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

Cell-autonomous clock of astrocytes drives circadian behavior in mammals

(2019) Marco Brancaccio et al.   SCIENCE

SOX2-Dependent Transcription in Clock Neurons Promotes the Robustness of the Central Circadian Pacemaker

(2019) Arthur H. Cheng et al.   Cell Reports

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Generation of circadian rhythms in the suprachiasmatic nucleus

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

Entrainment of Circadian Rhythms Depends on Firing Rates and Neuropeptide Release of VIP SCN Neurons

(2018) Cristina Mazuski et al.   NEURON

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Astrocytes Control Circadian Timekeeping in the Suprachiasmatic Nucleus via Glutamatergic Signaling

(2017) Marco Brancaccio et al.   NEURON

Astrocyte deletion of Bmal1 alters daily locomotor activity and cognitive functions via GABA signalling

(2017) Olga Barca-Mayo et al.   Nature Communications

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

MetaCycle: an integrated R package to evaluate periodicity in large scale data

(2016) Gang Wu et al.   BIOINFORMATICS

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes

(2016) Roman A Romanov et al.   NATURE NEUROSCIENCE

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

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Neuromedin S-Producing Neurons Act as Essential Pacemakers in the Suprachiasmatic Nucleus to Couple Clock Neurons and Dictate Circadian Rhythms

(2015) Ivan T. Lee et al.   NEURON

Cellular Clocks in AVP Neurons of the SCN Are Critical for Interneuronal Coupling Regulating Circadian Behavior Rhythm

(2015) Michihiro Mieda et al.   NEURON

Scalable and DiI-compatible optical clearance of the mammalian brain

(2015) Bing Hou et al.   Frontiers in Neuroanatomy

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

(2014) Raju Tomer et al.   Nature Protocols

The Nuclear Receptor REV-ERBα Regulates Fabp7 and Modulates Adult Hippocampal Neurogenesis

(2014) Anna Schnell et al.   PLoS One

Lhx1 maintains synchrony among circadian oscillator neurons of the SCN

(2014) Megumi Hatori et al.   eLife

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Quantitative Analysis of Phase Wave of Gene Expression in the Mammalian Central Circadian Clock Network

(2011) Hirokazu Fukuda et al.   PLoS One

Suprachiasmatic Nucleus: Cell Autonomy and Network Properties

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

Cholecystokinin (CCK)-expressing neurons in the suprachiasmatic nucleus: innervation, light responsiveness and entrainment in CCK-deficient mice

(2010) Jens Hannibal et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

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

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

(2008) Jun Yan et al.   PLoS Computational Biology