Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

(2016) Camille Sessegolo et al.   Biology Letters

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Fast and accurate detection of evolutionary shifts in Ornstein-Uhlenbeck models

(2016) Mohammad Khabbazian et al.   Methods in Ecology and Evolution

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Effects of Crossovers Between Homeologs on Inheritance and Population Genomics in Polyploid-Derived Salmonid Fishes

(2015) F. W. Allendorf et al.   JOURNAL OF HEREDITY

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

(2015) R. K. Waples et al.   Molecular Ecology Resources

Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein–Uhlenbeck Model

(2015) Clayton E. Cressler et al.   SYSTEMATIC BIOLOGY

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

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

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

(2014) D. J. Macqueen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposable element islands facilitate adaptation to novel environments in an invasive species

(2014) Lukas Schrader et al.   Nature Communications

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

(2013) Kentaro Yoshida et al.   eLife

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

(2012) Andreas W Schreiber et al.   BMC GENOMICS

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

(2012) Ross D Houston et al.   BMC GENOMICS

Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes

(2012) Yu-Tin Chen et al.   BMC GENOMICS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

(2011) N. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Competition and phylogeny determine community structure in Müllerian co-mimics

(2010) Markos A. Alexandrou et al.   NATURE

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum

(2008) T. Eilam et al.   GENOME

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

MicroRNAs and the advent of vertebrate morphological complexity

(2008) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA