NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior

Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding

(2021) Stefano Berto et al.   NATURE NEUROSCIENCE

Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

(2020) Shao’ang Wen et al.   NATURE NEUROSCIENCE

MEF2C Hypofunction in Neuronal and Neuroimmune Populations Produces MEF2C Haploinsufficiency Syndrome–like Behaviors in Mice

(2020) Adam J. Harrington et al.   BIOLOGICAL PSYCHIATRY

A noncanonical inhibitory circuit dampens behavioral sensitivity to light

(2020) Takuma Sonoda et al.   SCIENCE

Cell-autonomous clock of astrocytes drives circadian behavior in mammals

(2019) Marco Brancaccio et al.   SCIENCE

ARNT2 Tunes Activity-Dependent Gene Expression through NCoR2-Mediated Repression and NPAS4-Mediated Activation

(2019) Nikhil Sharma et al.   NEURON

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

(2019) G. Stefano Brigidi et al.   CELL

Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors

(2019) Shahriyar P. Majidi et al.   Cell Reports

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Generation of circadian rhythms in the suprachiasmatic nucleus

(2018) Michael H. Hastings et al.   NATURE REVIEWS NEUROSCIENCE

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

(2018) Jingkui Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SCN VIP Neurons Are Essential for Normal Light-Mediated Resetting of the Circadian System

(2018) Jeff R. Jones et al.   JOURNAL OF NEUROSCIENCE

The dynamics of GABA signaling: Revelations from the circadian pacemaker in the suprachiasmatic nucleus

(2017) H. Elliott Albers et al.   FRONTIERS IN NEUROENDOCRINOLOGY

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

A molecular census of arcuate hypothalamus and median eminence cell types

(2017) John N Campbell et al.   NATURE NEUROSCIENCE

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

(2017) Sinisa Hrvatin et al.   NATURE NEUROSCIENCE

Astrocytes Control Circadian Timekeeping in the Suprachiasmatic Nucleus via Glutamatergic Signaling

(2017) Marco Brancaccio et al.   NEURON

Membrane Currents, Gene Expression, and Circadian Clocks

(2017) Charles N. Allen et al.   Cold Spring Harbor Perspectives in Biology

Manipulating the Cellular Circadian Period of Arginine Vasopressin Neurons Alters the Behavioral Circadian Period

(2016) Michihiro Mieda et al.   CURRENT BIOLOGY

Sensory experience regulates cortical inhibition by inducing IGF1 in VIP neurons

(2016) A. R. Mardinly et al.   NATURE

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Architecture of retinal projections to the central circadian pacemaker

(2016) Diego Carlos Fernandez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks Involved in the Central Circadian Clock

(2016) James Park et al.   Frontiers in Neuroscience

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

FoxP1 orchestration of ASD-relevant signaling pathways in the striatum

(2015) Daniel J. Araujo et al.   GENES & DEVELOPMENT

GABA-mediated repulsive coupling between circadian clock neurons in the SCN encodes seasonal time

(2015) Jihwan Myung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) S. Anders et al.   BIOINFORMATICS

Npas4 Regulates Excitatory-Inhibitory Balance within Neural Circuits through Cell-Type-Specific Gene Programs

(2014) Ivo Spiegel et al.   CELL

Light as a central modulator of circadian rhythms, sleep and affect

(2014) Tara A. LeGates et al.   NATURE REVIEWS NEUROSCIENCE

Sensory-Related Neural Activity Regulates the Structure of Vascular Networks in the Cerebral Cortex

(2014) Baptiste Lacoste et al.   NEURON

Neuronal Activity Promotes Oligodendrogenesis and Adaptive Myelination in the Mammalian Brain

(2014) E. M. Gibson et al.   SCIENCE

Lhx1 maintains synchrony among circadian oscillator neurons of the SCN

(2014) Megumi Hatori et al.   eLife

Differential effects of light and feeding on circadian organization of peripheral clocks in a forebrain Bmal1 mutant

(2014) Mariko Izumo et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Wavelet Meets Actogram

(2013) Tanya L. Leise et al.   JOURNAL OF BIOLOGICAL RHYTHMS

The activity-dependent transcription factor NPAS4 regulates domain-specific inhibition

(2013) Brenda L. Bloodgood et al.   NATURE

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Neuroanatomy of the extended circadian rhythm system

(2012) Lawrence P. Morin   EXPERIMENTAL NEUROLOGY

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

(2012) N. Koike et al.   SCIENCE

Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR

(2011) Nan Hao et al.   NUCLEIC ACIDS RESEARCH

Npas4 Regulates a Transcriptional Program in CA3 Required for Contextual Memory Formation

(2011) K. Ramamoorthi et al.   SCIENCE

Suprachiasmatic Nucleus: Cell Autonomy and Network Properties

(2010) David K. Welsh et al.   Annual Review of Physiology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Physiology of Circadian Entrainment

(2010) Diego A. Golombek et al.   PHYSIOLOGICAL REVIEWS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Identification of plasticity-associated genes regulated by Pavlovian fear conditioning in the lateral amygdala

(2009) Jonathan E. Ploski et al.   JOURNAL OF NEUROCHEMISTRY

Casein Kinase 1 Delta Regulates the Pace of the Mammalian Circadian Clock

(2009) J.-P. Etchegaray et al.   MOLECULAR AND CELLULAR BIOLOGY

Temporal patterns of light-induced immediate-early gene expression in the suprachiasmatic nucleus

(2009) Veronica M. Porterfield et al.   NEUROSCIENCE LETTERS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Melanopsin cells are the principal conduits for rod–cone input to non-image-forming vision

(2008) Ali D. Güler et al.   NATURE

Activity-dependent regulation of inhibitory synapse development by Npas4

(2008) Yingxi Lin et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Setting Clock Speed in Mammals: The CK1ɛ tau Mutation in Mice Accelerates Circadian Pacemakers by Selectively Destabilizing PERIOD Proteins

(2008) Qing-Jun Meng et al.   NEURON

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY