Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

(2021) Le Zhang et al.   Horticulture Research

Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe

(2021) Wenbing Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

(2019) Qionghou Li et al.   Horticulture Research

Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

(2019) Romain Lannes et al.   Genes

DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts

(2019) Jaemyung Choi et al.   MOLECULAR CELL

Inferring synteny between genome assemblies: a systematic evaluation

(2018) Dang Liu et al.   BMC BIOINFORMATICS

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

(2018) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Fractionation and Function in the Ancient Subgenomes of Maize

(2017) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Patterns and Consequences of Subgenome Differentiation Provide Insights into the Nature of Paleopolyploidy in Plants

(2017) Meixia Zhao et al.   PLANT CELL

FractBias: a graphical tool for assessing fractionation bias following polyploidy

(2016) Blake L. Joyce et al.   BIOINFORMATICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Spatial mismatches between plant biodiversity facets and evolutionary legacy in the vicinity of a major Mediterranean city

(2016) M. Pouget et al.   ECOLOGICAL INDICATORS

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

(2016) Rie Shimizu-Inatsugi et al.   MOLECULAR ECOLOGY

The wondrous cycles of polyploidy in plants

(2015) Jonathan F. Wendel   AMERICAN JOURNAL OF BOTANY

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences

(2015) Michael Freeling et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution

(2015) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Control of transposable elements in Arabidopsis thaliana

(2014) Hidetaka Ito et al.   CHROMOSOME RESEARCH

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

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

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

(2013) M C Estep et al.   HEREDITY

Phylogenetic conservatism in plant phenology

(2013) T. Jonathan Davies et al.   JOURNAL OF ECOLOGY

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Transposon variation by order during allopolyploidisation betweenBrassica oleraceaandBrassica rapa

(2013) Z. An et al.   PLANT BIOLOGY

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

Single-Copy Nuclear Genes Place Haustorial Hydnoraceae within Piperales and Reveal a Cretaceous Origin of Multiple Parasitic Angiosperm Lineages

(2013) Julia Naumann et al.   PLoS One

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

(2012) Michael Freeling et al.   CURRENT OPINION IN PLANT BIOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

(2012) Feng Cheng et al.   PLoS One

Past Climate Change and Plant Evolution in Western North America: A Case Study in Rosaceae

(2012) Mats Töpel et al.   PLoS One

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A mystery unveiled

(2011) Yves Van de Peer   GENOME BIOLOGY

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids

(2008) M. Chen et al.   GENETICS