Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf

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

(2021) Xiaosa Xu et al.   DEVELOPMENTAL CELL

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

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

(2020) Zhixin Liu et al.   Molecular Plant

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

KIN10 promotes stomatal development through stabilization of the SPEECHLESS transcription factor

(2020) Chao Han et al.   Nature Communications

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

The plant stomatal lineage at a glance

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

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

The evolving concept of cell identity in the single cell era

(2019) Samantha A. Morris   DEVELOPMENT

Cell-type–specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage

(2019) Laura R. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Lineage- and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells

(2018) Annika K. Weimer et al.   DEVELOPMENT

MUTE Directly Orchestrates Cell-State Switch and the Single Symmetric Division to Create Stomata

(2018) Soon-Ki Han et al.   DEVELOPMENTAL CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

Modulation of Asymmetric Division Diversity through Cytokinin and SPEECHLESS Regulatory Interactions in the Stomatal Lineage

(2018) Anne Vatén et al.   DEVELOPMENTAL CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

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

A Transcriptional Lineage of the Early C. elegans Embryo

(2016) Sophia C. Tintori et al.   DEVELOPMENTAL CELL

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

25 Years of Cell Cycle Research: What's Ahead?

(2016) Crisanto Gutierrez   TRENDS IN PLANT SCIENCE

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

(2015) Jessika Adrian et al.   DEVELOPMENTAL CELL

Subspecialization of R2R3-MYB Repressors for Anthocyanin and Proanthocyanidin Regulation in Forage Legumes

(2015) Nick W. Albert   Frontiers in Plant Science

How the cell cycle impacts chromatin architecture and influences cell fate

(2015) Yiqin Ma et al.   Frontiers in Genetics

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

(2014) S. Anders et al.   BIOINFORMATICS

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

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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Arabidopsis Reduces Growth Under Osmotic Stress by Decreasing SPEECHLESS Protein

(2014) Archana Kumari et al.   PLANT AND CELL PHYSIOLOGY

Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family

(2014) D. Roppolo et al.   PLANT PHYSIOLOGY

MAB4-induced auxin sink generates local auxin gradients in Arabidopsis organ formation

(2014) M. Furutani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential

(2014) K. A. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct roles of SPEECHLESS in the specification of stomatal self-renewing cells

(2014) O. S. Lau et al.   SCIENCE

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

(2014) Juliana L Matos et al.   eLife

A Dof Transcription Factor, SCAP1, Is Essential for the Development of Functional Stomata in Arabidopsis

(2013) Juntaro Negi et al.   CURRENT BIOLOGY

A bHLH Complex Controls Embryonic Vascular Tissue Establishment and Indeterminate Growth in Arabidopsis

(2013) Bert De Rybel et al.   DEVELOPMENTAL CELL

Timely expression of the Arabidopsis stoma-fate master regulator MUTE is required for specification of other epidermal cell types

(2013) Magdalena Triviño et al.   PLANT JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division

(2012) Alfredo Cruz-Ramírez et al.   CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

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

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

Development of a Series of Gateway Binary Vectors Possessing a Tunicamycin Resistance Gene as a Marker for the Transformation ofArabidopsis thaliana

(2011) Yuji TANAKA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database

(2011) N. Kleinboelting et al.   NUCLEIC ACIDS RESEARCH

Sucrose Efflux Mediated by SWEET Proteins as a Key Step for Phloem Transport

(2011) L.-Q. Chen et al.   SCIENCE

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth

(2010) R. Sozzani et al.   NATURE

MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor

(2010) Alexandra Schlereth et al.   NATURE

The signalling peptide EPFL9 is a positive regulator of stomatal development

(2010) Lee Hunt et al.   NEW PHYTOLOGIST

Two Arabidopsis cyclin A3s possess G1 cyclin-like features

(2010) Ikuo Takahashi et al.   PLANT CELL REPORTS

SHORT-ROOT and SCARECROW Regulate Leaf Growth in Arabidopsis by Stimulating S-Phase Progression of the Cell Cycle

(2010) S. Dhondt et al.   PLANT PHYSIOLOGY

Variability in the Control of Cell Division Underlies Sepal Epidermal Patterning in Arabidopsis thaliana

(2010) Adrienne H. K. Roeder et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Stomagen positively regulates stomatal density in Arabidopsis

(2009) Shigeo S. Sugano et al.   NATURE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Stomatal Density is Controlled by a Mesophyll-Derived Signaling Molecule

(2009) Tatsuhiko Kondo et al.   PLANT AND CELL PHYSIOLOGY

Epidermal Cell Density is Autoregulated via a Secretory Peptide, EPIDERMAL PATTERNING FACTOR 2 in Arabidopsis Leaves

(2009) Kenta Hara et al.   PLANT AND CELL PHYSIOLOGY

Development of R4 Gateway Binary Vectors (R4pGWB) Enabling High-Throughput Promoter Swapping for Plant Research

(2008) Tsuyoshi NAKAGAWA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

SCREAM/ICE1 and SCREAM2 Specify Three Cell-State Transitional Steps Leading to Arabidopsis Stomatal Differentiation

(2008) M. M. Kanaoka et al.   PLANT CELL

Unique and Overlapping Expression Patterns among Members of Photosynthesis-Associated Nuclear Gene Families in Arabidopsis

(2008) M. G. Sawchuk et al.   PLANT PHYSIOLOGY

Arabidopsis Stomatal Initiation Is Controlled by MAPK-Mediated Regulation of the bHLH SPEECHLESS

(2008) G. R. Lampard et al.   SCIENCE