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

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Translational regulation shapes the molecular landscape of complex disease phenotypes

(2015) Sebastian Schafer et al.   Nature Communications

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

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

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

(2015) Dmitry E Andreev et al.   GENOME BIOLOGY

Nucleolar stress in Diamond Blackfan anemia pathophysiology

(2014) Steven R. Ellis   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

(2014) Andrea Pauli et al.   BIOESSAYS

Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei

(2014) Bryan C Jensen et al.   BMC GENOMICS

An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation

(2014) Arvind R. Subramaniam et al.   CELL

A Bicistronic MAVS Transcript Highlights a Class of Truncated Variants in Antiviral Immunity

(2014) Sky W. Brubaker et al.   CELL

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

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

(2014) Gene-Wei Li et al.   CELL

Remote Control of Gene Function by Local Translation

(2014) Hosung Jung et al.   CELL

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

(2014) Yan Han et al.   CELL RESEARCH

Translational profiling through biotinylation of tagged ribosomes in zebrafish

(2014) M. P. Housley et al.   DEVELOPMENT

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP)

(2014) Myriam Heiman et al.   Nature Protocols

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages

(2014) Juan-José Vasquez et al.   NUCLEIC ACIDS RESEARCH

The general mode of translation inhibition by macrolide antibiotics

(2014) Krishna Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence selectivity of macrolide-induced translational attenuation

(2014) A. R. Davis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

(2014) C. C. Williams et al.   SCIENCE

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

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

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

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

(2014) Jenna E. Smith et al.   Cell Reports

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

(2014) Iva Kronja 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

Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals

(2014) Fabian Schueren et al.   eLife

Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages

(2014) Florence Caro et al.   eLife

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Ribosome biogenesis in skeletal development and the pathogenesis of skeletal disorders

(2013) Paul A. Trainor et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Updating RNA-Seq analyses after re-annotation

(2013) Adam Roberts et al.   BIOINFORMATICS

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

Repeat-associated non-ATG (RAN) translation in neurological disease

(2013) J. D. Cleary et al.   HUMAN MOLECULAR GENETICS

Two Rapidly Evolving Genes Contribute to Male Fitness in Drosophila

(2013) Josephine A. Reinhardt et al.   JOURNAL OF MOLECULAR EVOLUTION

Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames

(2013) Adam G. Schwaid et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes

(2013) Botao Liu et al.   MOLECULAR CELL

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

(2013) Miler T. Lee et al.   NATURE

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

A Rapid Ribosome Profiling Method Elucidates Chloroplast Ribosome Behavior in Vivo

(2013) R. Zoschke et al.   PLANT CELL

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Ribosomal Protein SA Haploinsufficiency in Humans with Isolated Congenital Asplenia

(2013) A. Bolze et al.   SCIENCE

Mysterious Ribosomopathies

(2013) K. L. McCann et al.   SCIENCE

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

Ribosome profiling reveals features of normal and disease-associated mitochondrial translation

(2013) Koos Rooijers et al.   Nature Communications

Conserved Translatome Remodeling in Nematode Species Executing a Shared Developmental Transition

(2013) Michael Stadler et al.   PLoS Genetics

The Ecm11-Gmc2 Complex Promotes Synaptonemal Complex Formation through Assembly of Transverse Filaments in Budding Yeast

(2013) Neil Humphryes et al.   PLoS Genetics

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

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

Translational reprogramming in cellular stress response

(2013) Botao Liu et al.   Wiley Interdisciplinary Reviews-RNA

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel

(2012) Krishna Kannan et al.   CELL

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

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

(2012) Gene-Wei Li et al.   NATURE

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

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

A Versatile Method for Cell-Specific Profiling of Translated mRNAs in Drosophila

(2012) Amanda Thomas et al.   PLoS One

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee 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

Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I

(2012) S. R. Starck et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Decoding Human Cytomegalovirus

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

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

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

(2011) Eugene Oh et al.   CELL

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov 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

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

(2011) I. Jungreis et al.   GENOME RESEARCH

Wobble base-pairing slows in vivo translation elongation in metazoans

(2011) M. Stadler et al.   RNA

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Making Sense of Antisense: Seemingly Noncoding RNAs Antisense to the Master Regulator of Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication Do Not Regulate That Transcript but Serve as mRNAs Encoding Small Peptides

(2010) Y. Xu et al.   JOURNAL OF VIROLOGY

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Execution of nonsense-mediated mRNA decay: what defines a substrate?

(2009) Indrani Rebbapragada et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2009) N. T. Ingolia et al.   SCIENCE

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL