The proteome under translational control

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

ASaccharomyces cerevisiaeModel RevealsIn VivoFunctional Impairment of the Ogden Syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

(2014) Ranen Aviner et al.   Nature Protocols

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages

(2014) Juan-José Vasquez et al.   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

RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors

(2014) Queenie Wing-Lei Wong et al.   RNA Biology

Distinct functional classes of ram mutations in 16S rRNA

(2014) S. P. McClory et al.   RNA

In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism

(2014) Maria S. Robles et al.   PLoS Genetics

Adaptive Translation as a Mechanism of Stress Response and Adaptation

(2013) Tao Pan   Annual Review of Genetics

Expression changes of ribosomal proteins in phosphate- and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition

(2013) Jinyan Wang et al.   BMC GENOMICS

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

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

(2013) Mitchell Guttman et al.   CELL

Ribosome heterogeneity: another level of complexity in bacterial translation regulation

(2013) Konstantin Byrgazov et al.   CURRENT OPINION IN MICROBIOLOGY

Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation

(2013) R. Aviner et al.   GENES & DEVELOPMENT

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Protein synthesis rate is the predominant regulator of protein expression during differentiation

(2013) A. R. Kristensen et al.   Molecular Systems Biology

Erratum: Corrigendum: Global quantification of mammalian gene expression control

(2013) Björn Schwanhäusser et al.   NATURE

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

(2013) Teck Yew Low et al.   Cell Reports

The Circadian Clock Coordinates Ribosome Biogenesis

(2013) Céline Jouffe et al.   PLOS BIOLOGY

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

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

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

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

(2012) C. Fritsch et al.   GENOME RESEARCH

Up-regulation of Translation Eukaryotic Initiation Factor 4E in Nucleophosmin 1 Haploinsufficient Cells Results in Changes in CCAAT Enhancer-binding Protein α Activity

(2012) Arati Khanna-Gupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

(2012) Kang Ning et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Specialized ribosomes: a new frontier in gene regulation and organismal biology

(2012) Shifeng Xue et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Alternative translation initiation augments the human mitochondrial proteome

(2012) Lawrence Kazak 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

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

Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast

(2012) Daniel H Lackner et al.   GENOME BIOLOGY

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

(2011) Nicholas T. Ingolia et al.   CELL

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Bioinformatics Analysis of aSaccharomyces cerevisiaeN-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal Acetylation

(2011) Kenny Helsens et al.   JOURNAL OF PROTEOME RESEARCH

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

(2011) A. G. Hinnebusch   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

(2011) J. Munoz et al.   Molecular Systems Biology

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Quantification of mRNA and protein and integration with protein turnover in a bacterium

(2011) T. Maier et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

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

(2011) Ivaylo P. Ivanov 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

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

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Targeting Eukaryotic Translation Initiation Factor 4E (eIF4E) in Cancer

(2010) A. C. Hsieh et al.   CLINICAL CANCER RESEARCH

Expanding the Dipeptidyl Peptidase 4-Regulated Peptidome via an Optimized Peptidomics Platform

(2010) Arthur D. Tinoco et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An Upstream Open Reading Frame and the Context of the Two AUG Codons Affect the Abundance of Mitochondrial and Nuclear RNase H1

(2010) Y. Suzuki et al.   MOLECULAR AND CELLULAR BIOLOGY

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Alternative translation start sites are conserved in eukaryotic genomes

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

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells

(2010) Tamar Geiger et al.   PLoS Genetics

Combined analysis of eIF4E and 4E-binding protein expression predicts breast cancer survival and estimates eIF4E activity

(2009) L J Coleman et al.   BRITISH JOURNAL OF CANCER

eIF4E Activation Is Commonly Elevated in Advanced Human Prostate Cancers and Significantly Related to Reduced Patient Survival

(2009) J. R. Graff et al.   CANCER RESEARCH

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

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

Overexpression of eukaryotic initiation factor 5A2 enhances cell motility and promotes tumor metastasis in hepatocellular carcinoma

(2009) Dong-Jiang Tang et al.   HEPATOLOGY

Delayed Correlation of mRNA and Protein Expression in Rapamycin-treated Cells and a Role for Ggc1 in Cellular Sensitivity to Rapamycin

(2009) Marjorie L. Fournier et al.   MOLECULAR & CELLULAR PROTEOMICS

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

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

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

(2009) Sandra Goetze et al.   PLOS BIOLOGY

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

(2009) David G. Hendrickson et al.   PLOS BIOLOGY

Expression and amplification of eIF-5A2 in human epithelial ovarian tumors and overexpression of EIF-5A2 is a new independent predictor of outcome in patients with ovarian carcinoma

(2008) Guo-Fen Yang et al.   GYNECOLOGIC ONCOLOGY

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

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

(2008) Dierk Thomas et al.   NEURON

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA