The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons

Viral Nucleases Induce an mRNA Degradation-Transcription Feedback Loop in Mammalian Cells

(2015) Emma Abernathy et al.   Cell Host & Microbe

Connecting growth with gene expression: of noise and numbers

(2015) Vahid Shahrezaei et al.   CURRENT OPINION IN MICROBIOLOGY

Noise in gene expression is coupled to growth rate

(2015) Leeat Keren et al.   GENOME RESEARCH

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

(2015) Chien-Der Lee et al.   Cell Reports

Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts

(2015) Ophelia S. Venturelli et al.   PLOS BIOLOGY

Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff

(2015) Jue Wang et al.   PLOS BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Why, when, and how did yeast evolve alcoholic fermentation?

(2014) Sofia Dashko et al.   FEMS YEAST RESEARCH

The Switch from Fermentation to Respiration in Saccharomyces cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor

(2014) N. Gasmi et al.   GENETICS

Selection of non-Saccharomyces yeast strains for reducing alcohol levels in wine by sugar respiration

(2014) Manuel Quirós et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

A Role for the Mitochondrial Pyruvate Carrier as a Repressor of the Warburg Effect and Colon Cancer Cell Growth

(2014) John C. Schell et al.   MOLECULAR CELL

Cell cycle population effects in perturbation studies

(2014) E. O'Duibhir et al.   Molecular Systems Biology

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

(2014) I. Gupta et al.   Molecular Systems Biology

Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression

(2014) P. Eser et al.   Molecular Systems Biology

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

Flow Cytometry of Microencapsulated Colonies for Genetics Analysis of Filamentous Fungi

(2014) Lidia Delgado-Ramos et al.   G3-Genes Genomes Genetics

What do you mean by transcription rate?

(2013) José E. Pérez-Ortín et al.   BIOESSAYS

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

Eukaryotic mRNA Decay: Methodologies, Pathways, and Links to Other Stages of Gene Expression

(2013) José E. Pérez-Ortín et al.   JOURNAL OF MOLECULAR BIOLOGY

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

Carbon source-dependent alteration of Puf3p activity mediates rapid changes in the stabilities of mRNAs involved in mitochondrial function

(2013) Melanie A. Miller et al.   NUCLEIC ACIDS RESEARCH

Genetic Determinants of Cell Size at Birth and Their Impact on Cell Cycle Progression in Saccharomyces cerevisiae

(2013) Sandra K. Truong et al.   G3-Genes Genomes Genetics

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

(2012) Nikolai Slavov et al.   MOLECULAR BIOLOGY OF THE CELL

Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression

(2012) Nikolai Slavov et al.   MOLECULAR BIOLOGY OF THE CELL

TFIIS is required for the balanced expression of the genes encoding ribosomal components under transcriptional stress

(2012) Fernando Gómez-Herreros et al.   NUCLEIC ACIDS RESEARCH

Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

(2012) Sasha F. Levy et al.   PLOS BIOLOGY

Genome-wide studies of mRNA synthesis and degradation in eukaryotes

(2011) José E. Pérez-Ortín et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast

(2011) Nikolai Slavov et al.   MOLECULAR BIOLOGY OF THE CELL

Heat Shock Response in Yeast Involves Changes in Both Transcription Rates and mRNA Stabilities

(2011) Laia Castells-Roca et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

(2011) Ophir Shalem et al.   PLoS Genetics

The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression

(2010) Rodrigo Diaz-Ruiz et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Adaptive index models for marker-based risk stratification

(2010) L. Tian et al.   BIOSTATISTICS

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

(2010) Daniel P. Riordan et al.   NUCLEIC ACIDS RESEARCH

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano et al.   PLoS One

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

There is a steady-state transcriptome in exponentially growing yeast cells

(2010) Vicent Pelechano et al.   YEAST

Control of Transcription by Cell Size

(2010) Chia-Yung Wu et al.   PLOS BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress

(2009) C. Molin et al.   RNA

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Predicting Cellular Growth from Gene Expression Signatures

(2009) Edoardo M. Airoldi et al.   PLoS Computational Biology

Regulon-Specific Control of Transcription Elongation across the Yeast Genome

(2009) Vicent Pelechano et al.   PLoS Genetics

Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast

(2008) María Micaela Molina-Navarro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Slow Growth Induces Heat-Shock Resistance in Normal and Respiratory-deficient Yeast

(2008) Charles Lu et al.   MOLECULAR BIOLOGY OF THE CELL

A Generic Mechanism for Adaptive Growth Rate Regulation

(2008) Chikara Furusawa et al.   PLoS Computational Biology

Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization

(2008) Yann Saint-Georges et al.   PLoS One

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL