Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Evolution of Gene Regulation during Transcription and Translation

(2015) Zhe Wang et al.   Genome Biology and Evolution

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

Multidimensional proteomics for cell biology

(2015) Mark Larance et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

The utility of protein and mRNA correlation

(2015) Samuel H. Payne   TRENDS IN BIOCHEMICAL SCIENCES

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

(2014) M. Stoeckius et al.   EMBO JOURNAL

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

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

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

Coupling mRNA Synthesis and Decay

(2014) K. A. Braun et al.   MOLECULAR AND CELLULAR BIOLOGY

One third of dynamic protein expression profiles can be predicted by a simple rate equation

(2014) Konstantine Tchourine et al.   Molecular BioSystems

Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast

(2014) Brian M. Zid et al.   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

Determination of in vivo RNA kinetics using RATE-seq

(2014) Benjamin Neymotin et al.   RNA

Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe

(2014) Romain Christiano et al.   Cell Reports

Conservation of mRNA and Protein Expression during Development of C. elegans

(2014) Dominic Grün et al.   Cell Reports

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

(2014) Jenna E. Smith et al.   Cell Reports

The Not5 Subunit of the Ccr4-Not Complex Connects Transcription and Translation

(2014) Zoltan Villanyi et al.   PLoS Genetics

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

Genetic Influences on Translation in Yeast

(2014) Frank W. Albert et al.   PLoS Genetics

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

(2014) Tony Ly et al.   eLife

Evidence for the biogenesis of more than 1,000 novel human microRNAs

(2014) Marc R Friedländer et al.   GENOME BIOLOGY

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

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

(2013) Mitchell Guttman et al.   CELL

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

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

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

(2013) C. J. McManus et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

PECA: A Novel Statistical Tool for Deconvoluting Time-Dependent Gene Expression Regulation

(2013) Guoshou Teo et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Protein Expression Under Pressure

(2013) C. Vogel   SCIENCE

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Global Subcellular Characterization of Protein Degradation Using Quantitative Proteomics

(2012) Mark Larance et al.   MOLECULAR & CELLULAR PROTEOMICS

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells

(2012) Iván Ventoso et al.   PLoS One

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais 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

Widespread promoter-mediated coordination of transcription and mRNA degradation

(2012) Mally Dori-Bachash 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

Systems-wide Proteomic Analysis in Mammalian Cells Reveals Conserved, Functional Protein Turnover

(2011) Sidney B. Cambridge et al.   JOURNAL OF PROTEOME RESEARCH

Protein Expression Regulation under Oxidative Stress

(2011) Christine Vogel 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

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

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

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

(2011) Anagha Joshi et al.   NUCLEIC ACIDS RESEARCH

A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms

(2011) Sri Priya Ponnapalli et al.   PLoS One

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

(2011) G. A. Brar et al.   SCIENCE

Regulatory mechanisms and networks couple the different phases of gene expression

(2011) Orna Dahan et al.   TRENDS IN GENETICS

Coupled Evolution of Transcription and mRNA Degradation

(2011) Mally Dori-Bachash et al.   PLOS BIOLOGY

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

Transcriptional regulation is only half the story

(2010) Joshua B Plotkin   Molecular Systems Biology

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

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano et al.   PLoS One

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

Protein abundances are more conserved than mRNA abundances across diverse taxa

(2010) Jon M. Laurent et al.   PROTEOMICS

The emerging complexity of protein ubiquitination

(2009) David Komander   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Breaking the chains: structure and function of the deubiquitinases

(2009) David Komander et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

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

(2009) N. T. Ingolia et al.   SCIENCE

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

(2008) Mary K. Doherty et al.   JOURNAL OF PROTEOME RESEARCH

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

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Global Protein Stability Profiling in Mammalian Cells

(2008) H.-C. S. Yen et al.   SCIENCE

The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast

(2007) Vicent Pelechano et al.   YEAST