The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates

(2019) Rui Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Impact of whole-genome duplication events on diversification rates in angiosperms

(2018) Jacob B. Landis et al.   AMERICAN JOURNAL OF BOTANY

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

(2018) Daniel Lang et al.   PLANT JOURNAL

The timescale of early land plant evolution

(2018) Jennifer L. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris

(2018) Rachael E Workman et al.   GigaScience

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

(2017) Amanda R. De La Torre et al.   MOLECULAR BIOLOGY AND EVOLUTION

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research

(2016) Christopher H. Haufler et al.   BIOSCIENCE

A 4000-species dataset provides new insight into the evolution of ferns

(2016) Weston Testo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Expression of an insecticidal fern protein in cotton protects against whitefly

(2016) Anoop Kumar Shukla et al.   NATURE BIOTECHNOLOGY

Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny

(2016) James Clark et al.   NEW PHYTOLOGIST

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

A community-derived classification for extant lycophytes and ferns

(2016)   Journal of Systematics and Evolution

Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates

(2016) EIMEAR NIC LUGHADHA et al.   Phytotaxa

Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

(2015) Lindell Bromham et al.   AMERICAN NATURALIST

NxTrim: optimized trimming of Illumina mate pair reads: Table 1.

(2015) Jared O’Connell et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

An Exploration into Fern Genome Space

(2015) Paul G. Wolf et al.   Genome Biology and Evolution

High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba

(2015) Lorenzo Carretero-Paulet et al.   MOLECULAR BIOLOGY AND EVOLUTION

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Horsetails Are Ancient Polyploids: Evidence fromEquisetum giganteum

(2015) Kevin Vanneste et al.   PLANT CELL

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

Ever since Klekowski: Testing a set of radical hypotheses revives the genetics of ferns and lycophytes

(2014) C. H. Haufler   AMERICAN JOURNAL OF BOTANY

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers

(2014) Anna Rice et al.   NEW PHYTOLOGIST

Azolladomestication towards a biobased economy?

(2014) Paul Brouwer et al.   NEW PHYTOLOGIST

Insights into Conifer Giga-Genomes

(2014) A. R. De La Torre et al.   PLANT PHYSIOLOGY

Between Two Fern Genomes

(2014) Emily B Sessa et al.   GigaScience

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

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

(2013) M C Estep et al.   HEREDITY

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

An automated homology-based approach for identifying transposable elements

(2011) Ryan C Kennedy et al.   BMC BIOINFORMATICS

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics

(2010) Michael S. Barker et al.   Evolutionary Bioinformatics

The Effect of Rain Forest Canopy Architecture on the Distribution of Epiphytic Ferns (Aspleniumspp.) in Sabah, Malaysia

(2009) Tom M. Fayle et al.   BIOTROPICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

(2008) Michel Schneider et al.   Journal of Proteomics

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

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE