The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

(2019) Franziska Brüning et al.   SCIENCE

VGLUT1 Binding to Endophilin or Intersectin1 and Dynamin Phosphorylation in a Diurnal Context

(2018) Karin Richter et al.   NEUROSCIENCE

Transcriptomic Analysis of Ribosome-Bound mRNA in Cortical NeuritesIn Vivo

(2017) Rebecca Ouwenga et al.   JOURNAL OF NEUROSCIENCE

Ultrastructural evidence for synaptic scaling across the wake/sleep cycle

(2017) Luisa de Vivo et al.   SCIENCE

Homer1a drives homeostatic scaling-down of excitatory synapses during sleep

(2017) Graham H. Diering et al.   SCIENCE

Circadian actin dynamics drive rhythmic fibroblast mobilization during wound healing

(2017) Nathaniel P. Hoyle et al.   Science Translational Medicine

Circadian Posttranscriptional Regulatory Mechanisms in Mammals

(2017) Carla B. Green   Cold Spring Harbor Perspectives in Biology

RNA localization is a key determinant of neurite-enriched proteome

(2017) Alessandra Zappulo et al.   Nature Communications

Separating the Contribution of Glucocorticoids and Wakefulness to the Molecular and Electrophysiological Correlates of Sleep Homeostasis

(2017) Valérie Mongrain et al.   SLEEP

Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness

(2016) Sandipan Ray et al.   BIOESSAYS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Life at Low Copy Number: How Dendrites Manage with So Few mRNAs

(2016) Kenneth S. Kosik   NEURON

Circadian rhythmicity of synapses in mouse somatosensory cortex

(2015) Malgorzata Jasinska et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Hippocampal spine changes across the sleep–wake cycle: corticosterone and kinases

(2015) Muneki Ikeda et al.   JOURNAL OF ENDOCRINOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

PERIOD1 coordinates hippocampal rhythms and memory processing with daytime

(2014) Oliver Rawashdeh et al.   HIPPOCAMPUS

Network-Mediated Encoding of Circadian Time: The Suprachiasmatic Nucleus (SCN) from Genes to Neurons to Circuits, and Back

(2014) M. Brancaccio et al.   JOURNAL OF NEUROSCIENCE

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sleep and the Price of Plasticity: From Synaptic and Cellular Homeostasis to Memory Consolidation and Integration

(2014) Giulio Tononi et al.   NEURON

Circadian rhythm modulates long-term potentiation induced at CA1 in rat hippocampal slices

(2014) Hiroki Nakatsuka et al.   NEUROSCIENCE RESEARCH

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

Unmasking the messenger

(2014) Saskia Hutten et al.   RNA Biology

Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience

(2014) Joshua A. Ainsley et al.   Nature Communications

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

The diurnal variation of performance of the novel location recognition task in male rats

(2013) Yoshiyuki Takahashi et al.   BEHAVIOURAL BRAIN RESEARCH

The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging

(2012) Iván J. Cajigas et al.   NEURON

Circadian Rhythm of Redox State Regulates Excitability in Suprachiasmatic Nucleus Neurons

(2012) T. A. Wang et al.   SCIENCE

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

(2012) J. Morf et al.   SCIENCE

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

(2012) N. Koike et al.   SCIENCE

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

(2011) D. Feng et al.   SCIENCE

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

The mammalian clock component PERIOD2 coordinates circadian output by interaction with nuclear receptors

(2010) I. Schmutz et al.   GENES & DEVELOPMENT

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

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

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

Temporal dynamics of mouse hippocampal clock gene expression support memory processing

(2009) Antje Jilg et al.   HIPPOCAMPUS

Nogo receptor 1 regulates formation of lasting memories

(2009) A. Karlen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor

(2008) H. Reinke et al.   GENES & DEVELOPMENT

Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study

(2008) Thomas Dange et al.   JOURNAL OF CELL BIOLOGY

Circadian oscillation of hippocampal MAPK activity and cAMP: implications for memory persistence

(2008) Kristin L Eckel-Mahan et al.   NATURE NEUROSCIENCE

A rapid Percoll gradient procedure for preparation of synaptosomes

(2008) Peter R Dunkley et al.   Nature Protocols