High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

(2015) David J. Young et al.   CELL

Middle East Respiratory Syndrome Coronavirus: Another Zoonotic Betacoronavirus Causing SARS-Like Disease

(2015) Jasper F. W. Chan et al.   CLINICAL MICROBIOLOGY REVIEWS

X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions

(2015) Yafang Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evidence for an Ancestral Association of Human Coronavirus 229E with Bats

(2015) Victor Max Corman et al.   JOURNAL OF VIROLOGY

Deciphering Poxvirus Gene Expression by RNA Sequencing and Ribosome Profiling

(2015) Zhilong Yang et al.   JOURNAL OF VIROLOGY

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The awesome power of ribosome profiling

(2015) Richard Jackson et al.   RNA

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis

(2015) Betty Y. Chung et al.   RNA

Coronavirus envelope (E) protein remains at the site of assembly

(2015) Pavithra Venkatagopalan et al.   VIROLOGY

New insights on the role of paired membrane structures in coronavirus replication

(2015) Philip V’kovski et al.   VIRUS RESEARCH

Coronavirus nonstructural protein 1: Common and distinct functions in the regulation of host and viral gene expression

(2015) Krishna Narayanan et al.   VIRUS RESEARCH

Bats as reservoirs of severe emerging infectious diseases

(2015) Hui-Ju Han et al.   VIRUS RESEARCH

Functional non-coding RNAs derived from the flavivirus 3′ untranslated region

(2015) B.D. Clarke et al.   VIRUS RESEARCH

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

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

(2015) Cristian Del Campo et al.   PLoS Genetics

The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions

(2015) Osnat Tirosh et al.   PLoS Pathogens

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Programmed –1 Frameshifting by Kinetic Partitioning during Impeded Translocation

(2014) Neva Caliskan et al.   CELL

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation

(2014) Yan Han et al.   CELL RESEARCH

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

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

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

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

Dynamic pathways of −1 translational frameshifting

(2014) Jin Chen et al.   NATURE

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions

(2014) Teemu P. Miettinen et al.   NUCLEIC ACIDS RESEARCH

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

(2014) H.-K. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

(2014) Carolina Arias et al.   PLoS Pathogens

Arrest Peptides:Cis-Acting Modulators of Translation

(2013) Koreaki Ito et al.   Annual Review of Biochemistry

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

(2013) P. B. F. O'Connor et al.   BIOINFORMATICS

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Functional Analysis of the Murine Coronavirus Genomic RNA Packaging Signal

(2013) L. Kuo et al.   JOURNAL OF VIROLOGY

Reselection of a Genomic Upstream Open Reading Frame in Mouse Hepatitis Coronavirus 5'-Untranslated-Region Mutants

(2013) H.-Y. Wu et al.   JOURNAL OF VIROLOGY

Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes

(2013) Botao Liu et al.   MOLECULAR CELL

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

High-resolution view of bacteriophage lambda gene expression by ribosome profiling

(2013) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Severe Acute Respiratory Syndrome Coronavirus Nonstructural Proteins 3, 4, and 6 Induce Double-Membrane Vesicles

(2013) M. M. Angelini et al.   mBio

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

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

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale

(2013) Audrey M. Michel et al.   Wiley Interdisciplinary Reviews-RNA

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

Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U 6 A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting

(2012) Zhaoru Lin et al.   NUCLEIC ACIDS RESEARCH

Monitoring cotranslational protein folding in mammalian cells at codon resolution

(2012) Y. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

(2012) M. V. Gerashchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

(2012) Alexandra Dana et al.   PLoS Computational Biology

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Mouse Hepatitis Virus Stem-Loop 4 Functions as a Spacer Element Required To Drive Subgenomic RNA Synthesis

(2011) D. Yang et al.   JOURNAL OF VIROLOGY

Translation Goes Global

(2011) R. B. Weiss et al.   SCIENCE

Processive Selenocysteine Incorporation during Synthesis of Eukaryotic Selenoproteins

(2010) S.M. Fixsen et al.   JOURNAL OF MOLECULAR BIOLOGY

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins

(2010) E. P. Plant et al.   JOURNAL OF VIROLOGY

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Detection of Nonstructural Protein 6 in Murine Coronavirus-Infected Cells and Analysis of the Transmembrane Topology by Using Bioinformatics and Molecular Approaches

(2009) S. Baliji et al.   JOURNAL OF VIROLOGY

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

(2009) Gong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

Ribosomal footprints on a transcriptome landscape

(2009) David R Morris   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Proteomics Analysis Unravels the Functional Repertoire of Coronavirus Nonstructural Protein 3

(2008) B. W. Neuman et al.   JOURNAL OF VIROLOGY

Topology and Membrane Anchoring of the Coronavirus Replication Complex: Not All Hydrophobic Domains of nsp3 and nsp6 Are Membrane Spanning

(2008) M. Oostra et al.   JOURNAL OF VIROLOGY

Slow peptide bond formation by proline and other N-alkylamino acids in translation

(2008) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles

(2008) Mark A. Clementz et al.   VIROLOGY

SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

(2008) Kèvin Knoops et al.   PLOS BIOLOGY