Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration

Chromatin accessibility dynamics during cell fate reprogramming

(2021) Dongwei Li et al.   EMBO REPORTS

Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis

(2021) Sangrea Shim et al.   Epigenetics

Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

(2021) Anat Hendelman et al.   CELL

Phytochrome Signaling Networks

(2021) Mei-Chun Cheng et al.   Annual Review of Plant Biology

Model systems for regeneration:Arabidopsis

(2021) Mabel Maria Mathew et al.   DEVELOPMENT

Genetics of Shoot Meristem and Shoot Regeneration

(2021) Leor Eshed Williams   Annual Review of Genetics

A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation

(2020) Kun Zhang et al.   Nature Communications

The atypical histone variant H3.15 promotes callus formation in Arabidopsis thaliana

(2020) An Yan et al.   DEVELOPMENT

The Type-B Cytokinin Response Regulator ARR1 Inhibits Shoot Regeneration in an ARR12-Dependent Manner in Arabidopsis

(2020) Zhenhua Liu et al.   PLANT CELL

Integrative analysis of reference epigenomes in 20 rice varieties

(2020) Lun Zhao et al.   Nature Communications

Reprogramming of Cell Fate During Root Regeneration by Transcriptional and Epigenetic Networks

(2020) Tingting Jing et al.   Frontiers in Plant Science

Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis

(2020) Linhao Xu et al.   Frontiers in Plant Science

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

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

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

Gene regulatory programmes of tissue regeneration

(2020) Joseph A. Goldman et al.   NATURE REVIEWS GENETICS

De novo shoot regeneration controlled by HEN1 and TCP3/4 in Arabidopsis

(2020) Woorim Yang et al.   PLANT AND CELL PHYSIOLOGY

Brassinosteroid-Activated BRI1-EMS-SUPPRESSOR 1 Inhibits Flavonoid Biosynthesis and Coordinates Growth and UV-B Stress Responses in Plants

(2020) Tong Liang et al.   PLANT CELL

Advances in Plant Regeneration: Shake, Rattle and Roll

(2020) Sergio Ibáñez et al.   Plants-Basel

How do plants transduce wound signals to induce tissue repair and organ regeneration?

(2020) Momoko Ikeuchi et al.   CURRENT OPINION IN PLANT BIOLOGY

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Natural Variation in Plant Pluripotency and Regeneration

(2020) Robin Lardon et al.   Plants-Basel

Molecular Mechanisms of Plant Regeneration

(2019) Momoko Ikeuchi et al.   Annual Review of Plant Biology

Arabidopsis histone H3K4 demethylase JMJ 17 functions in dehydration stress response

(2019) Shuangzhan Huang et al.   NEW PHYTOLOGIST

Regeneration enhancers: Starting a journey to unravel regulatory events in tissue regeneration

(2019) Anjelica M. Rodriguez et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Primed histone demethylation regulates shoot regenerative competency

(2019) Hiroya Ishihara et al.   Nature Communications

Cell Reprogramming: The Many Roads to Success

(2019) Begüm Aydin et al.   Annual Review of Cell and Developmental Biology

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming

(2019) Nicole R. Stone et al.   Cell Stem Cell

BZR1 Family Transcription Factors Function Redundantly and Indispensably in BR Signaling but Exhibit BRI1-Independent Function in Regulating Anther Development in Arabidopsis

(2019) Lian-Ge Chen et al.   Molecular Plant

Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

(2019) Wenhao Yan et al.   Nature Communications

De novo shoot organogenesis during plant regeneration

(2019) Jinwoo Shin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Arabidopsis CAMTA Transcription Factors Regulate Pipecolic Acid Biosynthesis and Priming of Immunity Genes

(2019) Yongsig Kim et al.   Molecular Plant

Brassinosteroids: Multi-Dimensional Regulators of Plant Growth, Development, and Stress Responses

(2019) Trevor Nolan et al.   PLANT CELL

AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration

(2019) Bin-Bin Ye et al.   PLANT CELL

BES1 is activated by EMS1-TPD1-SERK1/2-mediated signaling to control tapetum development in Arabidopsis thaliana

(2019) Weiyue Chen et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

UVR8 Interacts with BES1 and BIM1 to Regulate Transcription and Photomorphogenesis in Arabidopsis

(2018) Tong Liang et al.   DEVELOPMENTAL CELL

A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration

(2018) Momoko Ikeuchi et al.   PLANT AND CELL PHYSIOLOGY

JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis

(2018) Kyounghee Lee et al.   PLANT JOURNAL

Thioredoxin-Mediated ROS Homeostasis Explains Natural Variation in Plant Regeneration

(2018) Hui Zhang et al.   PLANT PHYSIOLOGY

iPSCs: A Comparison between Animals and Plants

(2018) Ya Lin Sang et al.   TRENDS IN PLANT SCIENCE

Dynamic Epigenetic Changes during Plant Regeneration

(2018) Kyounghee Lee et al.   TRENDS IN PLANT SCIENCE

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development

(2018) Mingtang Xie et al.   Nature Communications

Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells

(2018) Junko Hasegawa et al.   Scientific Reports

Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition inArabidopsis

(2018) Ji‐Yun Kim et al.   EMBO JOURNAL

Tissue Regeneration Enhancer Elements: A Way to Unlock Endogenous Healing Power

(2018) KaHoua Yang et al.   DEVELOPMENTAL DYNAMICS

ARABIDOPSIS TRITHORAX 4 Facilitates Shoot Identity Establishment during the Plant Regeneration Process

