Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

Advances and Opportunities of Single-Cell Transcriptomics for Plant Research

(2021) Carolin Seyfferth et al.   Annual Review of Plant Biology

Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing

(2020) Zhixin Liu et al.   Molecular Plant

Distance-to-Time Conversion Using Gompertz Model Reveals Age-Dependent Aerenchyma Formation in Rice Roots

(2020) Takaki Yamauchi et al.   PLANT PHYSIOLOGY

Root Cortex Provides a Venue for Gas-Space Formation and Is Essential for Plant Adaptation to Waterlogging

(2019) Takaki Yamauchi et al.   Frontiers in Plant Science

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

(2019) Kunling Chen et al.   Annual Review of Plant Biology

Single cell RNA sequencing and its promise in reconstructing plant vascular cell lineages

(2019) Antia Rodriguez-Villalon et al.   CURRENT OPINION IN PLANT BIOLOGY

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

OsSPL3, a SBP-Domain Protein, Regulates Crown Root Development in Rice

(2019) Yanlin Shao et al.   PLANT CELL

Towards Building a Plant Cell Atlas

(2019) Seung Y. Rhee et al.   TRENDS IN PLANT SCIENCE

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

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

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

Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport

(2019) Takehiko Ogura et al.   CELL

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

(2019) Gina M. Turco et al.   Cell Reports

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

(2019) Leif S. Ludwig et al.   Cell Reports

Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

(2019) Kai Hua et al.   Molecular Plant

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

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

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

A single-cell view of tissue regeneration in plants

(2019) Victoria Mironova et al.   CURRENT OPINION IN PLANT BIOLOGY

CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing

(2019) Hakim Manghwar et al.   TRENDS IN PLANT SCIENCE

Genetic diversity of root system architecture in response to drought stress in grain legumes

(2018) Heng Ye et al.   JOURNAL OF EXPERIMENTAL BOTANY

Suberized transport barriers in Arabidopsis , barley and rice roots: From the model plant to crop species

(2018) Tino Kreszies et al.   JOURNAL OF PLANT PHYSIOLOGY

Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis

(2018) Daniela Ristova et al.   PLANT JOURNAL

Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

(2018) Maria Antonietta Tosches et al.   SCIENCE

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate

(2018) Jitender Giri et al.   Nature Communications

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

(2018) Yan Zhao et al.   PLoS Genetics

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Genome-wide Targeted Mutagenesis in Rice Using the CRISPR/Cas9 System

(2017) Yuming Lu et al.   Molecular Plant

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

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules

(2017) Kelsey A. Maher et al.   PLANT CELL

A Two-Step Model for de Novo Activation of WUSCHEL during Plant Shoot Regeneration

(2017) Tian-Qi Zhang et al.   PLANT CELL

Current and future editing reagent delivery systems for plant genome editing

(2017) Yidong Ran et al.   Science China-Life Sciences

Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation

(2017) Colleen Drapek et al.   TRENDS IN GENETICS

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

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

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

qRT9, a quantitative trait locus controlling root thickness and root length in upland rice

(2015) Junzhou Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Proline-rich protein-like PRPL1 controls elongation of root hairs in Arabidopsis thaliana

(2014) Agnieszka Karolina Boron et al.   JOURNAL OF EXPERIMENTAL BOTANY

Definition and stabilisation of the quiescent centre in rice roots

(2014) J. Ni et al.   PLANT BIOLOGY

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

LATERAL ROOTLESS2, a Cyclophilin Protein, Regulates Lateral Root Initiation and Auxin Signaling Pathway in Rice

(2013) Huakun Zheng et al.   Molecular Plant

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

OsCYP2, a chaperone involved in degradation of auxin-responsive proteins, plays crucial roles in rice lateral root initiation

(2013) Bo Kang et al.   PLANT JOURNAL

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Plant Stem Cell Niches

(2012) Ernst Aichinger et al.   Annual Review of Plant Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Stem cell function during plant vascular development

(2012) Shunsuke Miyashima et al.   EMBO JOURNAL

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Root hair-specific expansins modulate root hair elongation in rice

(2011) Yu ZhiMing et al.   PLANT JOURNAL

Coexpression-Based Clustering of Arabidopsis Root Genes Predicts Functional Modules in Early Phosphate Deficiency Signaling

(2011) W.-D. Lin et al.   PLANT PHYSIOLOGY

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

Genetic control of root development in rice, the model cereal

(2010) Yoan Coudert et al.   TRENDS IN PLANT SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

cis-Element- and Transcriptome-Based Screening of Root Hair-Specific Genes and Their Functional Characterization in Arabidopsis

(2009) S.-K. Won et al.   PLANT PHYSIOLOGY

ROOT HAIR DEFECTIVE4 Encodes a Phosphatidylinositol-4-Phosphate Phosphatase Required for Proper Root Hair Development in Arabidopsis thaliana

(2008) J. M. Thole et al.   PLANT CELL

Molecular Genetics of Rice Root Development

(2008) J. Rebouillat et al.   Rice

Conserved and diverse mechanisms in root development

(2007) Frank Hochholdinger et al.   CURRENT OPINION IN PLANT BIOLOGY