Related references
Note: Only part of the references are listed.Ribonuclease selection for ribosome profiling
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2017)
Detecting actively translated open reading frames in ribosome profiling data
Lorenzo Calviello et al.
NATURE METHODS (2016)
Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis
Ilya M. Terenin et al.
NUCLEIC ACIDS RESEARCH (2016)
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling
Shang-Qian Xie et al.
NUCLEIC ACIDS RESEARCH (2016)
sORFs.org: a repository of small ORFs identified by ribosome profiling
Volodimir Olexiouk et al.
NUCLEIC ACIDS RESEARCH (2016)
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
Hao Wang et al.
BIOINFORMATICS (2016)
Mapping the non-standardized biases of ribosome profiling
Alexander Bartholomaeus et al.
BIOLOGICAL CHEMISTRY (2016)
Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells
Alexandra Popa et al.
BMC GENOMICS (2016)
Redefining the Translational Status of 80S Monosomes
Erin E. Heyer et al.
CELL (2016)
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination
Estienne Carl Swart et al.
CELL (2016)
Ribosome Footprint Profiling of Translation throughout the Genome
Nicholas T. Ingolia
CELL (2016)
The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality
Aditya Radhakrishnan et al.
CELL (2016)
nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
Valentina Gandin et al.
GENOME RESEARCH (2016)
Evolutionary Dynamics of Abundant Stop Codon Readthrough
Irwin Jungreis et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum
Stephen M. Heaphy et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Cotranslational signal-independent SRP preloading during membrane targeting
Justin W. Chartron et al.
NATURE (2016)
Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor
Shintaro Iwasaki et al.
NATURE (2016)
Dynamics of ribosome scanning and recycling revealed by translation complex profiling
Stuart K. Archer et al.
NATURE (2016)
Tumour-specific proline vulnerability uncovered by differential ribosome codon reading
Fabricio Loayza-Puch et al.
NATURE (2016)
Transcriptome-scale RNase-footprinting of RNA-protein complexes
Zhe Ji et al.
NATURE BIOTECHNOLOGY (2016)
eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G
Neelam Dabas Sen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors
Rodrigo D. Requiao et al.
RNA BIOLOGY (2016)
RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data
Audrey M. Michel et al.
RNA BIOLOGY (2016)
Translational control by 5′-untranslated regions of eukaryotic mRNAs
Alan G. Hinnebusch et al.
SCIENCE (2016)
Comparative survey of the relative impact of mRNA features on local ribosome profiling read density
Patrick B. F. O'Connor et al.
NATURE COMMUNICATIONS (2016)
Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish
Guo-Liang Chew et al.
NATURE COMMUNICATIONS (2016)
Genome-wide assessment of differential translations with ribosome profiling data
Zhengtao Xiao et al.
NATURE COMMUNICATIONS (2016)
High frequency of+1 programmed ribosomal frameshifting in Euplotes octocarinatus
Ruanlin Wang et al.
SCIENTIFIC REPORTS (2016)
Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation
David E. Weinberg et al.
CELL REPORTS (2016)
Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling
Fuad Mohammad et al.
CELL REPORTS (2016)
The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs
Mary K. Thompson et al.
ELIFE (2016)
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Anil Raj et al.
ELIFE (2016)
Large-scale mass spectrometry-based analysis of Euplotes octocarinatus supports the high frequency of+1 programmed ribosomal frameshift
Ruanlin Wang et al.
SCIENTIFIC REPORTS (2016)
Ribosomal profiling adds new coding sequences to the proteome
Muhammad Ali S. Mumtaz et al.
BIOCHEMICAL SOCIETY TRANSACTIONS (2015)
RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis
Rachel Legendre et al.
BIOINFORMATICS (2015)
Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity
Danny D. Nedialkova et al.
CELL (2015)
Codon Optimality Is a Major Determinant of mRNA Stability
Vladimir Presnyak et al.
CELL (2015)
Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo
David J. Young et al.
CELL (2015)
Translational Tolerance of Mitochondrial Genes to Metabolic Energy Stress Involves TISU and eIF1-eIF4GI Cooperation in Start Codon Selection
Hadar Sinvani et al.
CELL METABOLISM (2015)
Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
Neelam Dabas Sen et al.
GENOME RESEARCH (2015)
Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
Peggy Janich et al.
GENOME RESEARCH (2015)
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
Can Cenik et al.
GENOME RESEARCH (2015)
Decoding Viral Infection by Ribosome Profiling
Noam Stern-Ginossar
JOURNAL OF VIROLOGY (2015)
Simple and inexpensive ribosome profiling analysis of mRNA translation
David W. Reid et al.
METHODS (2015)
A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation
Alexander P. Fields et al.
MOLECULAR CELL (2015)
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning
Pavel V. Baranov et al.
NATURE REVIEWS GENETICS (2015)
Ribosome profiling reveals the what, when, where and how of protein synthesis
Gloria A. Brar et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)
CDK1 substitutes for mTOR kinase to activate mitotic cap-dependent protein translation
Masahiro Shuda et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
Audrey M. Michel et al.
