Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells

Auxin canalization: From speculative models toward molecular players

(2022) Jakub Hajný et al.   CURRENT OPINION IN PLANT BIOLOGY

Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra

(2021) Chi-Fa Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Wen-Yu Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants

(2018) Carla P. Coelho et al.   TRENDS IN PLANT SCIENCE

Genome-Wide Identification of TCP Family Transcription Factors in Medicago truncatula Reveals Significant Roles of miR319-Targeted TCPs in Nodule Development

(2018) Hongfeng Wang et al.   Frontiers in Plant Science

The PIN-FORMED Auxin Efflux Carriers in Plants

(2018) Jing-Jing Zhou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Getting closer: vein density in C4 leaves

(2018) Dhinesh Kumar et al.   NEW PHYTOLOGIST

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

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

Elevated auxin biosynthesis and transport underlie high vein density in C4leaves

(2017) Chi-Fa Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positional distribution of transcription factor binding sites in Arabidopsis thaliana

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

RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

(2015) Junpeng Zhan et al.   PLANT CELL

Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway

(2015) Govinda Rizal et al.   PLANT JOURNAL

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

Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism

(2015) Hong-Zhe Wang et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Cracking the Kranz enigma with systems biology

(2014) J. P. Fouracre et al.   JOURNAL OF EXPERIMENTAL BOTANY

From proto-Kranz to C4 Kranz: building the bridge to C4 photosynthesis

(2014) Rowan F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Short-Root1 Plays a Role in the Development of Vascular Tissue and Kranz Anatomy in Maize Leaves

(2014) Thomas L. Slewinski et al.   Molecular Plant

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Increasing Leaf Vein Density by Mutagenesis: Laying the Foundations for C4 Rice

(2014) Aryo B. Feldman et al.   PLoS One

Ectopic Expression of a Maize Hybrid Down-Regulated Gene ZmARF25 Decreases Organ Size by Affecting Cellular Proliferation in Arabidopsis

(2014) Chuan Li et al.   PLoS One

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4Kranz anatomy

(2013) Peng Wang et al.   PLANT JOURNAL

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

The Plant-Specific Dof Transcription Factors Family: New Players Involved in Vascular System Development and Functioning in Arabidopsis

(2013) Rozenn Le Hir et al.   Frontiers in Plant Science

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Scarecrow Plays a Role in Establishing Kranz Anatomy in Maize Leaves

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

Anatomical enablers and the evolution of C4photosynthesis in grasses

(2012) Pascal-Antoine Christin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

(2011) Hongyan Xing et al.   BMC GENOMICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

The GATA Factor HANABA TARANU Is Required to Position the Proembryo Boundary in the Early Arabidopsis Embryo

(2010) Tal Nawy et al.   DEVELOPMENTAL CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Differentiating Arabidopsis Shoots from Leaves by Combined YABBY Activities

(2010) R. Sarojam et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Dof5.6/HCA2, a Dof Transcription Factor Gene, Regulates Interfascicular Cambium Formation and Vascular Tissue Development in Arabidopsis

(2009) Y. Guo et al.   PLANT CELL

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Auxin influx carriers stabilize phyllotactic patterning

(2008) K. Bainbridge et al.   GENES & DEVELOPMENT

Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana

(2008) Jalean Joyanne Petricka et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY