The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress

(2016) Amine Namouchi et al.   BMC GENOMICS

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

A streamlined ribosome profiling protocol for the characterization of microorganisms

(2015) Haythem Latif et al.   BIOTECHNIQUES

How do bacteria tune translation efficiency?

(2015) Gene-Wei Li   CURRENT OPINION IN MICROBIOLOGY

Structural basis for stop codon recognition in eukaryotes

(2015) Alan Brown et al.   NATURE

A functional role of Rv1738 inMycobacterium tuberculosispersistence suggested by racemic protein crystallography

(2015) Richard D. Bunker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP

(2015) Christopher J. Woolstenhulme et al.   Cell Reports

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

(2015) Cristian Del Campo et al.   PLoS Genetics

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Gene-Wei Li et al.   CELL

The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli

(2014) Rohan Balakrishnan et al.   NUCLEIC ACIDS RESEARCH

The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

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

Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression

(2013) Flora Picard et al.   BMC GENOMICS

The significance of translation regulation in the stress response

(2013) Flora Picard et al.   BMC GENOMICS

Integrated Analysis of Transcriptomic and Proteomic Data

(2013) Saad Haider et al.   CURRENT GENOMICS

Ribosome heterogeneity: another level of complexity in bacterial translation regulation

(2013) Konstantin Byrgazov et al.   CURRENT OPINION IN MICROBIOLOGY

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan 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

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

(2013) Teresa Cortes et al.   Cell Reports

Integrative “Omics”-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses

(2013) Bork A. Berghoff et al.   PLoS Genetics

The Dormancy Regulator DosR Controls Ribosome Stability in Hypoxic Mycobacteria

(2012) Andrej Trauner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Specialized ribosomes: a new frontier in gene regulation and organismal biology

(2012) Shifeng Xue et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Global analysis of mRNA stability in Mycobacterium tuberculosis

(2012) Tige R. Rustad et al.   NUCLEIC ACIDS RESEARCH

Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis during an Extended Intracellular Infection

(2012) Kyle H. Rohde et al.   PLoS Pathogens

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

(2011) Eugene Oh et al.   CELL

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

Evaluating the Sensitivity of Mycobacterium tuberculosis to Biotin Deprivation Using Regulated Gene Expression

(2011) Sae Woong Park et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Linear covariance models to examine the determinants of protein levels in Lactococcus lactis

(2010) Clémentine Dressaire et al.   Molecular BioSystems

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

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

(2010) Y. Taniguchi et al.   SCIENCE

The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes

(2010) Adamandia Kapopoulou et al.   TUBERCULOSIS

A Novel In Vitro Multiple-Stress Dormancy Model for Mycobacterium tuberculosis Generates a Lipid-Loaded, Drug-Tolerant, Dormant Pathogen

(2009) Chirajyoti Deb et al.   PLoS One

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS