Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain

Generation of circadian rhythms in the suprachiasmatic nucleus

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

Regulation of circadian clock transcriptional output by CLOCK:BMAL1

(2018) Alexandra J. Trott et al.   PLoS Genetics

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

(2017) Jake Yeung et al.   GENOME RESEARCH

Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity

(2017) Ying Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles for circadian orchestration of metabolic pathways

(2017) Kevin Thurley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

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

(2017) Katharine C. Abruzzi et al.   PLoS Genetics

Neurobiology of Monarch Butterfly Migration

(2016) Steven M. Reppert et al.   Annual Review of Entomology

Differential rhythmicity: detecting altered rhythmicity in biological data

(2016) Paul F. Thaben et al.   BIOINFORMATICS

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

(2016) Gang Wu et al.   BIOINFORMATICS

Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis

(2016) Matthew J. Markert et al.   G3-Genes Genomes Genetics

Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora

(2015) Cigdem Sancar et al.   BMC BIOLOGY

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Glial Glycolysis Is Essential for Neuronal Survival in Drosophila

(2015) Anne Volkenhoff et al.   Cell Metabolism

The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing

(2015) O. Bartok et al.   EMBO JOURNAL

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

CLOCK:BMAL1 is a pioneer-like transcription factor

(2014) J. S. Menet et al.   GENES & DEVELOPMENT

Detecting Rhythms in Time Series with RAIN

(2014) Paul F. Thaben et al.   JOURNAL OF BIOLOGICAL RHYTHMS

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

Extensive circadian and light regulation of the transcriptome in the malaria mosquito Anopheles gambiae

(2013) Samuel SC Rund et al.   BMC GENOMICS

Coldness Triggers Northward Flight in Remigrant Monarch Butterflies

(2013) Patrick A. Guerra et al.   CURRENT BIOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

The Antarctic Krill Euphausia superba Shows Diurnal Cycles of Transcription under Natural Conditions

(2013) Cristiano De Pittà et al.   PLoS One

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

An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection

(2012) Xingbin Wang et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Christopher Vollmers et al.   Cell Metabolism

Deleterious effects of neuronal accumulation of glycogen in flies and mice

(2012) Jordi Duran et al.   EMBO Molecular Medicine

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

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

Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases

(2012) C. Merlin et al.   GENOME RESEARCH

Reciprocal cholinergic and GABAergic modulation of the small ventrolateral pacemaker neurons of Drosophila's circadian clock neuron network

(2012) Katherine R. Lelito et al.   JOURNAL OF NEUROPHYSIOLOGY

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Acetylcholine as a Neuromodulator: Cholinergic Signaling Shapes Nervous System Function and Behavior

(2012) Marina R. Picciotto et al.   NEURON

MonarchBase: the monarch butterfly genome database

(2012) Shuai Zhan et al.   NUCLEIC ACIDS RESEARCH

bHLH-PAS heterodimer of methoprene-tolerant and Cycle mediates circadian expression of juvenile hormone-induced mosquito genes

(2012) S. W. Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) N. Koike et al.   SCIENCE

Discordant timing between antennae disrupts sun compass orientation in migratory monarch butterflies

(2012) Patrick A. Guerra et al.   Nature Communications

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

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

Crosstalk between Components of Circadian and Metabolic Cycles in Mammals

(2011) Gad Asher et al.   Cell Metabolism

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Sun Compass Integration of Skylight Cues in Migratory Monarch Butterflies

(2011) Stanley Heinze et al.   NEURON

Genome-wide profiling of diel and circadian gene expression in the malaria vectorAnopheles gambiae

(2011) Samuel S. C. Rund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Drosophila Pacemaker Neurons Require G Protein Signaling and GABAergic Inputs to Generate Twenty-Four Hour Behavioral Rhythms

(2010) David Dahdal et al.   NEURON

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

Navigational mechanisms of migrating monarch butterflies

(2010) Steven M. Reppert et al.   TRENDS IN NEUROSCIENCES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Antennal Circadian Clocks Coordinate Sun Compass Orientation in Migratory Monarch Butterflies

(2009) C. Merlin et al.   SCIENCE

The Meter of Metabolism

(2008) Carla B. Green et al.   CELL

The Clockwork Orange Drosophila Protein Functions as Both an Activator and a Repressor of Clock Gene Expression

(2008) Benjamin Richier et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Cryptochromes Define a Novel Circadian Clock Mechanism in Monarch Butterflies That May Underlie Sun Compass Navigation

(2008) Haisun Zhu et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY