Methods for monitoring and measurement of protein translation in time and space

HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification

(2017) Yuanhui Ma et al.   JOURNAL OF PROTEOME RESEARCH

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

(2017) Danny Incarnato et al.   TRENDS IN BIOTECHNOLOGY

RNA localization is a key determinant of neurite-enriched proteome

(2017) Alessandra Zappulo et al.   Nature Communications

Cell-specific Profiling of Nascent Proteomes Using Orthogonal Enzyme-mediated Puromycin Incorporation

(2016) Ruth M. Barrett et al.   ACS Chemical Biology

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation

(2016) Christopher J. Tape et al.   CELL

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

Gene‐specific correlation of RNA and protein levels in human cells and tissues

(2016) Fredrik Edfors et al.   Molecular Systems Biology

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Incorporation of non-canonical amino acids into the developing murine proteome

(2016) Sarah Calve et al.   Scientific Reports

Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions

(2015) Faraz K. Mardakheh et al.   DEVELOPMENTAL CELL

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Cell-specific proteomic analysis inCaenorhabditis elegans

(2015) Kai P. Yuet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RNA biosensor for imaging the first round of translation from single cells to living animals

(2015) J. M. Halstead et al.   SCIENCE

Cell-selective labelling of proteomes in Drosophila melanogaster

(2015) Ines Erdmann et al.   Nature Communications

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

(2015) Dmitry E Andreev et al.   GENOME BIOLOGY

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

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

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

Rapid Temporal Dynamics of Transcription, Protein Synthesis, and Secretion during Macrophage Activation

(2014) Katrin Eichelbaum et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture

(2014) John D. Bagert et al.   MOLECULAR & CELLULAR PROTEOMICS

Cell-specific Labeling Enzymes for Analysis of Cell–Cell Communication in Continuous Co-culture

(2014) Christopher J. Tape et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal

(2014) Thomas S Elliott et al.   NATURE BIOTECHNOLOGY

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP)

(2014) Myriam Heiman et al.   Nature Protocols

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

(2014) C. C. Williams et al.   SCIENCE

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

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

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

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

QuaNCAT: quantitating proteome dynamics in primary cells

(2013) Andrew J M Howden et al.   NATURE METHODS

Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments

(2013) Nicholas P Gauthier et al.   NATURE METHODS

uORFdb—a comprehensive literature database on eukaryotic uORF biology

(2013) Klaus Wethmar 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

Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells

(2013) J. T. Ngo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis

(2013) Sara Zanivan et al.   Cell Reports

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

(2013) Joshua G Dunn et al.   eLife

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

(2012) Sami Hocine et al.   NATURE METHODS

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

A Versatile Method for Cell-Specific Profiling of Translated mRNAs in Drosophila

(2012) Amanda Thomas 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

Decoding Human Cytomegalovirus

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

Noncanonical Amino Acid Labeling in Vivo to Visualize and Affinity Purify Newly Synthesized Proteins in Larval Zebrafish

(2011) Flora I. Hinz et al.   ACS Chemical Neuroscience

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell 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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin

(2011) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) G. A. Brar et al.   SCIENCE

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons

(2010) Daniela C Dieterich et al.   NATURE NEUROSCIENCE

Correlations between RNA and protein expression profiles in 23 human cell lines

(2009) Marcus Gry et al.   BMC GENOMICS

SUnSET, a nonradioactive method to monitor protein synthesis

(2009) Enrico K Schmidt et al.   NATURE METHODS

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

(2009) N. T. Ingolia et al.   SCIENCE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE