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

Domestication selected for deceleration of the circadian clock in cultivated tomato

(2015) Niels A Müller et al.   NATURE GENETICS

Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis

(2015) Marisa Miller et al.   Nature Communications

CONSTANS is a photoperiod regulated activator of flowering in sorghum

(2014) Shanshan Yang et al.   BMC PLANT BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis in Arabidopsis Intraspecific Hybrids

(2014) D. W.- K. Ng et al.   PLANT CELL

Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes

(2014) Michael Groszmann et al.   PLANT PHYSIOLOGY

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

(2014) Rajandeep S. Sekhon et al.   PLoS One

Progress Toward Understanding Heterosis in Crop Plants

(2013) Patrick S. Schnable et al.   Annual Review of Plant Biology

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Photosynthetic entrainment of the Arabidopsis thaliana circadian clock

(2013) Michael J. Haydon et al.   NATURE

Genomic and epigenetic insights into the molecular bases of heterosis

(2013) Z. Jeffrey Chen   NATURE REVIEWS GENETICS

Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development

(2013) M. Xin et al.   PLANT CELL

The circadian clock-associated genegigantea1affects maize developmental transitions

(2013) CLAIRE BENDIX et al.   PLANT CELL AND ENVIRONMENT

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Self-Regulatory Circuit of CIRCADIAN CLOCK-ASSOCIATED1 Underlies the Circadian Clock Regulation of Temperature Responses inArabidopsis

(2012) Pil Joon Seo et al.   PLANT CELL

Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

(2012) H. Shen et al.   PLANT CELL

Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids

(2012) Rhonda C. Meyer et al.   PLANT JOURNAL

PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants

(2012) Charles Chen et al.   PLoS One

Cozzarelli Prize Winner: Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior

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

Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity

(2012) R. Fujimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) N. Koike et al.   SCIENCE

Ploidy and Hybridity Effects on Growth Vigor and Gene Expression in Arabidopsis thaliana Hybrids and Their Parents

(2012) Marisa Miller et al.   G3-Genes Genomes Genetics

A Map-Based Cloning Strategy Employing a Residual Heterozygous Line Reveals that theGIGANTEAGene Is Involved in Soybean Maturity and Flowering

(2011) Satoshi Watanabe et al.   GENETICS

Timing of plant immune responses by a central circadian regulator

(2011) Wei Wang et al.   NATURE

Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species

(2011) David G.J. Mann et al.   PLANT BIOTECHNOLOGY JOURNAL

Systems Analysis of a Maize Leaf Developmental Gradient Redefines the Current C4 Model and Provides Candidates for Regulation

(2011) T. R. Pick et al.   PLANT CELL

CCA1 and ELF3 Interact in the Control of Hypocotyl Length and Flowering Time in Arabidopsis

(2011) S. X. Lu et al.   PLANT PHYSIOLOGY

Circadian oscillation of gibberellin signaling in Arabidopsis

(2011) M. V. Arana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

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

CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis

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

Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum

(2011) R. L. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordination of the maize transcriptome by a conserved circadian clock

(2010) Sadaf Khan et al.   BMC PLANT BIOLOGY

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

(2010) Gui-Sheng Song et al.   Molecular Plant

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding

(2010) Stephen A. Goff   NEW PHYTOLOGIST

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Cell Number Regulator1Affects Plant and Organ Size in Maize: Implications for Crop Yield Enhancement and Heterosis

(2010) Mei Guo et al.   PLANT CELL

Heterosis

(2010) J. A. Birchler et al.   PLANT CELL

Maize Global Transcriptomics Reveals Pervasive Leaf Diurnal Rhythms but Rhythms in Developing Ears Are Largely Limited to the Core Oscillator

(2010) Kevin R. Hayes et al.   PLoS One

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

The Circadian System in Higher Plants

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

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL Function Synergistically in the Circadian Clock of Arabidopsis

(2009) S. X. Lu et al.   PLANT PHYSIOLOGY

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants

(2008) Abdelaty Saleh et al.   Nature Protocols

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

(2008) Allan B. James et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY