RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

(2016) Alan Derr et al.   GENOME RESEARCH

A Neural Network Underlying Circadian Entrainment and Photoperiodic Adjustment of Sleep and Activity in Drosophila

(2016) M. Schlichting et al.   JOURNAL OF NEUROSCIENCE

Circadian neuron feedback controls the Drosophila sleep–activity profile

(2016) Fang Guo et al.   NATURE

Circadian rhythms in neuronal activity propagate through output circuits

(2016) Matthieu Cavey et al.   NATURE NEUROSCIENCE

Functional PDF Signaling in the Drosophila Circadian Neural Circuit Is Gated by Ral A-Dependent Modulation

(2016) Markus Klose et al.   NEURON

Memory-Relevant Mushroom Body Output Synapses Are Cholinergic

(2016) Oliver Barnstedt et al.   NEURON

Synchronous Drosophila circadian pacemakers display nonsynchronous Ca2+ rhythms in vivo

(2016) X. Liang et al.   SCIENCE

Acetylcholine from Visual Circuits Modulates the Activity of Arousal Neurons in Drosophila

(2015) N. I. Muraro et al.   JOURNAL OF NEUROSCIENCE

Erratum: Daytime spikes in dopaminergic activity drive rapid mood-cycling in mice

(2015) M M Sidor et al.   MOLECULAR PSYCHIATRY

Temporal transcriptomics suggest that twin-peaking genes reset the clock

(2015) William G Pembroke et al.   eLife

Identification of a Circadian Output Circuit for Rest:Activity Rhythms in Drosophila

(2014) Daniel J. Cavanaugh et al.   CELL

Calcitonin Gene-Related Peptide Neurons Mediate Sleep-Specific Circadian Output in Drosophila

(2014) Michael Kunst et al.   CURRENT BIOLOGY

Phosphorylation of the Transcription Activator CLOCK Regulates Progression through a ∼24-h Feedback Loop to Influence the Circadian Period inDrosophila

(2014) Guruswamy Mahesh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Studying circadian rhythms in Drosophila melanogaster

(2014) Ozgur Tataroglu et al.   METHODS

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

The Drosophila Circadian Clock Is a Variably Coupled Network of Multiple Peptidergic Units

(2014) Z. Yao et al.   SCIENCE

Dual PDF Signaling Pathways Reset Clocks Via TIMELESS and Acutely Excite Target Neurons to Control Circadian Behavior

(2014) Adam Seluzicki et al.   PLOS BIOLOGY

Differentially Timed Extracellular Signals Synchronize Pacemaker Neuron Clocks

(2014) Ben Collins et al.   PLOS BIOLOGY

NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes

(2013) Dan Ofer et al.   BIOINFORMATICS

cis -Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock

(2013) Antonio C.A. Meireles-Filho et al.   CURRENT BIOLOGY

Circadian timekeeping and output mechanisms in animals

(2013) Paul E Hardin et al.   CURRENT OPINION IN NEUROBIOLOGY

Short Neuropeptide F Is a Sleep-Promoting Inhibitory Modulator

(2013) Yuhua Shang et al.   NEURON

Nascent-Seq analysis ofDrosophilacycling gene expression

(2013) Joseph Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The Nuclear Receptor unfulfilled Is Required for Free-Running Clocks in Drosophila Pacemaker Neurons

(2012) Dirk Beuchle et al.   CURRENT BIOLOGY

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

(2012) M. E. Hughes et al.   GENOME RESEARCH

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Balance of Activity between LNvs and Glutamatergic Dorsal Clock Neurons Promotes Robust Circadian Rhythms in Drosophila

(2012) Ben Collins et al.   NEURON

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

Molecular Organization of Drosophila Neuroendocrine Cells by Dimmed

(2011) Dongkook Park et al.   CURRENT BIOLOGY

The novel gene twenty-four defines a critical translational step in the Drosophila clock

(2011) Chunghun Lim et al.   NATURE

Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine

(2011) Yuhua Shang et al.   NATURE NEUROSCIENCE

Cell autonomy and synchrony of suprachiasmatic nucleus circadian oscillators

(2011) Jennifer A. Mohawk et al.   TRENDS IN NEUROSCIENCES

Light and Temperature Control the Contribution of Specific DN1 Neurons to Drosophila Circadian Behavior

(2010) Yong Zhang et al.   CURRENT BIOLOGY

DN1p Circadian Neurons Coordinate Acute Light and PDF Inputs to Produce Robust Daily Behavior in Drosophila

(2010) Luoying Zhang et al.   CURRENT BIOLOGY

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

Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila

(2010) E. Kula-Eversole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Period Gene Expression in Four Neurons Is Sufficient for Rhythmic Activity of Drosophila melanogaster under Dim Light Conditions

(2009) Dirk Rieger et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Peptidergic clock neurons inDrosophila: Ion transport peptide and short neuropeptide F in subsets of dorsal and ventral lateral neurons

(2009) Helena A.D. Johard et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Endogenous Peptide Discovery of the Rat Circadian Clock

(2009) Ji Eun Lee et al.   MOLECULAR & CELLULAR PROTEOMICS

PDF-modulated visual inputs and cryptochrome define diurnal behavior in Drosophila

(2009) Paola Cusumano et al.   NATURE NEUROSCIENCE

Dissecting differential gene expression within the circadian neuronal circuit of Drosophila

(2009) Emi Nagoshi et al.   NATURE NEUROSCIENCE

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

(2009) Da Wei Huang et al.   Nature Protocols

CLOCK expression identifies developing circadian oscillator neurons in the brains of Drosophila embryos

(2008) Jerry H Houl et al.   BMC NEUROSCIENCE

Intrinsic neurons ofDrosophilamushroom bodies express short neuropeptide F: Relations to extrinsic neurons expressing different neurotransmitters

(2008) Helena A.D. Johard et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Cryptochrome is present in the compound eyes and a subset ofDrosophila's clock neurons

(2008) Taishi Yoshii et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Circadian Control of Membrane Excitability in Drosophila melanogaster Lateral Ventral Clock Neurons

(2008) G. Cao et al.   JOURNAL OF NEUROSCIENCE

PDF Cells Are a GABA-Responsive Wake-Promoting Component of the Drosophila Sleep Circuit

(2008) Katherine M. Parisky et al.   NEURON

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

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