The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens : introducing the ecotype Reute

(2017) Manuel Hiss et al.   PLANT JOURNAL

Dehydration-responsive features of Atrichum undulatum

(2016) Ruoyang Hu et al.   JOURNAL OF PLANT RESEARCH

A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

(2016) Carlos Ortiz-Ramírez et al.   Molecular Plant

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

(2016) Nicolas Devos et al.   NEW PHYTOLOGIST

Highly efficient gene tagging in the bryophytePhyscomitrella patensusing the tobacco (Nicotiana tabacum) Tnt1 retrotransposon

(2016) Cristina Vives et al.   NEW PHYTOLOGIST

Phytochromes: More Than Meets the Eye

(2016) Stefan A. Rensing et al.   TRENDS IN PLANT SCIENCE

A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction

(2016) Nelly A. Horst et al.   Nature Plants

PGSB PlantsDB: updates to the database framework for comparative plant genome research

(2015) Manuel Spannagl et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Horsetails Are Ancient Polyploids: Evidence fromEquisetum giganteum

(2015) Kevin Vanneste et al.   PLANT CELL

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex

(2014) Anna K Beike et al.   BMC EVOLUTIONARY BIOLOGY

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

De novoassembly and comparative analysis of theCeratodon purpureustranscriptome

(2014) Péter Szövényi et al.   Molecular Ecology Resources

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Epigenetic reprogramming in plant sexual reproduction

(2014) Tomokazu Kawashima et al.   NATURE REVIEWS GENETICS

The chromatin landscape of the mossPhyscomitrella patensand its dynamics during development and drought stress

(2014) Thomas Widiez et al.   PLANT JOURNAL

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Plant genomes enclose footprints of past infections by giant virus relatives

(2014) Florian Maumus et al.   Nature Communications

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

(2013) Andreas D Zimmer et al.   BMC GENOMICS

Gene duplication as a driver of plant morphogenetic evolution

(2013) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

Genome size increases in recently diverged hornwort clades

(2013) Jillian D. Bainard et al.   GENOME

Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss

(2013) Péter Szövényi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nuclear DNA content variation and evolution in liverworts

(2013) Jillian D. Bainard et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ThePpCMTchromomethylase affects cell growth and interacts with the homolog of LIKE HETEROCHROMATIN PROTEIN 1 in the mossPhyscomitrella patens

(2013) Meenakshi Dangwal et al.   PLANT JOURNAL

KNOX2 Genes Regulate the Haploid-to-Diploid Morphological Transition in Land Plants

(2013) K. Sakakibara et al.   SCIENCE

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

(2012) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

Developmental relaxation of transposable element silencing in plants: functional or byproduct?

(2012) Germán Martínez et al.   CURRENT OPINION IN PLANT BIOLOGY

Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification

(2012) Dries Vekemans et al.   MOLECULAR BIOLOGY AND EVOLUTION

DICER-LIKE3 Activity in Physcomitrella patens DICER-LIKE4 Mutants Causes Severe Developmental Dysfunction and Sterility

(2012) M. Asif Arif et al.   Molecular Plant

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

(2012) H. Stroud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

(2012) Guillaume Blanc et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao 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

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

(2010) Daniel Lang et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Improved criteria and comparative genomics tool provide new insights into grass paleogenomics

(2009) J. Salse et al.   BRIEFINGS IN BIOINFORMATICS

THE SPECIATION HISTORY OF THEPHYSCOMITRIUM-PHYSCOMITRELLASPECIES COMPLEX

(2009) Stuart F. McDaniel et al.   EVOLUTION

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

An overview of plant centromeres

(2009) Guixiang Wang et al.   Journal of Genetics and Genomics

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

A sequence-anchored genetic linkage map for the moss,Physcomitrella patens

(2008) Yasuko Kamisugi et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY