Reorganization of the 3D chromatin architecture of rice genomes during heat stress

Reorganization of the 3D chromatin architecture of rice genomes during heat stress

(2021) Zhe Liang et al.   BMC BIOLOGY

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

(2020) Linhua Sun et al.   Nature Communications

N6-methyladenine in DNA antagonizes SATB1 in early development

(2020) Zheng Li et al.   NATURE

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

(2019) Pengfei Dong et al.   Journal of Integrative Plant Biology

Long-range interactions between proximal and distal regulatory regions in maize

(2019) En Li et al.   Nature Communications

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

(2019) Alessandro Bertero et al.   Nature Communications

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

(2019) Lun Zhao et al.   Nature Communications

Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta

(2019) Zhe Liang et al.   Advanced Science

Epigenetic Modifications of mRNA and DNA in Plants

(2019) Zhe Liang et al.   Molecular Plant

DNA N 6 -Adenine Methylation in Arabidopsis thaliana

(2018) Zhe Liang et al.   DEVELOPMENTAL CELL

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

(2018) Paja Sijacic et al.   PLANT JOURNAL

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

A regulatory role of autophagy for resetting the memory of heat stress in plants

(2018) Mastoureh Sedaghatmehr et al.   PLANT CELL AND ENVIRONMENT

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Stress-induced structural changes in plant chromatin

(2015) Aline V Probst et al.   CURRENT OPINION IN PLANT BIOLOGY

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon 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

Role of plant glyoxylate reductases during stress: a hypothesis

(2009) Wendy L. Allan et al.   BIOCHEMICAL JOURNAL

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE