Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus

The Clock Takes Shape—24 h Dynamics in Genome Topology

(2022) Kévin Tartour et al.   Frontiers in Cell and Developmental Biology

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

(2021) Jérôme Mermet et al.   PLoS Genetics

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

(2021) Gareth Steed et al.   SCIENCE

Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

(2020) Andrés Romanowski et al.   PLANT JOURNAL

Diversified regulation of circadian clock gene expression following whole genome duplication

(2020) Alexander C. West et al.   PLoS Genetics

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

(2020) Kathleen Greenham et al.   eLife

Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus

(2020) Qing Zhang et al.   Molecular Plant

A Novel Loop: Mutual Regulation Between Epigenetic Modification and the Circadian Clock

(2019) Shenxiu Du et al.   Frontiers in Plant Science

Continuous dynamic adjustment of the plant circadian oscillator

(2019) Alex A. R. Webb et al.   Nature Communications

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

(2019) Hong An et al.   Nature Communications

Molecular mechanisms and physiological importance of circadian rhythms

(2019) Alina Patke et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive mapping of abiotic stress inputs into the soybean circadian clock

(2019) Meina Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The circadian clock coordinates plant development through specificity at the tissue and cellular level

(2019) Mark Greenwood et al.   CURRENT OPINION IN PLANT BIOLOGY

CircadiOmics: circadian omic web portal

(2018) Nicholas Ceglia et al.   NUCLEIC ACIDS RESEARCH

TPMCalculator: one-step software to quantify mRNA abundance of genomic features

(2018) Roberto Vera Alvarez et al.   BIOINFORMATICS

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

(2017) Kathleen Greenham et al.   eLife

Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes

(2016) J. Chris Pires et al.   Annual Review of Genetics

What time is it? Deep learning approaches for circadian rhythms

(2016) Forest Agostinelli et al.   BIOINFORMATICS

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Organ specificity in the plant circadian system is explained by different light inputs to the shoot and root clocks

(2016) Simon Bordage et al.   NEW PHYTOLOGIST

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis

(2016) Katja Baerenfaller et al.   PLANT CELL AND ENVIRONMENT

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Circadian Clock Genes Universally Control Key Agricultural Traits

(2015) Claire Bendix et al.   Molecular Plant

Integrating circadian dynamics with physiological processes in plants

(2015) Kathleen Greenham et al.   NATURE REVIEWS GENETICS

Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa

(2015) Yulia Yarkhunova et al.   NEW PHYTOLOGIST

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

(2015) Dawn H. Nagel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Tissue-specific clocks in Arabidopsis show asymmetric coupling

(2014) Motomu Endo et al.   NATURE

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome

(2012) Christopher Vollmers et al.   Cell Metabolism

Preferential Retention of Circadian Clock Genes during Diploidization following Whole Genome Triplication inBrassica rapa

(2012) Ping Lou et al.   PLANT CELL

Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

(2012) W. Huang et al.   SCIENCE

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

(2011) Yun Chen et al.   BMC GENOMICS

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY