Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates

Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second “Core” Gene,sxtG

(2013) Russell J. S. Orr et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Reevaluating the Green Contribution to Diatom Genomes

(2012) Philippe Deschamps et al.   Genome Biology and Evolution

ANALYSIS OFALEXANDRIUM TAMARENSE(DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE1

(2012) Cheong Xin Chan et al.   JOURNAL OF PHYCOLOGY

Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny

(2012) Huan Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alveolate Mitochondrial Metabolic Evolution: Dinoflagellates Force Reassessment of the Role of Parasitism as a Driver of Change in Apicomplexans

(2012) Jillian C. Danne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Saxitoxin Synthesis in Cyanobacteria and Dinoflagellates

(2012) Jeremiah D. Hackett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

(2011) Shinichiro Maruyama et al.   BMC EVOLUTIONARY BIOLOGY

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

(2011) John W Stiller   BMC EVOLUTIONARY BIOLOGY

Two internal type II NADH dehydrogenases of Toxoplasma gondii are both required for optimal tachyzoite growth

(2011) San San Lin et al.   MOLECULAR MICROBIOLOGY

Recent Gene Duplication and Subfunctionalization Produced a Mitochondrial GrpE, the Nucleotide Exchange Factor of the Hsp70 Complex, Specialized in Thermotolerance to Chronic Heat Stress in Arabidopsis

(2011) C. Hu et al.   PLANT PHYSIOLOGY

Discovery of Nuclear-Encoded Genes for the Neurotoxin Saxitoxin in Dinoflagellates

(2011) Anke Stüken et al.   PLoS One

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

(2011) C. J. Gobler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Dinoflagellate Genome Evolution

(2010) Jennifer H. Wisecaver et al.   Annual Review of Microbiology

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum

(2010) Marianne A Minge et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata

(2010) Jennifer H Wisecaver et al.   BMC GENOMICS

Central carbon metabolism of Plasmodium parasites

(2010) Kellen L. Olszewski et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) J. Mark Cock et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

(2010) Ahmed Moustafa et al.   PLoS One

Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

(2010) S. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

(2010) J. Janouskovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

(2010) J. Gordon Burleigh et al.   SYSTEMATIC BIOLOGY

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

(2010) Laura Wegener Parfrey et al.   SYSTEMATIC BIOLOGY

Gene Transfer and Diversification of Microbial Eukaryotes

(2009) Jan O. Andersson   Annual Review of Microbiology

Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology

(2009) Ross F. Waller et al.   BIOESSAYS

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

The Puzzle of Plastid Evolution

(2009) John M. Archibald   CURRENT BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

(2009) Yubo Hou et al.   PLoS One

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

(2009) A. Z. Worden et al.   SCIENCE

Metabolic Function of Corynebacterium glutamicum Aminotransferases AlaT and AvtA and Impact on L-Valine Production

(2008) J. Marienhagen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas

(2008) Ahmed Moustafa et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Biochemical characterization of a mitochondrial-like organelle from Blastocystis sp. subtype 7

(2008) Y. Lantsman et al.   MICROBIOLOGY-SGM

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

From Stop to Start: Tandem Gene Arrangement, Copy Number and Trans-Splicing Sites in the Dinoflagellate Amphidinium carterae

(2008) Tsvetan R. Bachvaroff et al.   PLoS One