Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1

(2020) Andrew B. Gipson et al.   Plants-Basel

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

(2020) John Lee et al.   NUCLEIC ACIDS RESEARCH

Multi-Trait Genome-Wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture

(2020) Brian R Rice et al.   PLANT AND CELL PHYSIOLOGY

UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize

(2020) Yanfang Du et al.   PLoS Genetics

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

(2020) Liya Wang et al.   Frontiers in Plant Science

Mobile PEAR transcription factors integrate positional cues to prime cambial growth

(2019) Shunsuke Miyashima et al.   NATURE

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

Evolution of buffering in a genetic circuit controlling plant stem cell proliferation

(2019) Daniel Rodriguez-Leal et al.   NATURE GENETICS

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

The Arabidopsis glutathione transferases, AtGSTF8 and AtGSTU19 are involved in the maintenance of root redox homeostasis affecting meristem size and salt stress sensitivity

(2019) Edit Horváth et al.   PLANT SCIENCE

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

(2019) Steffen Knauer et al.   GENOME RESEARCH

Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics

(2019) Charlotte Rich-Griffin et al.   TRENDS IN PLANT SCIENCE

The maize heterotrimeric G protein β subunit controls shoot meristem development and immune responses

(2019) Qingyu Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

(2018) Niels Aerts et al.   BMC PLANT BIOLOGY

Single-cell RNA sequencing for the study of development, physiology and disease

(2018) S. Steven Potter   Nature Reviews Nephrology

A Comprehensive Toolkit for Inducible, Cell Type-Specific Gene Expression in Arabidopsis

(2018) Ann-Kathrin Schürholz et al.   PLANT PHYSIOLOGY

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems

(2018) Masaru Fujimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and expression characterization of the Phloem Protein 2 (PP2) genes in ramie (Boehmeria nivea L. Gaudich)

(2018) Pingan Guo et al.   Scientific Reports

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

(2018) Dijun Chen et al.   Nature Communications

Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture

(2017) Josh Strable et al.   PLANT CELL

Cell type boundaries organize plant development

(2017) Monica Pia Caggiano et al.   eLife

Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits

(2016) Byoung Il Je et al.   NATURE GENETICS

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

Polyamine Resistance Is Increased by Mutations in a Nitrate Transporter Gene NRT1.3 (AtNPF6.4) in Arabidopsis thaliana

(2016) Wurina Tong et al.   Frontiers in Plant Science

Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered and drought conditions

(2015) Michael L Nuccio et al.   NATURE BIOTECHNOLOGY

Plant vascular development: from early specification to differentiation

(2015) Bert De Rybel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The MaizePI/GLOOrthologZmm16/sterile tassel silky ear1Interacts with the Zygomorphy and Sex Determination Pathways in Flower Development

(2015) Madelaine E. Bartlett et al.   PLANT CELL

FASCIATED EAR4Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize

(2015) Michael Pautler et al.   PLANT CELL

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

(2015) Charlotte Herzeel et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MaizeSBP-boxtranscription factorsunbranched2andunbranched3affect yield traits by regulating the rate of lateral primordia initiation

(2014) George S. Chuck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory modules controlling maize inflorescence architecture

(2013) A. L. Eveland et al.   GENOME RESEARCH

Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus

(2013) Peter Bommert et al.   NATURE GENETICS

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Improved Heritability Estimation from Genome-wide SNPs

(2012) Doug Speed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Unraveling the KNOTTED1 regulatory network in maize meristems

(2012) N. Bolduc et al.   GENES & DEVELOPMENT

Ontogeny of the Maize Shoot Apical Meristem

(2012) E. M. Takacs et al.   PLANT CELL

Pod Corn Is Caused by Rearrangement at the Tunicate1 Locus

(2012) J.-J. Han et al.   PLANT CELL

The Phytochrome-Interacting VASCULAR PLANT ONE-ZINC FINGER1 and VOZ2 Redundantly Regulate Flowering in Arabidopsis

(2012) Y. Yasui et al.   PLANT CELL

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

(2012) J. Lloyd et al.   PLANT PHYSIOLOGY

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis

(2011) M. Javelle et al.   PLANT PHYSIOLOGY

ZmPep1, an Ortholog of Arabidopsis Elicitor Peptide 1, Regulates Maize Innate Immunity and Enhances Disease Resistance

(2011) A. Huffaker et al.   PLANT PHYSIOLOGY

myo-Inositol-1-phosphate Synthase Is Required for Polar Auxin Transport and Organ Development

(2010) Hao Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Evidence of selection at theramosa1locus during maize domestication

(2010) BRANDI SIGMON et al.   MOLECULAR ECOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Divergence in function and expression of the NOD26-like intrinsic proteins in plants

(2009) Qingpo Liu et al.   BMC GENOMICS

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

(2009) BethA. Krizek   PLANT PHYSIOLOGY

Maps of random walks on complex networks reveal community structure

(2008) M. Rosvall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA