Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth

The Arabidopsis transcription factor AINTEGUMENTA orchestrates patterning genes and auxin signaling in the establishment of floral growth and form

(2020) Beth A. Krizek et al.   PLANT JOURNAL

Arabidopsis and sunflower plants with increased xylem area show enhanced seed yield

(2019) Julieta V. Cabello et al.   PLANT JOURNAL

Sigma factor 1 in chloroplast gene transcription and photosynthetic light acclimation

(2019) Lauren A Macadlo et al.   JOURNAL OF EXPERIMENTAL BOTANY

LLM-Domain B-GATA Transcription Factors Play Multifaceted Roles in Controlling Greening in Arabidopsis

(2018) Emmanouil Bastakis et al.   PLANT CELL

Coordination of Chloroplast Development through the Action of the GNC and GLK Transcription Factor Families

(2018) Yan Zubo et al.   PLANT PHYSIOLOGY

Mapping genome-wide transcription-factor binding sites using DAP-seq

(2017) Anna Bartlett et al.   Nature Protocols

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

The Plastid Lipocalin LCNP Is Required for Sustained Photoprotective Energy Dissipation in Arabidopsis

(2017) Alizée Malnoë et al.   PLANT CELL

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways

(2016) Beth A. Krizek et al.   PLANT PHYSIOLOGY

Tetrapyrrole Signaling in Plants

(2016) Robert M. Larkin   Frontiers in Plant Science

Positional distribution of transcription factor binding sites in Arabidopsis thaliana

(2016) Chun-Ping Yu et al.   Scientific Reports

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

(2015) Sonia Tarazona et al.   NUCLEIC ACIDS RESEARCH

GROWTH REGULATING FACTOR5 Stimulates Arabidopsis Chloroplast Division, Photosynthesis, and Leaf Longevity

(2015) Liesbeth Vercruyssen et al.   PLANT PHYSIOLOGY

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

(2015) Chun-Ping Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins

(2015) R. S. Randall et al.   Biology Open

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processes associated with growth and responses to water stress

(2014) Delfina A Ré et al.   BMC PLANT BIOLOGY

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

(2014) Hui-Li Xing et al.   BMC PLANT BIOLOGY

ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development

(2014) L. Vercruyssen et al.   PLANT CELL

A Molecular Framework for Auxin-Mediated Initiation of Flower Primordia

(2013) Nobutoshi Yamaguchi et al.   DEVELOPMENTAL CELL

The Arabidopsis B-BOX Protein BBX25 Interacts with HY5, Negatively Regulating BBX22 Expression to Suppress Seedling Photomorphogenesis

(2013) S. N. Gangappa et al.   PLANT CELL

Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

(2013) W.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo

(2012) Mitsumasa Hanaoka et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Scarecrow Plays a Role in Establishing Kranz Anatomy in Maize Leaves

(2012) Thomas L. Slewinski et al.   PLANT AND CELL PHYSIOLOGY

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

(2012) J. Lloyd et al.   PLANT PHYSIOLOGY

Functional Characterization of the GATA Transcription Factors GNC and CGA1 Reveals Their Key Role in Chloroplast Development, Growth, and Division in Arabidopsis

(2012) Y.-H. Chiang et al.   PLANT PHYSIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Overexpression of HEMA1 encoding glutamyl-tRNA reductase

(2011) Judith Schmied et al.   JOURNAL OF PLANT PHYSIOLOGY

GNC and CGA1 Modulate Chlorophyll Biosynthesis and Glutamate Synthase (GLU1/Fd-GOGAT) Expression in Arabidopsis

(2011) Darryl Hudson et al.   PLoS One

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Polar auxin transport together with AINTEGUMENTA and REVOLUTA coordinate early Arabidopsis gynoecium development

(2010) Staci Nole-Wilson et al.   DEVELOPMENTAL BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Setaria viridis: A Model for C4 Photosynthesis

(2010) T. P. Brutnell et al.   PLANT CELL

VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation inArabidopsis

(2010) Masatoshi Yamaguchi et al.   PLANT CELL

The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants

(2010) José G. García-Cerdán et al.   PLANT JOURNAL

Sigma factor phosphorylation in the photosynthetic control of photosystem stoichiometry

(2010) M. Shimizu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

AINTEGUMENTA and AINTEGUMENTA-LIKE6 Act Redundantly to Regulate Arabidopsis Floral Growth and Patterning

(2009) BethA. Krizek   PLANT PHYSIOLOGY

The Arabidopsis GRF-INTERACTING FACTOR Gene Family Performs an Overlapping Function in Determining Organ Size as Well as Multiple Developmental Properties

(2009) B. H. Lee et al.   PLANT PHYSIOLOGY

Regulation and evolution of chlorophyll metabolism

(2008) Tatsuru Masuda et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Two GATA Transcription Factors Are Downstream Effectors of Floral Homeotic Gene Action in Arabidopsis

(2008) C. D. Mara et al.   PLANT PHYSIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY