Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling

PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5

(2014) Judit Soy et al.   JOURNAL OF EXPERIMENTAL BOTANY

SAUR Inhibition of PP2C-D Phosphatases Activates Plasma Membrane H+-ATPases to Promote Cell Expansion in Arabidopsis

(2014) A. K. Spartz et al.   PLANT CELL

PIFs: Systems Integrators in Plant Development

(2014) P. Leivar et al.   PLANT CELL

Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany

(2013) C. Wasternack et al.   ANNALS OF BOTANY

Photoreceptor Signaling Networks in Plant Responses to Shade

(2013) Jorge J. Casal   Annual Review of Plant Biology

Image analysis is driving a renaissance in growth measurement

(2013) Edgar P Spalding et al.   CURRENT OPINION IN PLANT BIOLOGY

Canopy light cues affect emission of constitutive and methyl jasmonate-induced volatile organic compounds inArabidopsis thaliana

(2013) Wouter Kegge et al.   NEW PHYTOLOGIST

Auxin-mediated plant architectural changes in response to shade and high temperature

(2013) Mieke de Wit et al.   PHYSIOLOGIA PLANTARUM

COP1 re-accumulates in the nucleus under shade

(2013) Manuel Pacín et al.   PLANT JOURNAL

The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings

(2013) Nicolás Cifuentes-Esquivel et al.   PLANT JOURNAL

Jasmonate Controls Leaf Growth by Repressing Cell Proliferation and the Onset of Endoreduplication while Maintaining a Potential Stand-By Mode

(2013) S. Noir et al.   PLANT PHYSIOLOGY

Abscisic Acid Regulates Axillary Bud Outgrowth Responses to the Ratio of Red to Far-Red Light

(2013) S. K. Reddy et al.   PLANT PHYSIOLOGY

Flowering time regulation: photoperiod- and temperature-sensing in leaves

(2013) Young Hun Song et al.   TRENDS IN PLANT SCIENCE

Multiple bHLH Proteins form Heterodimers to Mediate CRY2-Dependent Regulation of Flowering-Time in Arabidopsis

(2013) Yawen Liu et al.   PLoS Genetics

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis

(2013) Yu Zhang et al.   PLoS Genetics

Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis - a novel phenotyping approach using laser scanning

(2012) Tino Dornbusch et al.   FUNCTIONAL PLANT BIOLOGY

Linking photoreceptor excitation to changes in plant architecture

(2012) L. Li et al.   GENES & DEVELOPMENT

Light-dependent, Dark-promoted Interaction betweenArabidopsisCryptochrome 1 and Phytochrome B Proteins

(2012) Robert M. Hughes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Inhibition of arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner

(2012) Jing Chen et al.   JOURNAL OF PLANT RESEARCH

Transcription factor PIF4 controls the thermosensory activation of flowering

(2012) S. Vinod Kumar et al.   NATURE

A Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA

(2012) M. C. Reymond et al.   PLANT CELL

The Arabidopsis Mediator Subunit MED25 Differentially Regulates Jasmonate and Abscisic Acid Signaling through Interacting with the MYC2 and ABI5 Transcription Factors

(2012) R. Chen et al.   PLANT CELL

Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network inArabidopsis

(2012) Pablo Leivar et al.   PLANT CELL

Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling

(2012) Patricia Hornitschek et al.   PLANT JOURNAL

Arabidopsis COP1 and SPA Genes Are Essential for Plant Elongation But Not for Acceleration of Flowering Time in Response to a Low Red Light to Far-Red Light Ratio

(2012) S. Rolauffs et al.   PLANT PHYSIOLOGY

The Mediator Complex Subunit PFT1 Interferes with COP1 and HY5 in the Regulation of Arabidopsis Light Signaling

(2012) C. Klose et al.   PLANT PHYSIOLOGY

MEDIATOR25 Acts as an Integrative Hub for the Regulation of Jasmonate-Responsive Gene Expression in Arabidopsis

(2012) V. Cevik et al.   PLANT PHYSIOLOGY

Stem Transcriptome Reveals Mechanisms to Reduce the Energetic Cost of Shade-Avoidance Responses in Tomato

(2012) J. I. Cagnola et al.   PLANT PHYSIOLOGY

Low Red/Far-Red Ratios Reduce Arabidopsis Resistance to Botrytis cinerea and Jasmonate Responses via a COI1-JAZ10-Dependent, Salicylic Acid-Independent Mechanism

(2012) I. Cerrudo et al.   PLANT PHYSIOLOGY

Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade

(2012) D.-L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response

(2012) Daniele L. Filiault et al.   PLoS Genetics

A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis

(2012) Angela Bruex et al.   PLoS Genetics

A High-Throughput Method for Illumina RNA-Seq Library Preparation

(2012) Ravi Kumar et al.   Frontiers in Plant Science

Technologies for Micromanipulating, Imaging, and Phenotyping Small Invertebrates and Vertebrates

(2011) Mehmet Fatih Yanik et al.   Annual Review of Biomedical Engineering

A High-Resolution C. elegans Essential Gene Network Based on Phenotypic Profiling of a Complex Tissue

(2011) Rebecca A. Green et al.   CELL

Blue Light-Dependent Interaction of CRY2 with SPA1 Regulates COP1 activity and Floral Initiation in Arabidopsis

(2011) Zecheng Zuo et al.   CURRENT BIOLOGY

Functional Profiling Identifies Genes Involved in Organ-Specific Branches of the PIF3 Regulatory Network inArabidopsis

(2011) Maria Sentandreu et al.   PLANT CELL

TheArabidopsisbHLH Transcription Factors MYC3 and MYC4 Are Targets of JAZ Repressors and Act Additively with MYC2 in the Activation of Jasmonate Responses

(2011) Patricia Fernández-Calvo et al.   PLANT CELL

Arabidopsis thaliana TERMINAL FLOWER2 is involved in light-controlled signalling during seedling photomorphogenesis

(2011) ANA ELISA VALDÉS et al.   PLANT CELL AND ENVIRONMENT

The trafficking protein SYP121 of Arabidopsis connects programmed stomatal closure and K+ channel activity with vegetative growth

(2011) Cornelia Eisenach et al.   PLANT JOURNAL

Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades

(2011) Mercedes M. Keller et al.   PLANT JOURNAL

Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings

(2011) Diederik H. Keuskamp et al.   PLANT JOURNAL

Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis

(2011) K. Nozue et al.   PLANT PHYSIOLOGY

Intronic T-DNA Insertion Renders Arabidopsis opr3 a Conditional Jasmonic Acid-Producing Mutant

(2011) E. W. Chehab et al.   PLANT PHYSIOLOGY

PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature

(2011) K. A. Franklin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis

(2011) C. Won et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The main auxin biosynthesis pathway in Arabidopsis

(2011) K. Mashiguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The action mechanisms of plant cryptochromes

(2011) Hongtao Liu et al.   TRENDS IN PLANT SCIENCE

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

(2011) Reetika Rawat et al.   PLoS Genetics

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

(2011) Rosangela Sozzani et al.   GENOME BIOLOGY

DELLAs Modulate Jasmonate Signaling via Competitive Binding to JAZs

(2010) Xingliang Hou et al.   DEVELOPMENTAL CELL

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Jasmonate and Phytochrome A Signaling inArabidopsisWound and Shade Responses Are Integrated through JAZ1 Stability

(2010) Frances Robson et al.   PLANT CELL

AtBBX21 and COP1 genetically interact in the regulation of shade avoidance

(2010) Carlos D. Crocco et al.   PLANT JOURNAL

Involvement of Auxin and Brassinosteroid in the Regulation of Petiole Elongation under the Shade

(2010) T. Kozuka et al.   PLANT PHYSIOLOGY

Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis

(2010) José M. Jiménez-Gómez et al.   PLoS Genetics

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Blue Light Induces Degradation of the Negative Regulator Phytochrome Interacting Factor 1 to Promote Photomorphogenic Development of Arabidopsis Seedlings

(2009) A. Castillon et al.   GENETICS

Phytochrome functions in Arabidopsis development

(2009) K. A. Franklin et al.   JOURNAL OF EXPERIMENTAL BOTANY

The bHLH Transcription Factor SPATULA Controls Final Leaf Size in Arabidopsis thaliana

(2009) Yasunori Ichihashi et al.   PLANT AND CELL PHYSIOLOGY

ATHB4, a regulator of shade avoidance, modulates hormone response in Arabidopsis seedlings

(2009) Céline Sorin et al.   PLANT JOURNAL

Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity

(2009) J. E. Moreno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants

(2008) Yi Tao et al.   CELL

Acceleration of Flowering during Shade Avoidance in Arabidopsis Alters the Balance between FLOWERING LOCUS C-Mediated Repression and Photoperiodic Induction of Flowering

(2008) A. C. Wollenberg et al.   PLANT PHYSIOLOGY

Regulation of CONSTANS and FLOWERING LOCUS T Expression in Response to Changing Light Quality

(2008) S. Y. Kim et al.   PLANT PHYSIOLOGY