A single-cell analysis of the Arabidopsis vegetative shoot apex

SUPPRESSOR OF MAX2 1‐LIKE 5 promotes secondary phloem formation during radial stem growth

(2020) Eva‐Sophie Wallner et al.   PLANT JOURNAL

Gravity-Sensing Tissues for Gravitropism Are Required for “Anti-Gravitropic” Phenotypes of lzy Multiple Mutants in Arabidopsis

(2020) Nozomi Kawamoto et al.   Plants-Basel

Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

(2020) Fu-Xiang Wang et al.   DEVELOPMENTAL CELL

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

(2020) Zhixin Liu et al.   Molecular Plant

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Mobile PEAR transcription factors integrate positional cues to prime cambial growth

(2019) Shunsuke Miyashima et al.   NATURE

High levels of auxin signalling define the stem-cell organizer of the vascular cambium

(2019) Ondřej Smetana et al.   NATURE

A gene expression map of shoot domains reveals regulatory mechanisms

(2019) Caihuan Tian et al.   Nature Communications

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

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng 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

The Root Cap Cuticle: A Cell Wall Structure for Seedling Establishment and Lateral Root Formation

(2019) Alice Berhin et al.   CELL

Control of Meristem Size

(2019) Munenori Kitagawa et al.   Annual Review of Plant Biology

The plant stomatal lineage at a glance

(2019) Laura R. Lee et al.   JOURNAL OF CELL SCIENCE

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

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

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

To Divide or Differentiate: It Is about Scaffolding

(2019) Xiaoyu Guo et al.   TRENDS IN PLANT SCIENCE

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

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

Linking cell cycle to stomatal differentiation

(2019) Soon-Ki Han et al.   CURRENT OPINION IN PLANT BIOLOGY

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Regulation of Division and Differentiation of Plant Stem Cells

(2018) Edith Pierre-Jerome et al.   Annual Review of Cell and Developmental Biology

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

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges

(2018) Xavier Pichon et al.   MOLECULAR CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis LAZY1 Family Plays a Key Role in Gravity Signaling within Statocytes and in Branch Angle Control of Roots and Shoots

(2017) Masatoshi Taniguchi 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

DRO1 influences root system architecture in Arabidopsis and Prunus species

(2017) Jessica M. Guseman et al.   PLANT JOURNAL

Stem Cell Differentiation as a Non-Markov Stochastic Process

(2017) Patrick S. Stumpf et al.   Cell Systems

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Plant Stem Cells

(2016) Thomas Greb et al.   CURRENT BIOLOGY

O Cell, Where Art Thou? The mechanisms of shoot meristem patterning

(2015) Christophe Gaillochet et al.   CURRENT OPINION IN PLANT BIOLOGY

Transcriptome Dynamics of the Stomatal Lineage: Birth, Amplification, and Termination of a Self-Renewing Population

(2015) Jessika Adrian et al.   DEVELOPMENTAL CELL

50 years of Arabidopsis research: highlights and future directions

(2015) Nicholas J. Provart et al.   NEW PHYTOLOGIST

Transit-Amplifying Cells Orchestrate Stem Cell Activity and Tissue Regeneration

(2014) Ya-Chieh Hsu et al.   CELL

A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche

(2014) R. K. Yadav et al.   DEVELOPMENT

Plant and animal stem cells: similar yet different

(2014) Renze Heidstra et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Unique HEAT Repeat-Containing Protein SHOOT GRAVITROPISM6 is Involved in Vacuolar Membrane Dynamics in Gravity-Sensing Cells of Arabidopsis Inflorescence Stem

(2014) Yasuko Hashiguchi et al.   PLANT AND CELL PHYSIOLOGY

Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

(2014) Juliana L Matos et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Signaling in shoot and flower meristems of Arabidopsis thaliana

(2013) Anna L Holt et al.   CURRENT OPINION IN PLANT BIOLOGY

Members of the NPF3 Transporter Subfamily Encode Pathogen-Inducible Nitrate/Nitrite Transporters in Grapevine and Arabidopsis

(2013) Sharon Pike et al.   PLANT AND CELL PHYSIOLOGY

AtLAZY1 is a signaling component required for gravitropism of theArabidopsis thalianainflorescence

(2013) Takeshi Yoshihara et al.   PLANT JOURNAL

Arabidopsis 2010 and beyond—big science with a small weed

(2013) Klaus Harter et al.   Frontiers in Plant Science

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

Stem cell function during plant vascular development

(2012) Shunsuke Miyashima et al.   EMBO JOURNAL

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Identification of an Arabidopsis Fatty Alcohol:Caffeoyl-Coenzyme A Acyltransferase Required for the Synthesis of Alkyl Hydroxycinnamates in Root Waxes

(2012) D. K. Kosma et al.   PLANT PHYSIOLOGY

Arabidopsis LATERAL ORGAN BOUNDARIES negatively regulates brassinosteroid accumulation to limit growth in organ boundaries

(2012) E. M. Bell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stem cell maintenance in shoot apical meristems

(2011) Mariano Perales et al.   CURRENT OPINION IN PLANT BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Plant stem cell niches: from signalling to execution

(2010) Robert Sablowski   CURRENT OPINION IN PLANT BIOLOGY

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

(2010) Jelle Van Leene et al.   Molecular Systems Biology

How a Plant Builds Leaves

(2010) Siobhan A. Braybrook et al.   PLANT CELL

The development of Arabidopsis as a model plant

(2010) Maarten Koornneef et al.   PLANT JOURNAL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Signals and prepatterns: new insights into organ polarity in plants

(2009) A. Y. Husbands et al.   GENES & DEVELOPMENT

Stomagen positively regulates stomatal density in Arabidopsis

(2009) Shigeo S. Sugano et al.   NATURE

Two Arabidopsis 3-ketoacyl CoA synthase genes,KCS20andKCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress

(2009) Saet-Buyl Lee et al.   PLANT JOURNAL

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

(2009) R. K. Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant Stem Cell Niches: Standing the Test of Time

(2008) José R. Dinneny et al.   CELL