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

Rev-erb  and Rev-erb  coordinately protect the circadian clock and normal metabolic function

(2012) A. Bugge et al.   GENES & DEVELOPMENT

Clocks, Metabolism, and the Epigenome

(2012) Dan Feng et al.   MOLECULAR CELL

Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β

(2012) Han Cho et al.   NATURE

Feedback Regulation of Transcriptional Termination by the Mammalian Circadian Clock PERIOD Complex

(2012) K. Padmanabhan et al.   SCIENCE

Biochemical Analysis of the Canonical Model for the Mammalian Circadian Clock

(2011) Rui Ye et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Post-transcriptional control of circadian rhythms

(2011) S. Kojima et al.   JOURNAL OF CELL SCIENCE

Understanding systems-level properties: timely stories from the study of clocks

(2011) John B. Hogenesch et al.   NATURE REVIEWS GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2011) D. Feng et al.   SCIENCE

A Molecular Mechanism for Circadian Clock Negative Feedback

(2011) H. A. Duong 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

Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation

(2010) R. Yang et al.   BIOINFORMATICS

WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit

(2010) Dexter Duncan et al.   BMC BIOINFORMATICS

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Spotlight on post-transcriptional control in the circadian system

(2010) Dorothee Staiger et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Flexible phase adjustment of circadian albumin D site-binding protein (Dbp) gene expression by CRYPTOCHROME1

(2010) M. Stratmann et al.   GENES & DEVELOPMENT

Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA

(2010) J. S. Menet et al.   GENES & DEVELOPMENT

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

Coactivation of the CLOCK-BMAL1 complex by CBP mediates resetting of the circadian clock

(2010) Y. Lee et al.   JOURNAL OF CELL SCIENCE

Genome-Wide Profiling of the Core Clock Protein BMAL1 Targets Reveals a Strict Relationship with Metabolism

(2010) F. Hatanaka et al.   MOLECULAR AND CELLULAR BIOLOGY

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Plasticity and specificity of the circadian epigenome

(2010) Selma Masri et al.   NATURE NEUROSCIENCE

Deconstructing repression: evolving models of co-repressor action

(2010) Valentina Perissi et al.   NATURE REVIEWS GENETICS

The histone methyltransferase MLL1 permits the oscillation of circadian gene expression

(2010) Sayako Katada et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

(2009) Eric E. Zhang et al.   CELL

Rhythmic PER Abundance Defines a Critical Nodal Point for Negative Feedback within the Circadian Clock Mechanism

(2009) Rongmin Chen et al.   MOLECULAR CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

CBP/p300 is a cell type-specific modulator of CLOCK/BMAL1-mediated transcription

(2009) Hiroshi Hosoda et al.   Molecular Brain

Harmonics of Circadian Gene Transcription in Mammals

(2009) Michael E. Hughes et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY