Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Linking Core Promoter Classes to Circadian Transcription

(2016) Pål O. Westermark   PLoS Genetics

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

(2015) Florian Atger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

CREB and FoxO1: two transcription factors for the regulation of hepatic gluconeogenesis

(2014) Kyoung-Jin Oh et al.   BMB Reports

Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae

(2014) Lorena Magraner-Pardo et al.   BMC GENOMICS

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

CLOCK:BMAL1 is a pioneer-like transcription factor

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

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

(2014) Galip Gürkan Yardımcı et al.   NUCLEIC ACIDS RESEARCH

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

(2014) Fabrice P. A. David et al.   PLoS One

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals

(2014) Federica Gilardi et al.   PLoS Genetics

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver

(2013) Logan J Everett et al.   BMC GENOMICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Blood-Borne Circadian Signal Stimulates Daily Oscillations in Actin Dynamics and SRF Activity

(2013) Alan Gerber et al.   CELL

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He 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

Glucocorticoid-mediated Period2 induction delays the phase of circadian rhythm

(2013) Solmi Cheon et al.   NUCLEIC ACIDS RESEARCH

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

(2013) D. Mauvoisin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Circadian Clock Coordinates Ribosome Biogenesis

(2013) Céline Jouffe et al.   PLOS BIOLOGY

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice

(2013) Kazuhiro Shimomura et al.   eLife

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

(2012) Christopher Vollmers et al.   Cell Metabolism

Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA

(2012) Zixi Wang et al.   CELL RESEARCH

Simulated body temperature rhythms reveal the phase-shifting behavior and plasticity of mammalian circadian oscillators

(2012) C. Saini et al.   GENES & DEVELOPMENT

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

(2012) Housheng Hansen He et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

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

(2012) Han Cho et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Genome-wide analysis of FoxO1 binding in hepatic chromatin: Potential involvement of FoxO1 in linking retinoid signaling to hepatic gluconeogenesis

(2012) Dong-Ju Shin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) N. Koike et al.   SCIENCE

Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex

(2012) N. Huang 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

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function

(2011) Maki Ukai-Tadenuma et al.   CELL

FoxO6 Integrates Insulin Signaling With Gluconeogenesis in the Liver

(2011) Dae Hyun Kim et al.   DIABETES

Transcription factors and coactivators controlling nutrient and hormonal regulation of hepatic gluconeogenesis

(2011) Sarawut Jitrapakdee   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

The Mammalian Circadian Timing System: Organization and Coordination of Central and Peripheral Clocks

(2010) Charna Dibner et al.   Annual Review of Physiology

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Characterization of the Core Mammalian Clock Component, NPAS2, as a REV-ERBα/RORα Target Gene

(2010) Christine Crumbley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional Repressor E4-binding Protein 4 (E4BP4) Regulates Metabolic Hormone Fibroblast Growth Factor 21 (FGF21) during Circadian Cycles and Feeding

(2010) Xin Tong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cryptochrome mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis

(2010) Eric E Zhang et al.   NATURE MEDICINE

The Fox Genes in the Liver: From Organogenesis to Functional Integration

(2010) John Le lay et al.   PHYSIOLOGICAL REVIEWS

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

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

(2010) Kenzie D. MacIsaac et al.   PLoS Computational Biology

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin 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

Regulation of Clock-Controlled Genes in Mammals

(2009) Katarzyna Bozek et al.   PLoS One

Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression

(2009) Christopher Vollmers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

REV-ERBα Participates in Circadian SREBP Signaling and Bile Acid Homeostasis

(2009) Gwendal Le Martelot et al.   PLOS BIOLOGY

A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes

(2008) Yasukazu Nakahata et al.   BMC MOLECULAR BIOLOGY

The Meter of Metabolism

(2008) Carla B. Green et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Inactivation of Hepatic Foxo1 by Insulin Signaling Is Required for Adaptive Nutrient Homeostasis and Endocrine Growth Regulation

(2008) Xiaocheng C. Dong et al.   Cell Metabolism

Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor

(2008) H. Reinke et al.   GENES & DEVELOPMENT

Glucocorticoids and the circadian clock

(2008) Thomas Dickmeis   JOURNAL OF ENDOCRINOLOGY

Evidence for an Overlapping Role of CLOCK and NPAS2 Transcription Factors in Liver Circadian Oscillators

(2008) C. Bertolucci et al.   MOLECULAR AND CELLULAR BIOLOGY

Modeling an Evolutionary Conserved Circadian Cis-Element

(2008) Eric R. Paquet et al.   PLoS Computational Biology

Physiological significance of a peripheral tissue circadian clock

(2008) K. A. Lamia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Occupancy of SREBP1 and Its Partners NFY and SP1 Reveals Novel Functional Roles and Combinatorial Regulation of Distinct Classes of Genes

(2008) Brian D. Reed et al.   PLoS Genetics

Redundant Function of REV-ERBα and β and Non-Essential Role for Bmal1 Cycling in Transcriptional Regulation of Intracellular Circadian Rhythms

(2008) Andrew C. Liu et al.   PLoS Genetics