Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context

Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins

(2019) Geoffray Monteuuis et al.   NUCLEIC ACIDS RESEARCH

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

(2019) Sanne Boersma et al.   CELL

Multimapping confounds ribosome profiling analysis: A case‐study of the Hsp90 molecular chaperone

(2019) Jackson C. Halpin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

(2018) Marie A. Brunet et al.   GENOME RESEARCH

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

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

Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection

(2018) Gary Loughran et al.   PLoS One

Protein Synthesis Initiation in Eukaryotic Cells

(2018) William C. Merrick et al.   Cold Spring Harbor Perspectives in Biology

Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions

(2018) Nikolay E. Shirokikh et al.   Wiley Interdisciplinary Reviews-RNA

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

(2018) Stephen J Kiniry et al.   NUCLEIC ACIDS RESEARCH

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

(2017) Daria Fijałkowska et al.   NUCLEIC ACIDS RESEARCH

APPRIS 2017: principal isoforms for multiple gene sets

(2017) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz: 2018 update

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

nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs

(2016) Valentina Gandin et al.   GENOME RESEARCH

Positional proteomics reveals differences in N-terminal proteoform stability

(2016) D. Gawron et al.   Molecular Systems Biology

Ribonuclease selection for ribosome profiling

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

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

Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18

(2015) Xingqian Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18

(2015) Xingqian Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

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

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men

(2014) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative analysis of mammalian translation initiation sites by FACS-seq

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

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

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

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

A perspective on mammalian upstream open reading frame function

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

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

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

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

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

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

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

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

(2011) Nicholas T. Ingolia et al.   CELL

Functional Elements in Initiation Factors 1, 1A, and 2  Discriminate against Poor AUG Context and Non-AUG Start Codons

(2011) P. Martin-Marcos et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

The mechanism of eukaryotic translation initiation and principles of its regulation

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

Alternative translation start sites are conserved in eukaryotic genomes

(2010) G. A. Bazykin et al.   NUCLEIC ACIDS RESEARCH

Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)

(2010) I. P. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic translation initiation factor 1 (eIF1), the inspector of good AUG context for translation initiation, has an extremely bad AUG context

(2009) Hitoshi Miyasaka et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING