PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation

(2018) Martina M. Yordanova et al.   NATURE

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

(2017) Elvis Ndah et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz: 2018 update

(2017) Audrey M Michel et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae

(2017) Renana Sabi et al.   RNA

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

(2017) Lorenzo Calviello et al.   TRENDS IN GENETICS

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

(2017) Yoshitaka Matsuo et al.   Nature Communications

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

(2016) Yi Zhong et al.   BIOINFORMATICS

SPECtre: a spectral coherence-­based classifier of actively translated transcripts from ribosome profiling sequence data

(2016) Sang Y. Chun et al.   BMC BIOINFORMATICS

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

(2016) Joshua G. Dunn et al.   BMC GENOMICS

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae

(2016) Seda Yerlikaya et al.   MOLECULAR BIOLOGY OF THE CELL

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

(2016) Dmitry E. Andreev et al.   NUCLEIC ACIDS RESEARCH

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation

(2016) Mayuki Tanaka et al.   PLANT CELL

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data

(2016) Audrey M. Michel et al.   RNA Biology

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

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis

(2015) Rachel Legendre et al.   BIOINFORMATICS

Pausing on Polyribosomes: Make Way for Elongation in Translational Control

(2015) Joel D. Richter et al.   CELL

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling

(2015) Shang-Qian Xie et al.   NUCLEIC ACIDS RESEARCH

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms

(2015) Audrey M. Michel et al.   PROTEOMICS

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

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

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide

(2014) Stefan Arenz et al.   Nature Communications

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

(2014) Liana F Lareau et al.   eLife

Assessing gene-level translational control from ribosome profiling

(2013) Adam B. Olshen et al.   BIOINFORMATICS

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

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

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

(2013) Koos Rooijers et al.   Nature Communications

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

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

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

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

(2012) Gene-Wei Li et al.   NATURE

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

(2011) Eugene Oh 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

mRNA pseudoknot structures can act as ribosomal roadblocks

(2011) Jesper Tholstrup et al.   NUCLEIC ACIDS RESEARCH

Translational Pausing Ensures Membrane Targeting and Cytoplasmic Splicing of XBP1u mRNA

(2011) K. Yanagitani et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY