Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate

Chromatin features constrain structural variation across evolutionary timescales

(2019) Geoff Fudenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

(2019) Alexandre P. Marand et al.   PLANT CELL

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

(2018) Qianli Dong et al.   PLANT JOURNAL

Entering the Next Dimension: Plant Genomes in 3D

(2018) Mariana Sotelo-Silveira et al.   TRENDS IN PLANT SCIENCE

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans

(2018) Jedidiah Carlson et al.   Nature Communications

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Pengfei Dong et al.   Molecular Plant

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

MethBank 3.0: a database of DNA methylomes across a variety of species

(2017) Rujiao Li et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Preferential Protection of Genetic Fidelity within Open Chromatin by the Mismatch Repair Machinery

(2016) Lue Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

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(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Rice SNP-seek database update: new SNPs, indels, and queries

(2016) Locedie Mansueto et al.   NUCLEIC ACIDS RESEARCH

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

Unraveling the mechanisms of chromatin fibril packaging

(2016) Alexey A. Gavrilov et al.   Nucleus

Unraveling the mechanisms of chromatin fibril packaging

(2016) Alexey A. Gavrilov et al.   Nucleus

Nucleotide diversity analysis highlights functionally important genomic regions

(2016) Tatiana V. Tatarinova et al.   Scientific Reports

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F2plants

(2015) Weina Si et al.   NEW PHYTOLOGIST

PlantDHS: a database for DNase I hypersensitive sites in plants

(2015) Tao Zhang et al.   NUCLEIC ACIDS RESEARCH

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

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

Refining analyses of copy number variation identifies specific genes associated with developmental delay

(2014) Bradley P Coe et al.   NATURE GENETICS

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

(2012) W. Qu et al.   GENOME RESEARCH

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

(2011) Carina F Mugal et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Condensin and cohesin complexity: the expanding repertoire of functions

(2010) Andrew J. Wood et al.   NATURE REVIEWS GENETICS