PROTEOMICS (2015)
The awesome power of ribosome profiling
Richard Jackson et al.
RNA (2015)
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis
Betty Y. Chung et al.
RNA (2015)
Mutations in a translation initiation factor identify the target of a memory-enhancing compound
Yusuke Sekine et al.
SCIENCE (2015)
Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast
Jeffrey A. Hussmann et al.
PLOS GENETICS (2015)
The small molecule ISRIB reverses the effects of elF2α phosphorylation on translation and stress granule assembly
Carmela Sidrauski et al.
ELIFE (2015)
Translation of 5' leaders is pervasive in genes resistant to eIF2 repression
Dmitry E. Andreev et al.
ELIFE (2015)
Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes
Dmitry E. Andreev et al.
GENOME BIOLOGY (2015)
Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions
Teemu P. Miettinen et al.
NUCLEIC ACIDS RESEARCH (2015)
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Jeroen Crappe et al.
NUCLEIC ACIDS RESEARCH (2015)
Impact of regulatory variation from RNA to protein
Alexis Battle et al.
SCIENCE (2015)
The Scanning Mechanism of Eukaryotic Translation Initiation
Alan G. Hinnebusch
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)
Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning
Audrey M. Michel et al.
BMC BIOINFORMATICS (2014)
Programmed Translational Readthrough Generates Antiangiogenic VEGF-Ax
Sandeepa M. Eswarappa et al.
CELL (2014)
Dom34 Rescues Ribosomes in 3′ Untranslated Regions
Nicholas R. Guydosh et al.
CELL (2014)
Transcriptome-wide studies uncover the diversity of modes of mRNA recruitment to eukaryotic ribosomes
Ivan N. Shatsky et al.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2014)
Stress-induced Start Codon Fidelity Regulates Arsenite-inducible Regulatory Particle-associated Protein (AIRAP) Translation
Lolita Zach et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2014)
Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors
Christian Gonzalez et al.
JOURNAL OF NEUROSCIENCE (2014)
Optimal Translational Termination Requires C4 Lysyl Hydroxylation of eRF1
Tianshu Feng et al.
MOLECULAR CELL (2014)
Quantitative analysis of mammalian translation initiation sites by FACS-seq
William L. Noderer et al.
MOLECULAR SYSTEMS BIOLOGY (2014)
RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
Andrew L. Wolfe et al.
NATURE (2014)
Ribosome profiling: new views of translation, from single codons to genome scale APPLICATIONS OF NEXT-GENERATION SEQUENCING - INNOVATION
Nicholas T. Ingolia
NATURE REVIEWS GENETICS (2014)
Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo
Sebastian Pechmann et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)
GWIPS-viz: development of a ribo-seq genome browser
Audrey M. Michel et al.
NUCLEIC ACIDS RESEARCH (2014)
TISdb: a database for alternative translation initiation in mammalian cells
Ji Wan et al.
NUCLEIC ACIDS RESEARCH (2014)
Identification of a Mg2+-sensitive ORF in the 5′-leader of TRPM7 magnesium channel mRNA
Inna A. Nikonorova et al.
NUCLEIC ACIDS RESEARCH (2014)
Translation inhibitors cause abnormalities in ribosome profiling experiments
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2014)
Evidence of efficient stop codon readthrough in four mammalian genes
Gary Loughran et al.
NUCLEIC ACIDS RESEARCH (2014)
Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy
Christoph Loenarz et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling
Christopher C. Williams et al.
SCIENCE (2014)
Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling
Calvin H. Jan et al.
SCIENCE (2014)
The ever-evolving role of mTOR in translation
Bruno D. Fonseca et al.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2014)
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
Nicholas T. Ingolia et al.
CELL REPORTS (2014)
Genome-wide Translational Changes Induced by the Prion [PSI+]
Agnes Baudin-Baillieu et al.
CELL REPORTS (2014)
Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals
Alina C. Stiebler et al.
PLOS GENETICS (2014)
Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals
Fabian Schueren et al.
ELIFE (2014)
Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages
Florence Caro et al.
ELIFE (2014)
Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
Liana F. Lareau et al.
ELIFE (2014)
Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
Julie L. Aspden et al.
ELIFE (2014)
Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation
Claudia A. Rubio et al.
GENOME BIOLOGY (2014)
Many roads from mTOR to eIF4F
Carson C. Thoreen
BIOCHEMICAL SOCIETY TRANSACTIONS (2013)
Assessing gene-level translational control from ribosome profiling
Adam B. Olshen et al.
BIOINFORMATICS (2013)
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
Patrick B. F. O'Connor et al.
BIOINFORMATICS (2013)
Rate-Limiting Steps in Yeast Protein Translation
Premal Shah et al.
CELL (2013)
Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes
Botao Liu et al.
MOLECULAR CELL (2013)
The Translational Landscape of the Mammalian Cell Cycle
Craig R. Stumpf et al.
MOLECULAR CELL (2013)
Widespread Regulation of Translation by Elongation Pausing in Heat Shock
Reut Shalgi et al.
MOLECULAR CELL (2013)
Translational Landscape of Photomorphogenic Arabidopsis
Ming-Jung Liu et al.
PLANT CELL (2013)
Tying up loose ends: ribosome recycling in eukaryotes and archaea
Elina Nuerenberg et al.
TRENDS IN BIOCHEMICAL SCIENCES (2013)
Ribosome profiling reveals features of normal and disease-associated mitochondrial translation
Koos Rooijers et al.
NATURE COMMUNICATIONS (2013)
Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale
Audrey M. Michel et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)
Pharmacological brake-release of mRNA translation enhances cognitive memory
Carmela Sidrauski et al.
ELIFE (2013)
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
Joshua G. Dunn et al.
ELIFE (2013)
Observation of dually decoded regions of the human genome using ribosome profiling data
Audrey M. Michel et al.
GENOME RESEARCH (2012)
Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
Claudia Fritsch et al.
GENOME RESEARCH (2012)
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Gene-Wei Li et al.
NATURE (2012)
A unifying model for mTORC1-mediated regulation of mRNA translation
Carson C. Thoreen et al.
NATURE (2012)
The translational landscape of mTOR signalling steers cancer initiation and metastasis
Andrew C. Hsieh et al.
NATURE (2012)
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nicholas T. Ingolia et al.
NATURE PROTOCOLS (2012)
Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5
Gary Loughran et al.
NUCLEIC ACIDS RESEARCH (2012)
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
Sooncheol Lee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling
Gloria A. Brar et al.
SCIENCE (2012)
Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish
Ariel A. Bazzini et al.
SCIENCE (2012)
Decoding Human Cytomegalovirus
Noam Stern-Ginossar et al.
SCIENCE (2012)
Eukaryotic Initiation Factor 2 Phosphorylation and Translational Control in Metabolism
Thomas D. Baird et al.
ADVANCES IN NUTRITION (2012)
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells
Alexandra Dana et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
anota: analysis of differential translation in genome-wide studies
Ola Larsson et al.
BIOINFORMATICS (2011)
Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo
Eugene Oh et al.
CELL (2011)
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
Nicholas T. Ingolia et al.
CELL (2011)
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes
Vera P. Pisareva et al.
EMBO JOURNAL (2011)
Evidence of abundant stop codon readthrough in Drosophila and other metazoa
Irwin Jungreis et al.
GENOME RESEARCH (2011)
Phosphorylation of eIF2 Facilitates Ribosomal Bypass of an Inhibitory Upstream ORF to Enhance CHOP Translation
Lakshmi Reddy Palam et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2011)
mRNA helicases: the tacticians of translational control
Armen Parsyan et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2011)
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences
Ivaylo P. Ivanov et al.
NUCLEIC ACIDS RESEARCH (2011)
Unique translation initiation of mRNAs-containing TISU element
Rofa Elfakess et al.
NUCLEIC ACIDS RESEARCH (2011)
Wobble base-pairing slows in vivo translation elongation in metazoans
Michael Stadler et al.
RNA (2011)
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
Tamir Tuller et al.
CELL (2010)
mTOR binds to the promoters of RNA polymerase I- and III-transcribed genes
Chi Kwan Tsang et al.
CELL CYCLE (2010)
Mammalian microRNAs predominantly act to decrease target mRNA levels
Huili Guo et al.
NATURE (2010)
Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)
Ivaylo P. Ivanov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
mTOR associates with TFIIIC, is found at tRNA and 5S rRNA genes, and targets their repressor Maf1
Theodoros Kantidakis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Antitumor Activity and Mechanism of Action of the Cyclopenta[b]benzofuran, Silvestrol
Regina Cencic et al.
PLOS ONE (2009)
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Nicholas T. Ingolia et al.
SCIENCE (2009)
uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs
Ivaylo P. Ivanov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Recycling of eukaryotic posttermination ribosomal complexes
Andrey V. Pisarev et al.
CELL (2007)
The mTOR pathway in the control of protein synthesis
Xuemin Wang et al.
PHYSIOLOGY (2006)
Ribosome biogenesis and cell growth: mTOR coordinates transcription by all three classes of nuclear RNA polymerases
C. Mayer et al.
ONCOGENE (2006)
Inhibition of eukaryotic translation initiation by the marine natural product pateamine A
WK Low et al.
MOLECULAR CELL (2005)
CK2 phosphorylation of eukaryotic translation initiation factor 5 potentiates cell cycle progression
MK Homma et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
The role of alternative translation start sites in the generation of human protein diversity
AV Kochetov et al.
MOLECULAR GENETICS AND GENOMICS (2005)
The transformation suppressor Pdcd4 is a novel eukaryotic translation initiation factor 4A binding protein that inhibits translation
HS Yang et al.
MOLECULAR AND CELLULAR BIOLOGY (2003)
DUG is a novel homologue of translation initiation factor 4G that binds eIF4A
A Göke et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2002)
Phosphorylation of mammalian translation initiation factor 5 (eIF5) in vitro and in vivo
R Majumdar et al.
NUCLEIC ACIDS RESEARCH (2002)
XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor
H Yoshida et al.
CELL (2001)
Isolation of translationally controlled mRNAs by differential screening
W Mikulits et al.
FASEB JOURNAL (2000)
Share Paper
