Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication.

(2021) Manas R. Prusty et al.   NEW PHYTOLOGIST

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

(2021) Gareth Steed et al.   SCIENCE

Plant metabolism paves the way for breeding crops with high nutritional value and stable yield

(2021) Cheng Jin et al.   Science China-Life Sciences

Rice functional genomics: decades’ efforts and roads ahead

(2021) Rongzhi Chen et al.   Science China-Life Sciences

A UV-B-responsive glycosyltransferase, OsUGT706C2, modulates flavonoid metabolism in rice

(2020) Feng Zhang et al.   Science China-Life Sciences

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Natural variation in the OsbZIP18 promoter contributes to branched‐chain amino acid levels in rice

(2020) Yangyang Sun et al.   NEW PHYTOLOGIST

Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing

(2020) Fang Wang et al.   PLANT CELL

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

(2019) Camilla Ferrari et al.   Nature Communications

Continuous dynamic adjustment of the plant circadian oscillator

(2019) Alex A. R. Webb et al.   Nature Communications

Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings

(2019) R. Glen Uhrig et al.   PLANT JOURNAL

Public-transcriptome-database-assisted selection and validation of reliable reference genes for qRT-PCR in rice

(2019) Zhe Zhao et al.   Science China-Life Sciences

Metabolite-mediated TOR signaling regulates the circadian clock inArabidopsis

(2019) Nan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

(2018) Daniel D Seaton et al.   Molecular Systems Biology

3′-Phosphoadenosine 5′-Phosphate Accumulation Delays the Circadian System

(2018) Suzanne Litthauer et al.   PLANT PHYSIOLOGY

Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions

(2018) Akiva Shalit-Kaneh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Kenneth A. Dyar et al.   CELL

Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment

(2018) Maria Grazia Annunziata et al.   JOURNAL OF EXPERIMENTAL BOTANY

Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets

(2018) Sally Adams et al.   NEW PHYTOLOGIST

OsTSD2 ‐mediated cell wall modification affects ion homeostasis and salt tolerance

(2018) Chuanying Fang et al.   PLANT CELL AND ENVIRONMENT

Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways

(2018) Jennifer M. Hurley et al.   Cell Systems

The Importance of the Circadian Clock in Regulating Plant Metabolism

(2017) Jin Kim et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Jasmonate regulates leaf senescence and tolerance to cold stress: crosstalk with other phytohormones

(2017) Yanru Hu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Parallel analysis ofArabidopsiscircadian clock mutants reveals different scales of transcriptome and proteome regulation

(2017) Alexander Graf et al.   Open Biology

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

(2017) Kathleen Greenham et al.   eLife

The Pentose Phosphate Pathway Regulates the Circadian Clock

(2016) Guillaume Rey et al.   Cell Metabolism

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MBROLE 2.0—functional enrichment of chemical compounds

(2016) Javier López-Ibáñez et al.   NUCLEIC ACIDS RESEARCH

Circadian clock regulation of mRNA translation through eukaryotic elongation factor eEF-2

(2016) Stephen Z. Caster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MYB96 shapes the circadian gating of ABA signaling in Arabidopsis

(2016) Hong Gil Lee et al.   Scientific Reports

Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids

(2016) Dae Kwan Ko et al.   PLoS Genetics

Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light–Dark Conditions

(2016) Takanobu Higashi et al.   Frontiers in Plant Science

Circadian Clock Control by Polyamine Levels through a Mechanism that Declines with Age

(2015) Ziv Zwighaft et al.   Cell Metabolism

Metabolite-based genome-wide association studies in plants

(2015) Jie Luo   CURRENT OPINION IN PLANT BIOLOGY

Circadian Clock Genes Universally Control Key Agricultural Traits

(2015) Claire Bendix et al.   Molecular Plant

Domestication selected for deceleration of the circadian clock in cultivated tomato

(2015) Niels A Müller et al.   NATURE GENETICS

Integrating circadian dynamics with physiological processes in plants

(2015) Kathleen Greenham et al.   NATURE REVIEWS GENETICS

The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading

(2015) Anamika Missra et al.   PLANT CELL

Punctual Transcriptional Regulation by the Rice Circadian Clock under Fluctuating Field Conditions

(2015) Jun Matsuzaki et al.   PLANT CELL

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

(2015) Dawn H. Nagel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural variation in transcriptional rhythms modulates photoperiodic responses

(2015) Akane Kubota et al.   TRENDS IN PLANT SCIENCE

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

(2014) Amaury de Montaigu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism

(2014) Maria S. Robles et al.   PLoS Genetics

Circadian Redox Signaling in Plant Immunity and Abiotic Stress

(2013) Steven H. Spoel et al.   ANTIOXIDANTS & REDOX SIGNALING

The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns

(2013) R. Noguchi et al.   Molecular Systems Biology

Photosynthetic entrainment of the Arabidopsis thaliana circadian clock

(2013) Michael J. Haydon et al.   NATURE

Metabolism and the Circadian Clock Converge

(2013) Kristin Eckel-Mahan et al.   PHYSIOLOGICAL REVIEWS

Jasmonate Regulates the INDUCER OF CBF EXPRESSION-C-REPEAT BINDING FACTOR/DRE BINDING FACTOR1 Cascade and Freezing Tolerance in Arabidopsis

(2013) Y. Hu et al.   PLANT CELL

The interactions between the circadian clock and primary metabolism

(2012) Eva M Farré et al.   CURRENT OPINION IN PLANT BIOLOGY

Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci

(2012) Hae-Ryong Song et al.   MOLECULES AND CELLS

Peroxiredoxins are conserved markers of circadian rhythms

(2012) Rachel S. Edgar et al.   NATURE

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

(2012) A. R. Fernie et al.   PLANT PHYSIOLOGY

Proteomic identification of rhythmic proteins in rice seedlings

(2011) Heeyoun Hwang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Timing of plant immune responses by a central circadian regulator

(2011) Wei Wang et al.   NATURE

Homeostasis of plasma membrane viscosity in fluctuating temperatures

(2011) Alexandre Martinière et al.   NEW PHYTOLOGIST

Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves

(2011) Wenying Xu et al.   PLoS One

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

(2011) Sergei A. Filichkin et al.   PLoS One

REVEILLE8 and PSEUDO-REPONSE REGULATOR5 Form a Negative Feedback Loop within the Arabidopsis Circadian Clock

(2011) Reetika Rawat et al.   PLoS Genetics

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

Interaction with Diurnal and Circadian Regulation Results in Dynamic Metabolic and Transcriptional Changes during Cold Acclimation in Arabidopsis

(2010) Carmen Espinoza et al.   PLoS One

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

The Circadian System in Higher Plants

(2009) Stacey L. Harmer   Annual Review of Plant Biology

Evolutionarily Conserved Regulatory Motifs in the Promoter of the Arabidopsis Clock Gene LATE ELONGATED HYPOCOTYL

(2009) M. Spensley et al.   PLANT CELL

Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

(2009) P. Armengaud et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

Interactions between circadian and hormonal signalling in plants

(2008) Fiona C. Robertson et al.   PLANT MOLECULAR BIOLOGY

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

(2008) Todd P. Michael et al.   PLoS Genetics

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

(2008) Michael F Covington et al.   GENOME BIOLOGY