Increased evolutionary rates and conserved transcriptional response following allopolyploidization in brown algae

Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat

(2016) Huakun Zhang et al.   Scientific Reports

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

(2015) Wandrille Duchemin et al.   BMC BIOINFORMATICS

Seascape drivers ofMacrocystis pyriferapopulation genetic structure in the northeast Pacific

(2015) Mattias L. Johansson et al.   MOLECULAR ECOLOGY

Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing

(2015) Xutong Wang et al.   NEW PHYTOLOGIST

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The legacy of diploid progenitors in allopolyploid gene expression patterns

(2014) R. J. A. Buggs et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing

(2014) Filipe de Sousa et al.   PLoS One

An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns

(2014) Murray P. Cox et al.   PLoS Genetics

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Gene duplication as a driver of plant morphogenetic evolution

(2013) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton

(2012) Lex E Flagel et al.   BMC GENOMICS

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Drifting fronds and drifting alleles: range dynamics, local dispersal and habitat isolation shape the population structure of the estuarine seaweed Fucus ceranoides

(2012) João Neiva et al.   JOURNAL OF BIOGEOGRAPHY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat

(2012) E. D. Akhunov et al.   PLANT PHYSIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation

(2011) Fernando G Cánovas et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant

(2011) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature

(2011) Amélie Bardil et al.   NEW PHYTOLOGIST

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

(2011) Shaowei Dong et al.   NEW PHYTOLOGIST

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ALLOPOLYPLOIDY IN NATURAL AND CULTIVATED POPULATIONS OF PORPHYRA (BANGIALES, RHODOPHYTA)1

(2010) Kyosuke Niwa et al.   JOURNAL OF PHYCOLOGY

A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the “brown algal crown radiation”

(2010) Thomas Silberfeld et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Clues to the Evolutionary Success of Polyploid Plants

(2008) Matthew J. Hegarty et al.   CURRENT BIOLOGY

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE