The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain

Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions

(2018) Eugenio F. Fornasiero et al.   Nature Communications

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

(2017) Fangzhou Zhao et al.   NUCLEIC ACIDS RESEARCH

Sequence-based analysis of protein degradation rates

(2017) Miguel Correa Marrero et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cis -regulatory elements explain most of the mRNA stability variation across genes in yeast

(2017) Jun Cheng et al.   RNA

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Beyond the Triplet Code: Context Cues Transform Translation

(2016) Gloria A. Brar   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Codon usage affects the structure and function of theDrosophilacircadian clock protein PERIOD

(2016) Jingjing Fu et al.   GENES & DEVELOPMENT

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

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

(2016) Fredrik Edfors et al.   Molecular Systems Biology

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Proteome complexity and the forces that drive proteome imbalance

(2016) J. Wade Harper et al.   NATURE

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Role of mRNA structure in the control of protein folding

(2016) Guilhem Faure et al.   NUCLEIC ACIDS RESEARCH

Codon usage is an important determinant of gene expression levels largely through its effects on transcription

(2016) Zhipeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ribosome in action: Tuning of translational efficiency and protein folding

(2016) Marina V. Rodnina   PROTEIN SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system

(2016) Mainak Guharoy et al.   Nature Communications

A large dataset of protein dynamics in the mammalian heart proteome

(2016) Edward Lau et al.   Scientific Data

The Biology of Proteostasis in Aging and Disease

(2015) Johnathan Labbadia et al.   Annual Review of Biochemistry

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

(2015) Mian Zhou et al.   MOLECULAR MICROBIOLOGY

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

(2015) Rashi Halder et al.   NATURE NEUROSCIENCE

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations

(2015) Beena M. Kadakkuzha et al.   Frontiers in Cellular Neuroscience

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

(2015) Alessandro Ori et al.   Cell Systems

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Properties and determinants of codon decoding time distributions

(2014) Alexandra Dana et al.   BMC GENOMICS

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

Translational profiling through biotinylation of tagged ribosomes in zebrafish

(2014) M. P. Housley et al.   DEVELOPMENT

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

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

REST and stress resistance in ageing and Alzheimer’s disease

(2014) Tao Lu et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Effects of Codon Context on In Vivo Translation Speed

(2014) Fabienne F. V. Chevance et al.   PLoS Genetics

Lysine and Arginine Content of Proteins: Computational Analysis Suggests a New Tool for Solubility Design

(2013) Jim Warwicker et al.   MOLECULAR PHARMACEUTICS

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

Metabolic Turnover of Synaptic Proteins: Kinetics, Interdependencies and Implications for Synaptic Maintenance

(2013) Laurie D. Cohen et al.   PLoS One

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

(2013) S. Dvir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N-terminal Protein Processing: A Comparative Proteogenomic Analysis

(2012) Stefano Bonissone et al.   MOLECULAR & CELLULAR PROTEOMICS

The Effect of Long Term Calorie Restriction onin VivoHepatic Proteostatis: A Novel Combination of Dynamic and Quantitative Proteomics

(2012) John C. Price et al.   MOLECULAR & CELLULAR PROTEOMICS

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

Alpha-synuclein: from secretion to dysfunction and death

(2012) O Marques et al.   Cell Death & Disease

Proteome Scale Turnover Analysis in Live Animals Using Stable Isotope Metabolic Labeling

(2011) Yaoyang Zhang et al.   ANALYTICAL CHEMISTRY

Parkinson's Disease: Genetics and Pathogenesis

(2011) Joshua M. Shulman et al.   Annual Review of Pathology-Mechanisms of Disease

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The N-end rule pathway and regulation by proteolysis

(2011) Alexander Varshavsky   PROTEIN SCIENCE

Wobble base-pairing slows in vivo translation elongation in metazoans

(2011) M. Stadler et al.   RNA

Proteome Half-Life Dynamics in Living Human Cells

(2011) E. Eden et al.   SCIENCE

Protein N-Terminal Processing: Substrate Specificity ofEscherichia coliand Human Methionine Aminopeptidases

(2010) Qing Xiao et al.   BIOCHEMISTRY

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

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

(2010) Yedael Y. Waldman et al.   NUCLEIC ACIDS RESEARCH

Analysis of proteome dynamics in the mouse brain

(2010) J. C. Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

GC level and expression of human coding sequences

(2008) Stilianos Arhondakis et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Tools for analyzing and predicting N-terminal protein modifications

(2008) Thierry Meinnel et al.   PROTEOMICS