TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response

Polyamine Control of Translation Elongation Regulates Start Site Selection on Antizyme Inhibitor mRNA via Ribosome Queuing

(2018) Ivaylo P. Ivanov et al.   MOLECULAR CELL

GWIPS-viz: 2018 update

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

In vivoevidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation

(2017) Mahabub Pasha Mohammad et al.   NUCLEIC ACIDS RESEARCH

Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs

(2017) Boris Zinshteyn et al.   RNA

mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4

(2017) Yeonwoo Park et al.   Cell Reports

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain

(2017) Nathanael G. Lintner et al.   PLOS BIOLOGY

Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome

(2016) Baoshan Xu et al.   BMC GENOMICS

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Ribosome Elongation Stall Directs Gene-specific Translation in the Integrated Stress Response

(2016) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response

(2016) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

(2016) Jong-Eun Park et al.   MOLECULAR CELL

Dynamics of ribosome scanning and recycling revealed by translation complex profiling

(2016) Stuart K. Archer et al.   NATURE

Quantitative assessment of ribosome drop-off inE. coli

(2016) Celine Sin et al.   NUCLEIC ACIDS RESEARCH

In-depth analysis ofcis-determinants that either promote or inhibit reinitiation onGCN4mRNA after translation of its four short uORFs

(2016) Stanislava Gunišová et al.   RNA

Translation from the 5' untranslated region shapes the integrated stress response

(2016) S. R. Starck et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

New Peptides Under the s(ORF)ace of the Genome

(2016) Jose I. Pueyo et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

(2016) Sekyung Oh et al.   Oncotarget

Systematic analysis of thePTEN5′ leader identifies a major AUU initiated proteoform

(2016) Ioanna Tzani et al.   Open Biology

Ribosome Reinitiation Directs Gene-specific Translation and Regulates the Integrated Stress Response

(2015) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell-fate determination by ubiquitin-dependent regulation of translation

(2015) Achim Werner et al.   NATURE

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

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

(2015) Osnat Tirosh et al.   PLoS Pathogens

The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly

(2015) Carmela Sidrauski et al.   eLife

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

(2015) Dmitry E Andreev et al.   eLife

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

(2015) Dmitry E Andreev et al.   GENOME BIOLOGY

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

(2014) Audrey M Michel et al.   BMC BIOINFORMATICS

mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach

(2014) Yun-Bo Zhao et al.   BMC Systems Biology

Stress-induced Start Codon Fidelity Regulates Arsenite-inducible Regulatory Particle-associated Protein (AIRAP) Translation

(2014) Lolita Zach et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fail-safe mechanism of GCN4 translational control—uORF2 promotes reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression

(2014) Stanislava Gunišová et al.   NUCLEIC ACIDS RESEARCH

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

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

(2014) Liana F Lareau et al.   eLife

The eEF2 Kinase Confers Resistance to Nutrient Deprivation by Blocking Translation Elongation

(2013) Gabriel Leprivier et al.   CELL

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

A perspective on mammalian upstream open reading frame function

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

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

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

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

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Stability Analysis of the Ribosome Flow Model

(2012) Michael Margaliot et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

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

Eukaryotic Initiation Factor 2 Phosphorylation and Translational Control in Metabolism

(2012) Thomas D. Baird et al.   Advances in Nutrition

MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW

(2012) Tobias von der Haar   Computational and Structural Biotechnology Journal

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

Phosphorylation of eIF2 Facilitates Ribosomal Bypass of an Inhibitory Upstream ORF to EnhanceCHOPTranslation

(2011) Lakshmi Reddy Palam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation

(2011) Konstantin S. Vassilenko et al.   NUCLEIC ACIDS RESEARCH

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

(2011) Ivaylo P. Ivanov et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

(2011) Shlomi Reuveni et al.   PLoS Computational Biology

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Role of the particle’s stepping cycle in an asymmetric exclusion process: A model of mRNA translation

(2010) L. Ciandrini et al.   PHYSICAL REVIEW E

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

Cap and cap-binding proteins in the control of gene expression

(2010) Ivan Topisirovic et al.   Wiley Interdisciplinary Reviews-RNA

An Upstream Open Reading Frame Regulates Translation of GADD34 during Cellular Stresses That Induce eIF2α Phosphorylation

(2009) Yun-Young Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions

(2009) Yi-Jiun Chen 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

Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes

(2008) Andrey V Pisarev et al.   EMBO JOURNAL

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs

(2008) I. P. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA