Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Metabolic clock generates nutrient anticipation rhythms in mTOR signaling

(2016) Rohini V. Khapre et al.   Aging-US

BMAL1-dependent regulation of the mTOR signaling pathway delays aging

(2016) Rohini V. Khapre et al.   Aging-US

The race to decipher the top secrets of TOP mRNAs

(2015) Oded Meyuhas et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Time for Food: The Intimate Interplay between Nutrition, Metabolism, and the Circadian Clock

(2015) Gad Asher et al.   CELL

The Circadian Protein BMAL1 Regulates Translation in Response to S6K1-Mediated Phosphorylation

(2015) Jonathan O. Lipton et al.   CELL

Translational Tolerance of Mitochondrial Genes to Metabolic Energy Stress Involves TISU and eIF1-eIF4GI Cooperation in Start Codon Selection

(2015) Hadar Sinvani et al.   Cell Metabolism

Mitochondrial division and fusion in metabolism

(2015) Madhuparna Roy et al.   CURRENT OPINION IN CELL BIOLOGY

Circadian Metabolism in the Light of Evolution

(2015) Zachary Gerhart-Hines et al.   ENDOCRINE REVIEWS

Circadian timing of metabolism in animal models and humans

(2015) C. Dibner et al.   JOURNAL OF INTERNAL MEDICINE

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Interactive Features of Proteins Composing Eukaryotic Circadian Clocks

(2014) Brian R. Crane et al.   Annual Review of Biochemistry

Time-Restricted Feeding Is a Preventative and Therapeutic Intervention against Diverse Nutritional Challenges

(2014) Amandine Chaix et al.   Cell Metabolism

Circadian Clocks and Feeding Time Regulate the Oscillations and Levels of Hepatic Triglycerides

(2014) Yaarit Adamovich et al.   Cell Metabolism

Phosphorylation of Eukaryotic Translation Initiation Factor 4E and Eukaryotic Translation Initiation Factor 4E-binding Protein (4EBP) and Their Upstream Signaling Components Undergo Diurnal Oscillation in the Mouse Hippocampus

(2014) Amit Saraf et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome Biogenesis: Emerging Evidence for a Central Role in the Regulation of Skeletal Muscle Mass

(2014) Thomas Chaillou et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Mitochondrial dynamics in the central regulation of metabolism

(2014) Carole M. Nasrallah et al.   Nature Reviews Endocrinology

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

The Circadian Clock Maintains Cardiac Function by Regulating Mitochondrial Metabolism in Mice

(2014) Akira Kohsaka et al.   PLoS One

Hepatic mTORC1 controls locomotor activity, body temperature, and lipid metabolism through FGF21

(2014) M. Cornu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals

(2014) Federica Gilardi et al.   PLoS Genetics

MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale

(2014) Ngoc-Hien Du et al.   eLife

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

mTORC1 Controls Mitochondrial Activity and Biogenesis through 4E-BP-Dependent Translational Regulation

(2013) Masahiro Morita et al.   Cell Metabolism

Growth control and ribosomopathies

(2013) Teng Teng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

(2013) John L. Woolford et al.   GENETICS

Translational Redefinition of UGA Codons Is Regulated by Selenium Availability

(2013) Michael T. Howard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Translational Control of Entrainment and Synchrony of the Suprachiasmatic Circadian Clock by mTOR/4E-BP1 Signaling

(2013) Ruifeng Cao et al.   NEURON

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

(2013) D. Mauvoisin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian acetylome reveals regulation of mitochondrial metabolic pathways

(2013) Selma Masri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Clock NAD+ Cycle Drives Mitochondrial Oxidative Metabolism in Mice

(2013) C. B. Peek et al.   SCIENCE

The Circadian Clock Coordinates Ribosome Biogenesis

(2013) Céline Jouffe et al.   PLOS BIOLOGY

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet

(2012) Megumi Hatori et al.   Cell Metabolism

Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome

(2012) Christopher Vollmers et al.   Cell Metabolism

Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

(2012) S. Kojima et al.   GENES & DEVELOPMENT

A unifying model for mTORC1-mediated regulation of mRNA translation

(2012) Carson C. Thoreen et al.   NATURE

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

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Shift work and vascular events: systematic review and meta-analysis

(2012) M. V. Vyas et al.   BMJ-British Medical Journal

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Brain-Specific Rescue of Clock Reveals System-Driven Transcriptional Rhythms in Peripheral Tissue

(2012) Michael E. Hughes et al.   PLoS Genetics

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

Modulating protein activity and cellular function by methionine residue oxidation

(2011) Zong Jie Cui et al.   AMINO ACIDS

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

(2011) Nicholas T. Ingolia et al.   CELL

Circadian regulation of mammalian target of rapamycin signaling in the mouse suprachiasmatic nucleus

(2011) R. Cao et al.   NEUROSCIENCE

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

(2011) R. Yamashita et al.   NUCLEIC ACIDS RESEARCH

Unique translation initiation of mRNAs-containing TISU element

(2011) Rofa Elfakess et al.   NUCLEIC ACIDS RESEARCH

Circadian Clock-Coordinated 12 Hr Period Rhythmic Activation of the IRE1α Pathway Controls Lipid Metabolism in Mouse Liver

(2010) Gaspard Cretenet et al.   Cell Metabolism

Mammalian Target of Rapamycin Signaling Modulates Photic Entrainment of the Suprachiasmatic Circadian Clock

(2010) R. Cao et al.   JOURNAL OF NEUROSCIENCE

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

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

Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression

(2009) Christopher Vollmers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Control of the NAD+ Salvage Pathway by CLOCK-SIRT1

(2009) Y. Nakahata et al.   SCIENCE

AMPK Regulates the Circadian Clock by Cryptochrome Phosphorylation and Degradation

(2009) K. A. Lamia et al.   SCIENCE

Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD+ Biosynthesis

(2009) K. M. Ramsey et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

A Translation Initiation Element Specific to mRNAs with Very Short 5′UTR that Also Regulates Transcription

(2008) Rofa Elfakess et al.   PLoS One