Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms

Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms

(2021) Benjamin D. Weger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Regulation of Adult Stem Cell Homeostasis and Aging

(2020) Salvador Aznar Benitah et al.   Cell Stem Cell

The hepatocyte clock and feeding control chronophysiology of multiple liver cell types

(2020) Dongyin Guan et al.   SCIENCE

Myokines mediate the cross talk between skeletal muscle and other organs

(2020) Wentao Chen et al.   JOURNAL OF CELLULAR PHYSIOLOGY

S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling

(2020) Carolina Magdalen Greco et al.   Science Advances

Mechanisms of Communication in the Mammalian Circadian Timing System

(2019) Mariana Astiz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Systems-based approaches for investigation of inter-tissue communication

(2019) Marcus M. Seldin et al.   JOURNAL OF LIPID RESEARCH

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

(2019) Joshua R. Beytebiere et al.   GENES & DEVELOPMENT

Oxygen and Carbon Dioxide Rhythms Are Circadian Clock Controlled and Differentially Directed by Behavioral Signals

(2019) Yaarit Adamovich et al.   Cell Metabolism

Insulin/IGF-1 Drives PERIOD Synthesis to Entrain Circadian Rhythms with Feeding Time

(2019) Priya Crosby et al.   CELL

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice

(2019) Ben J. Greenwell et al.   Cell Reports

Defining the Independence of the Liver Circadian Clock

(2019) Kevin B. Koronowski et al.   CELL

BMAL1-Driven Tissue Clocks Respond Independently to Light to Maintain Homeostasis

(2019) Patrick-Simon Welz et al.   CELL

Medicine in the Fourth Dimension

(2019) Christopher R. Cederroth et al.   Cell Metabolism

Cistromic Reprogramming of the Diurnal Glucocorticoid Hormone Response by High-Fat Diet

(2019) Fabiana Quagliarini et al.   MOLECULAR CELL

Loss of sirtuin 1 and mitofusin 2 contributes to enhanced ischemia/reperfusion injury in aged livers

(2018) Sung Kook Chun et al.   AGING CELL

A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism

(2018) Marcus M. Seldin et al.   Cell Metabolism

The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding

(2018) Giorgia Benegiamo et al.   Cell Metabolism

CircadiOmics: circadian omic web portal

(2018) Nicholas Ceglia et al.   NUCLEIC ACIDS RESEARCH

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

(2018) Jingkui Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disorders of mitochondrial long-chain fatty acid oxidation and the carnitine shuttle

(2018) Suzan J. G. Knottnerus et al.   REVIEWS IN ENDOCRINE & METABOLIC DISORDERS

A proteomics landscape of circadian clock in mouse liver

(2018) Yunzhi Wang et al.   Nature Communications

Regulation of circadian clock transcriptional output by CLOCK:BMAL1

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

Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks

(2018) Kenneth A. Dyar et al.   CELL

Time-Restricted Feeding Prevents Obesity and Metabolic Syndrome in Mice Lacking a Circadian Clock

(2018) Amandine Chaix et al.   Cell Metabolism

Deletion of Bmal1 Prevents Diet-Induced Ectopic Fat Accumulation by Controlling Oxidative Capacity in the Skeletal Muscle

(2018) Taira Wada et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock

(2018) Kenneth Allen Dyar et al.   PLOS BIOLOGY

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data

(2018) Jordan M. Singer et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Circadian blueprint of metabolic pathways in the brain

(2018) Carolina Magdalen Greco et al.   NATURE REVIEWS NEUROSCIENCE

Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks

(2018) Meng Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Guidelines for Genome-Scale Analysis of Biological Rhythms

(2017) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

A Metabolomic Signature of Acute Caloric Restriction

(2017) Tinh-Hai Collet et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Body Temperature Cycles Control Rhythmic Alternative Splicing in Mammals

(2017) Marco Preußner et al.   MOLECULAR CELL

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Circadian Metabolomics in Time and Space

(2017) Kenneth A. Dyar   Frontiers in Neuroscience

What time is it? Deep learning approaches for circadian rhythms

(2016) Forest Agostinelli et al.   BIOINFORMATICS

Peripheral circadian clocks are diversely affected by adrenalectomy

(2016) M. Soták et al.   CHRONOBIOLOGY INTERNATIONAL

Circadian Clock Control of Liver Metabolic Functions

(2016) Hans Reinke et al.   GASTROENTEROLOGY

Circadian and feeding cues integrate to drive rhythms of physiology in Drosophila insulin-producing cells

(2016) Annika F. Barber et al.   GENES & DEVELOPMENT

The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits

(2016) Aldons J. Lusis et al.   JOURNAL OF LIPID RESEARCH

Lipidomics Analyses Reveal Temporal and Spatial Lipid Organization and Uncover Daily Oscillations in Intracellular Organelles

(2016) Rona Aviram et al.   MOLECULAR CELL

Genomic footprinting

(2016) Jeff Vierstra et al.   NATURE METHODS

Insulin induction of SREBP-1c in rodent liver requires LXRα-C/EBPβ complex

(2016) Jing Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian physiology of metabolism

(2016) Satchidananda Panda   SCIENCE

Circadian time signatures of fitness and disease

(2016) Joseph Bass et al.   SCIENCE

Fatty acid oxidation and carnitine palmitoyltransferase I: emerging therapeutic targets in cancer

(2016) Q Qu et al.   Cell Death & Disease

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

(2016) Yehudit Hasin-Brumshtein et al.   eLife

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Genetic Architecture of Insulin Resistance in the Mouse

(2015) Brian W. Parks et al.   Cell Metabolism

Impairment of Circadian Rhythms in Peripheral Clocks by Constant Light Is Partially Reversed by Scheduled Feeding or Exercise

(2015) Yutaro Hamaguchi et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

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

Human skeletal myotubes display a cell-autonomous circadian clock implicated in basal myokine secretion

(2015) Laurent Perrin et al.   Molecular Metabolism

The Extracellular Redox State Modulates Mitochondrial Function, Gluconeogenesis, and Glycogen Synthesis in Murine Hepatocytes

(2015) Laura Nocito et al.   PLoS One

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Circadian Clocks and Feeding Time Regulate the Oscillations and Levels of Hepatic Triglycerides

(2014) Yaarit Adamovich et al.   Cell Metabolism

Effects of adrenalectomy on daily gene expression rhythms in the rat suprachiasmatic and paraventricular hypothalamic nuclei and in white adipose tissue

(2014) Yan Su et al.   CHRONOBIOLOGY INTERNATIONAL

The light-dark cycle controls peripheral rhythmicity in mice with a genetically ablated suprachiasmatic nucleus clock

(2014) Jana Husse et al.   FASEB JOURNAL

Differential effects of light and feeding on circadian organization of peripheral clocks in a forebrain Bmal1 mutant

(2014) Mariko Izumo et al.   eLife

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

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

(2013) Alan Gerber et al.   CELL

C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

(2013) Lars Grøntved et al.   EMBO JOURNAL

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

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

(2013) Kenneth A. Dyar et al.   Molecular Metabolism

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Obesity in mice with adipocyte-specific deletion of clock component Arntl

(2012) Georgios K Paschos et al.   NATURE MEDICINE

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics

(2012) Vishal R Patel et al.   NATURE METHODS

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2012) N. Koike et al.   SCIENCE

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA

(2011) Atanas Kamburov et al.   BIOINFORMATICS

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

(2011) Kenneth Daily et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Temporal orchestration of circadian autophagy rhythm by C/EBPβ

(2011) Di Ma et al.   EMBO JOURNAL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An intrinsic circadian clock of the pancreas is required for normal insulin release and glucose homeostasis in mice

(2010) L. A. Sadacca et al.   DIABETOLOGIA

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

Organization of GC/MS and LC/MS metabolomics data into chemical libraries

(2010) Corey D DeHaven et al.   Journal of Cheminformatics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Da Wei Huang et al.   Nature Protocols

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

Sympathetic input modulates, but does not determine, phase of peripheral circadian oscillators

(2008) Nina Vujović et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY