Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts

Plant evolution at the interface of paleontology and developmental biology: An organism-centered paradigm

(2014) Gar W. Rothwell et al.   AMERICAN JOURNAL OF BOTANY

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

(2014) L. Zhou et al.   MOLECULAR ECOLOGY

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

(2014) Cymon J. Cox et al.   SYSTEMATIC BIOLOGY

A synthesis of hornwort diversity: Patterns, causes and future work

(2014) J. C. Villarreal et al.   Phytotaxa

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Early evolution of the vascular plant body plan — the missing mechanisms

(2013) Alexandru MF Tomescu et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome size increases in recently diverged hornwort clades

(2013) Jillian D. Bainard et al.   GENOME

Major transitions in the evolution of early land plants: a bryological perspective

(2012) Roberto Ligrone et al.   ANNALS OF BOTANY

The origin of the sporophyte shoot in land plants: a bryological perspective

(2012) Roberto Ligrone et al.   ANNALS OF BOTANY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years

(2012) J. C. Villarreal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set

(2011) Y. Chang et al.   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

The Earliest Land Plants

(2008) Patricia G. Gensel   Annual Review of Ecology Evolution and Systematics

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

(2008) Yasuko Kamisugi et al.   PLANT JOURNAL