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

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

(2013) Mitchell Guttman et al.   CELL

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

Control of Protein Quality and Stoichiometries by N-Terminal Acetylation and the N-End Rule Pathway

(2013) Anna Shemorry et al.   MOLECULAR CELL

Translational Landscape of Photomorphogenic Arabidopsis

(2013) M.-J. Liu et al.   PLANT CELL

A Rapid Ribosome Profiling Method Elucidates Chloroplast Ribosome Behavior in Vivo

(2013) R. Zoschke et al.   PLANT CELL

A Cryptic Targeting Signal Creates a Mitochondrial FEN1 Isoform with Tailed R-Loop Binding Properties

(2013) Lawrence Kazak et al.   PLoS One

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

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

(2012) C. Fritsch et al.   GENOME RESEARCH

Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets

(2012) M. Stadler et al.   GENOME RESEARCH

Interrelations between the Nucleotide Context of Human Start AUG Codon, N-end Amino Acids of the Encoded Protein and Initiation of Translation

(2012) Oxana A. Volkova et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The DegraBase: A Database of Proteolysis in Healthy and Apoptotic Human Cells

(2012) Emily D. Crawford et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2012) Gene-Wei Li et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

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

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events

(2012) Niklaas Colaert et al.   NUCLEIC ACIDS RESEARCH

Alternative translation initiation augments the human mitochondrial proteome

(2012) Lawrence Kazak et al.   NUCLEIC ACIDS RESEARCH

Two Isoforms of the mRNA Binding Protein IGF2BP2 Are Generated by Alternative Translational Initiation

(2012) Hang T. T. Le 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

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB

(2012) P. Van Damme 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

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

(2012) A. A. Bazzini et al.   SCIENCE

Decoding Human Cytomegalovirus

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

Protein N-terminal acetyltransferases: when the start matters

(2012) Kristian K. Starheim et al.   TRENDS IN BIOCHEMICAL SCIENCES

Tricks an IRES uses to enslave ribosomes

(2012) Sunnie R. Thompson   TRENDS IN MICROBIOLOGY

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

Protein alpha-N-acetylation studied by N-terminomics

(2011) Petra Van Damme et al.   FEBS Journal

Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling

(2011) David W. Reid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Nuclear Variant of ErbB3 Receptor Tyrosine Kinase Regulates Ezrin Distribution and Schwann Cell Myelination

(2011) T. Adilakshmi et al.   JOURNAL OF NEUROSCIENCE

Cap-Assisted Internal Initiation of Translation of Histone H4

(2011) Franck Martin et al.   MOLECULAR CELL

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function

(2011) P. F. Lange et al.   NUCLEIC ACIDS RESEARCH

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2011) N. D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Localization of Human RNase Z Isoforms: Dual Nuclear/Mitochondrial Targeting of the ELAC2 Gene Product by Alternative Translation Initiation

(2011) Walter Rossmanith   PLoS One

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

(2011) G. A. Brar et al.   SCIENCE

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

(2011) Petra Van Damme et al.   PLoS Genetics

A Quantitative Proteomics Design for Systematic Identification of Protease Cleavage Events

(2010) Francis Impens et al.   MOLECULAR & CELLULAR PROTEOMICS

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

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

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

(2010) Kenny Helsens et al.   PROTEOMICS

N-Terminal Acetylation of Cellular Proteins Creates Specific Degradation Signals

(2010) C.-S. Hwang et al.   SCIENCE

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

(2010) Wanjun Gu et al.   PLoS Computational Biology

Translation Initiation from Two In-Frame AUGs Generates Mitochondrial and Cytoplasmic Forms of the p43 Component of the Multisynthetase Complex

(2009) Vyacheslav Shalak et al.   BIOCHEMISTRY

Differential use of an in-frame translation initiation codon regulates human mu opioid receptor (OPRM1)

(2009) Kyu Young Song et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Targeted mass spectrometric analysis of N-terminally truncated isoforms generated via alternative translation initiation

(2009) Ryuji Kobayashi et al.   FEBS LETTERS

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

(2009) T. Arnesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

Cotranslational processing mechanisms: towards a dynamic 3D model

(2009) Carmela Giglione et al.   TRENDS IN BIOCHEMICAL SCIENCES

Re-capping the message

(2009) Daniel R. Schoenberg et al.   TRENDS IN BIOCHEMICAL SCIENCES

Identification and Functional Characterization of N-Terminally Acetylated Proteins in Drosophila melanogaster

(2009) Sandra Goetze et al.   PLOS BIOLOGY

Alternative translation start sites and hidden coding potential of eukaryotic mRNAs

(2008) Alex V. Kochetov   BIOESSAYS

uORFs, reinitiation and alternative translation start sites in human mRNAs

(2008) Alex V. Kochetov et al.   FEBS LETTERS

A novel mutation in NFKBIA/IKBA results in a degradation-resistant N-truncated protein and is associated with ectodermal dysplasia with immunodeficiency

(2008) Eduardo Lopez-Granados et al.   HUMAN MUTATION

Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs

(2008) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Peptidecentric Proteomics Reveals Caspase-7 as a Substrate of the Caspase-1 Inflammasomes

(2008) Mohamed Lamkanfi et al.   MOLECULAR & CELLULAR PROTEOMICS

Alternative Translation Initiation in Rat Brain Yields K2P2.1 Potassium Channels Permeable to Sodium

(2008) Dierk Thomas et al.   NEURON

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

(2008) An Staes et al.   PROTEOMICS

Re-programming of translation following cell stress allows IRES-mediated translation to predominate

(2007) Keith A. Spriggs et al.   BIOLOGY OF THE CELL