Cycles in spatial and temporal chromosomal organization driven by the circadian clock

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

The circadian epigenome: how metabolism talks to chromatin remodeling

(2013) Lorena Aguilar-Arnal et al.   CURRENT OPINION IN CELL BIOLOGY

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Central and Peripheral Circadian Clocks in Mammals

(2012) Jennifer A. Mohawk et al.   Annual Review of Neuroscience

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

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

(2012) Christopher Vollmers et al.   Cell Metabolism

Revisiting higher-order and large-scale chromatin organization

(2012) Qian Bian et al.   CURRENT OPINION IN CELL BIOLOGY

Transcription factories: genetic programming in three dimensions

(2012) Lucas Brandon Edelman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation

(2012) O. Hakim et al.   GENOME RESEARCH

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

(2012) Markus Stratmann et al.   MOLECULAR CELL

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

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Circadian topology of metabolism

(2012) Joseph Bass   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Coordination of the transcriptome and metabolome by the circadian clock

(2012) K. L. Eckel-Mahan 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

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

(2011) Kenneth Daily et al.   BMC BIOINFORMATICS

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

On emerging nuclear order

(2011) Indika Rajapakse et al.   JOURNAL OF CELL BIOLOGY

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Histone Lysine Demethylase JARID1a Activates CLOCK-BMAL1 and Influences the Circadian Clock

(2011) L. DiTacchio 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

Circadian Control of Global Gene Expression Patterns

(2010) Colleen J. Doherty et al.   Annual Review of Genetics

PER2 Controls Lipid Metabolism by Direct Regulation of PPARγ

(2010) Benedetto Grimaldi et al.   Cell Metabolism

3D shortcuts to gene regulation

(2010) Ofir Hakim et al.   CURRENT OPINION IN CELL BIOLOGY

The transcriptional interactome: gene expression in 3D

(2010) Stefan Schoenfelder et al.   CURRENT OPINION IN GENETICS & 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

The histone methyltransferase MLL1 permits the oscillation of circadian gene expression

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

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

(2009) R. Nogales-Cadenas et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation

(2009) Tom Sexton et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

MotifMap: a human genome-wide map of candidate regulatory motif sites

(2008) Xiaohui Xie et al.   BIOINFORMATICS

The NAD+-Dependent Deacetylase SIRT1 Modulates CLOCK-Mediated Chromatin Remodeling and Circadian Control

(2008) Yasukazu Nakahata et al.   CELL

SIRT1 Regulates Circadian Clock Gene Expression through PER2 Deacetylation

(2008) Gad Asher et al.   CELL