Single-cell transcriptome atlas of the leaf and root of rice seedlings

A single-cell analysis of the Arabidopsis vegetative shoot apex

(2021) Tian-Qi Zhang et al.   DEVELOPMENTAL CELL

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

(2021) Tian-Qi Zhang et al.   Nature Communications

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

(2020) Zhixin Liu et al.   Molecular Plant

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Transcriptional landscape of rice roots at the single-cell resolution

(2020) Qing Liu et al.   Molecular Plant

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

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

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

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

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

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

Synchronized replication of genes encoding the same protein complex in fast-proliferating cells

(2019) Ying Chen 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

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing

(2018) Binbin Lai et al.   NATURE

HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation

(2018) Qing Huan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

(2017) Li-Juan Zhou et al.   PLANT PHYSIOLOGY

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Physiological, anatomical and antioxidant responses to salinity in the Mediterranean pastoral grass plant Stipa lagascae

(2017) Raoudha Abdellaoui et al.   Crop & Pasture Science

Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

(2017) Yingying Han et al.   Science Bulletin

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Stem cell lineage in body layer specialization and vascular patterning of rice root and leaf

(2016) Minhuan Zeng et al.   Science Bulletin

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Cell-specific transcriptomic analyses of three-dimensional shoot development in the mossPhyscomitrella patens

(2015) Margaret H. Frank et al.   PLANT JOURNAL

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

(2011) Hinako Takehisa et al.   PLANT JOURNAL

Functional Characterization of Evolutionarily Divergent 4-Coumarate:Coenzyme A Ligases in Rice

(2011) J. Gui et al.   PLANT PHYSIOLOGY

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

CO2 regulator SLAC1 and its homologues are essential for anion homeostasis in plant cells

(2008) Juntaro Negi et al.   NATURE

SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling

(2008) Triin Vahisalu et al.   NATURE

Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

(2008) J. R. Dinneny et al.   SCIENCE

Molecular Genetics of Rice Root Development

(2008) J. Rebouillat et al.   Rice

Gene expression profiling of single epidermal, basal and trichome cells of Arabidopsis thaliana

(2007) Elke Lieckfeldt et al.   JOURNAL OF PLANT PHYSIOLOGY