(2018) Kyounghee Lee et al.   PLANT AND CELL PHYSIOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

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

Type-B ARABIDOPSIS RESPONSE REGULATORs Is Critical to the Specification of Shoot Stem Cell Niche by Dual Regulation of WUSCHEL

(2017) Wenjing Meng et al.   PLANT CELL

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Phytochromes and Phytochrome Interacting Factors

(2017) Vinh Ngoc Pham et al.   PLANT PHYSIOLOGY

Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis

(2017) Estefano Bustillo-Avendaño et al.   PLANT PHYSIOLOGY

Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development inArabidopsis

(2017) Yan O. Zubo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ArabidopsisATXR2 deposits H3K36me3 at the promoters ofLBDgenes to facilitate cellular dedifferentiation

(2017) Kyounghee Lee et al.   Science Signaling

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

(2017) Orly L. Wapinski et al.   Cell Reports

ArabidopsisATXR2 deposits H3K36me3 at the promoters ofLBDgenes to facilitate cellular dedifferentiation

(2017) Kyounghee Lee et al.   Science Signaling

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

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

Information Integration and Communication in Plant Growth Regulation

(2016) Juthamas Chaiwanon et al.   CELL

Plant regeneration: cellular origins and molecular mechanisms

(2016) Momoko Ikeuchi et al.   DEVELOPMENT

Chromatin Control of Developmental Dynamics and Plasticity

(2016) Matteo Perino et al.   DEVELOPMENTAL CELL

Genome-wide analyses for dissecting gene regulatory networks in the shoot apical meristem

(2016) Mariana Bustamante et al.   JOURNAL OF EXPERIMENTAL BOTANY

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis

(2016) Akira Iwase et al.   PLANT CELL

Wound signaling of regenerative cell reprogramming

(2016) Samuel Daniel Lup et al.   PLANT SCIENCE

Very-long-chain fatty acids restrict regeneration capacity by confining pericycle competence for callus formation inArabidopsis

(2016) Baoshuan Shang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

PLETHORA Genes Control Regeneration by a Two-Step Mechanism

(2015) Abdul Kareem et al.   CURRENT BIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

An Intrinsic MicroRNA Timer Regulates Progressive Decline in Shoot Regenerative Capacity in Plants

(2015) Tian-Qi Zhang et al.   PLANT CELL

Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light

(2015) Dingbang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes

(2014) Ignacio Rubio-Somoza et al.   CURRENT BIOLOGY

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Interaction between MYC2 and ETHYLENE INSENSITIVE3 Modulates Antagonism between Jasmonate and Ethylene Signaling in Arabidopsis

(2014) S. Song et al.   PLANT CELL

A mechanistic framework for noncell autonomous stem cell induction inArabidopsis

(2014) Gabor Daum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Y. Liao et al.   BIOINFORMATICS

Chromatin dynamics during cellular reprogramming

(2013) Effie Apostolou et al.   NATURE

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration

(2012) Mingzhu Fan et al.   CELL RESEARCH

MYC2: The Master in Action

(2012) Kemal Kazan et al.   Molecular Plant

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

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

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

Incipient stem cell niche conversion in tissue culture: using a systems approach to probe early events inWUSCHEL-dependent conversion of lateral root primordia into shoot meristems

(2012) Steven P. Chatfield et al.   PLANT JOURNAL

Pattern of Auxin and Cytokinin Responses for Shoot Meristem Induction Results from the Regulation of Cytokinin Biosynthesis by AUXIN RESPONSE FACTOR3

(2012) Z. J. Cheng et al.   PLANT PHYSIOLOGY

Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues

(2012) Chongsheng He et al.   PLoS Genetics

The Epigenome and Plant Development

(2011) Guangming He et al.   Annual Review of Plant Biology

The AP2/ERF Transcription Factor WIND1 Controls Cell Dedifferentiation in Arabidopsis

(2011) Akira Iwase et al.   CURRENT BIOLOGY

WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex

(2011) R. K. Yadav et al.   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Regeneration in plants and animals: dedifferentiation, transdifferentiation, or just differentiation?

(2011) Kaoru Sugimoto et al.   TRENDS IN CELL BIOLOGY

De novo shoot organogenesis: from art to science

(2011) Jérôme Duclercq et al.   TRENDS IN PLANT SCIENCE

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytokinin signaling and transcriptional networks

(2010) Cristiana T Argueso et al.   CURRENT OPINION IN PLANT BIOLOGY

Arabidopsis Regeneration from Multiple Tissues Occurs via a Root Development Pathway

(2010) Kaoru Sugimoto et al.   DEVELOPMENTAL CELL

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

(2010) Marco Todesco et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Slicing across Kingdoms: Regeneration in Plants and Animals

(2008) Kenneth D. Birnbaum et al.   CELL

Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grownin vitro

(2008) Ramzy Atta et al.   PLANT JOURNAL

Cytokinin signaling: two-components and more

(2008) Jennifer P.C. To et al.   TRENDS IN PLANT SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Three Type-B Response Regulators, ARR1, ARR10 and ARR12, Play Essential but Redundant Roles in Cytokinin Signal Transduction Throughout the Life Cycle of Arabidopsis thaliana

(2007) Kai Ishida et al.   PLANT AND CELL PHYSIOLOGY