Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

(2018) Teofil Nakov et al.   NEW PHYTOLOGIST

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

(2017) Matthew B Parks et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary significance of polyploidy

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

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

(2017) Swaraj Basu et al.   NEW PHYTOLOGIST

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

No evidence for the radiation time lag model after whole genome duplications in Teleostei

(2017) Sacha Laurent et al.   PLoS One

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Phylogenetic evidence for cladogenetic polyploidization in land plants

(2016) Shing H. Zhan et al.   AMERICAN JOURNAL OF BOTANY

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data

(2016) George P. Tiley et al.   Genome Biology and Evolution

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

(2016) Matthew G. Johnson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta

(2016) Sara Moeys et al.   Scientific Reports

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

(2015) Edward C. Theriot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

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

Oil Accumulation by the Oleaginous DiatomFistulifera solarisas Revealed by the Genome and Transcriptome

(2015) Tsuyoshi Tanaka et al.   PLANT CELL

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

(2015) Jun Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare interspecific breeding in Pseudo-nitzschia (Bacillariophyceae)

(2015) Alberto Amato et al.   Phytotaxa

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

(2015) Li Song et al.   GigaScience

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

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

Polyploidy and novelty: Gottlieb's legacy

(2014) Pamela S. Soltis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

An Inordinate Fondness? The Number, Distributions, and Origins of Diatom Species

(2013) David G. Mann et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis

(2013) D.-Y. Chao et al.   SCIENCE

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Metabolomics Enables the Structure Elucidation of a Diatom Sex Pheromone

(2012) Jeroen Gillard et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology

(2012) Kerry A Whittaker et al.   BMC EVOLUTIONARY BIOLOGY

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

(2012) M Eric Schranz et al.   CURRENT OPINION IN PLANT BIOLOGY

HOW MANY SPECIES OF ALGAE ARE THERE?

(2012) Michael D. Guiry   JOURNAL OF PHYCOLOGY

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Novel Sex Cells and Evidence for Sex Pheromones in Diatoms

(2011) Shinya Sato et al.   PLoS One

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

(2010) Julie A Koester et al.   BMC EVOLUTIONARY BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Polyploidy and angiosperm diversification

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

(2009) Francesco Santini et al.   BMC EVOLUTIONARY BIOLOGY

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

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

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Hybrids in the Marine Diatom Pseudo-nitzschia pungens (Bacillariophyceae): Genetic and Morphological Evidence

(2009) Griet Casteleyn et al.   PROTIST

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

In search of new tractable diatoms for experimental biology

(2008) Victor A. Chepurnov et al.   BIOESSAYS

A MOLECULAR SYSTEMATIC APPROACH TO EXPLORE DIVERSITY WITHIN THESELLAPHORA PUPULASPECIES COMPLEX (BACILLARIOPHYTA)

(2008) Katharine M. Evans et al.   JOURNAL OF PHYCOLOGY

INTER- AND INTRASPECIFIC RELATIONSHIPS BETWEEN NUCLEAR DNA CONTENT AND CELL SIZE IN SELECTED MEMBERS OF THE CENTRIC DIATOM GENUSTHALASSIOSIRA(BACILLARIOPHYCEAE)

(2008) Peter von Dassow et al.   JOURNAL OF PHYCOLOGY

CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)

(2008) Jessica A. Connolly et al.   JOURNAL OF PHYCOLOGY

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

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Genetic Divergence and Reproductive Barriers among Morphologically Heterogeneous Sympatric Clones of Eunotia bilunaris Sensu Lato (Bacillariophyta)

(2007) Pieter Vanormelingen et al.   PROTIST