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

Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE

(2016) Mani K. Choudhary et al.   Frontiers in Plant Science

Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways

(2015) Mani Kant Choudhary et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

(2015) Anna Flis et al.   Open Biology

SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome

(2014) Cornelia M. Hooper et al.   BIOINFORMATICS

CaMKII is essential for the cellular clock and coupling between morning and evening behavioral rhythms

(2014) N. Kon et al.   GENES & DEVELOPMENT

Tissue-specific clocks in Arabidopsis show asymmetric coupling

(2014) Motomu Endo et al.   NATURE

Ubiquitin Ligase ATL31 Functions in Leaf Senescence in Response to the Balance Between Atmospheric CO2 and Nitrogen Availability in Arabidopsis

(2014) Shoki Aoyama et al.   PLANT AND CELL PHYSIOLOGY

Ambient Temperature Signal Feeds into the Circadian Clock Transcriptional Circuitry Through the EC Night-Time Repressor in Arabidopsis thaliana

(2014) Takeshi Mizuno et al.   PLANT AND CELL PHYSIOLOGY

Multiple Layers of Posttranslational Regulation Refine Circadian Clock Activity in Arabidopsis

(2014) P. J. Seo et al.   PLANT CELL

Correlation of mRNA and protein abundance in the developing maize leaf

(2014) Lalit Ponnala et al.   PLANT JOURNAL

Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis

(2013) Eva Vranová et al.   Annual Review of Plant Biology

Zeitlupe Senses Blue-Light Fluence To Mediate Circadian Timing in Arabidopsis thaliana

(2013) Ashutosh Pudasaini et al.   BIOCHEMISTRY

Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model

(2013) Alexandra Pokhilko et al.   Molecular BioSystems

Photosynthetic entrainment of the Arabidopsis thaliana circadian clock

(2013) Michael J. Haydon et al.   NATURE

The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis

(2013) Antony N. Dodd et al.   NEW PHYTOLOGIST

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

A fast circadian clock at high temperatures is a conserved feature acrossArabidopsisaccessions and likely to be important for vegetative yield

(2013) JELENA KUSAKINA et al.   PLANT CELL AND ENVIRONMENT

Ubiquitin-Specific Proteases UBP12 and UBP13 Act in Circadian Clock and Photoperiodic Flowering Regulation in Arabidopsis

(2013) X. Cui et al.   PLANT PHYSIOLOGY

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

(2013) Juliana Marcolino-Gomes et al.   PLoS One

Global approaches for telling time: Omics and the Arabidopsis circadian clock

(2013) Brenda Y. Chow et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Circadian clock-regulated physiological outputs: Dynamic responses in nature

(2013) Hannah A. Kinmonth-Schultz et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Wheels within wheels: the plant circadian system

(2013) Polly Yingshan Hsu et al.   TRENDS IN PLANT SCIENCE

Why measure enzyme activities in the era of systems biology?

(2013) Mark Stitt et al.   TRENDS IN PLANT SCIENCE

Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants

(2013) Mohammed Nuruzzaman et al.   Frontiers in Microbiology

Complexity in the Wiring and Regulation of Plant Circadian Networks

(2012) Dawn H. Nagel et al.   CURRENT BIOLOGY

Starch turnover: pathways, regulation and role in growth

(2012) Mark Stitt et al.   CURRENT OPINION IN PLANT BIOLOGY

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

(2012) C. Smaczniak et al.   DEVELOPMENT

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

(2012) Katja Baerenfaller et al.   Molecular Systems Biology

The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops

(2012) Alexandra Pokhilko et al.   Molecular Systems Biology

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

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

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

The genetic basis of flowering responses to seasonal cues

(2012) Fernando Andrés et al.   NATURE REVIEWS GENETICS

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

(2012) Sandra K. Tanz et al.   NUCLEIC ACIDS RESEARCH

Circadian Clock Regulates Dynamic Chromatin Modifications Associated with Arabidopsis CCA1/LHY and TOC1 Transcriptional Rhythms

(2012) Hans Hemmes et al.   PLANT AND CELL PHYSIOLOGY

EARLY FLOWERING4 Recruitment of EARLY FLOWERING3 in the Nucleus Sustains the Arabidopsis Circadian Clock

(2012) E. Herrero et al.   PLANT CELL

Ordered changes in histone modifications at the core of the Arabidopsis circadian clock

(2012) J. Malapeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

(2012) W. Huang et al.   SCIENCE

ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis

(2012) Zhaojun Ding et al.   Nature Communications

Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis

(2012) Clara Bourbousse et al.   PLoS Genetics

The endoplasmic reticulum in plant immunity and cell death

(2012) Ruth Eichmann et al.   Frontiers in Plant Science

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth

(2011) Dmitri A. Nusinow et al.   NATURE

Identification of 14-3-3 proteins as a target of ATL31 ubiquitin ligase, a regulator of the C/N response in Arabidopsis

(2011) Takeo Sato et al.   PLANT JOURNAL

Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation

(2011) Benoit Farinas et al.   PLANT JOURNAL

AtIPD: A Curated Database of Arabidopsis Isoprenoid Pathway Models and Genes for Isoprenoid Network Analysis

(2011) E. Vranova et al.   PLANT PHYSIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Regulation of starch metabolism: the age of enlightenment?

(2010) Oliver Kötting et al.   CURRENT OPINION IN PLANT BIOLOGY

Quantitative analysis of regulatory flexibility under changing environmental conditions

(2010) Kieron D Edwards et al.   Molecular Systems Biology

Clocks not winding down: unravelling circadian networks

(2010) Eric E. Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

(2010) Antje Feller et al.   PLANT JOURNAL

Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana

(2010) S. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis

(2010) A. Shapiguzov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian control of carbohydrate availability for growth in Arabidopsis plants at night

(2010) A. Graf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling

(2010) Karl-Josef Dietz et al.   PROTOPLASMA

Role of Plastid Protein Phosphatase TAP38 in LHCII Dephosphorylation and Thylakoid Electron Flow

(2010) Mathias Pribil et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The plant endoplasmic reticulum: a cell-wide web

(2009) Imogen A. Sparkes et al.   BIOCHEMICAL JOURNAL

Snf1-related protein kinases (SnRKs) act within an intricate network that links metabolic and stress signalling in plants

(2009) Nigel G. Halford et al.   BIOCHEMICAL JOURNAL

TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought

(2009) Tommaso Legnaioli et al.   EMBO JOURNAL

Delayed Correlation of mRNA and Protein Expression in Rapamycin-treated Cells and a Role for Ggc1 in Cellular Sensitivity to Rapamycin

(2009) Marjorie L. Fournier et al.   MOLECULAR & CELLULAR PROTEOMICS

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

CNI1/ATL31, a RING-type ubiquitin ligase that functions in the carbon/nitrogen response for growth phase transition in Arabidopsis seedlings

(2009) Takeo Sato et al.   PLANT JOURNAL

REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways

(2009) R. Rawat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endoplasmic reticulum bodies: solving the insoluble

(2008) Eliot M Herman   CURRENT OPINION IN PLANT BIOLOGY

Post-translational Regulation of theArabidopsisCircadian Clock through Selective Proteolysis and Phosphorylation of Pseudo-response Regulator Proteins

(2008) Sumire Fujiwara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

XAP5 CIRCADIAN TIMEKEEPER Coordinates Light Signals for Proper Timing of Photomorphogenesis and the Circadian Clock in Arabidopsis

(2008) E. L. Martin-Tryon et al.   PLANT CELL

Circadian Clock Proteins LHY and CCA1 Regulate SVP Protein Accumulation to Control Flowering in Arabidopsis

(2008) S. Fujiwara et al.   PLANT CELL

VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation

(2008) Teresa Ceserani et al.   PLANT JOURNAL

Global Transcript Levels Respond to Small Changes of the Carbon Status during Progressive Exhaustion of Carbohydrates in Arabidopsis Rosettes

(2008) B. Usadel et al.   PLANT PHYSIOLOGY

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

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

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

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

The Circadian Clock inArabidopsisRoots Is a Simplified Slave Version of the Clock in Shoots

(2008) Allan B. James et al.   SCIENCE

The CBL–CIPK network in plant calcium signaling

(2008) Sheng Luan   TRENDS IN PLANT SCIENCE

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

(2008) Michael F Covington et al.   GENOME BIOLOGY