Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

(2017) Seungho Kang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

(2017) Lucie Gallot-Lavallée et al.   Viruses-Basel

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

(2017) Richard G Dorrell et al.   eLife

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

(2016) Romain Derelle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles

(2016) Fumiya Noguchi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

(2015) Rahul Sharma et al.   BMC GENOMICS

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

Bacterial proteins pinpoint a single eukaryotic root

(2015) Romain Derelle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of Horizontal Gene Transfer in the Evolution of the Oomycetes

(2015) Fiona Savory et al.   PLoS Pathogens

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases

(2015) Arne Schwelm et al.   Scientific Reports

Clotrimazole as a Potent Agent for Treating the Oomycete Fish Pathogen Saprolegnia parasitica through Inhibition of Sterol 14α-Demethylase (CYP51)

(2014) Andrew G. S. Warrilow et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A network-based approach to identify substrate classes of bacterial glycosyltransferases

(2014) Aminael Sánchez-Rodríguez et al.   BMC GENOMICS

A Rhodopsin-Guanylyl Cyclase Gene Fusion Functions in Visual Perception in a Fungus

(2014) Gabriela M. Avelar et al.   CURRENT BIOLOGY

The Secreted Proteins of Achlya hypogyna and Thraustotheca clavata Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer

(2014) Ian Misner et al.   Genome Biology and Evolution

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proteomics Analysis of Heterogeneous Flagella in Brown Algae (Stramenopiles)

(2014) Gang Fu et al.   PROTIST

opm: an R package for analysing OmniLog(R) phenotype microarray data

(2013) L. A. I. Vaas et al.   BIOINFORMATICS

Ultrafast Approximation for Phylogenetic Bootstrap

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

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The nexin-dynein regulatory complex subunit DRC1 is essential for motile cilia function in algae and humans

(2013) Maureen Wirschell et al.   NATURE GENETICS

Horizontal gene transfer in osmotrophs: playing with public goods

(2013) Thomas A. Richards et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Identification of Plasmopara viticola Genes Potentially Involved in Pathogenesis on Grapevine Suggests New Similarities Between Oomycetes and True Fungi

(2013) P. Luis et al.   PHYTOPATHOLOGY

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

(2013) Marcelo M. Zerillo et al.   PLoS One

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

(2013) Bishwo N. Adhikari et al.   PLoS One

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

(2013) M. W. Brown et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

(2013) Rays H. Y. Jiang et al.   PLoS Genetics

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types

(2012) Hugo Mélida et al.   EUKARYOTIC CELL

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

(2012) G. Leonard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

No jacket required - new fungal lineage defies dress code

(2011) Timothy Y. James et al.   BIOESSAYS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Myosin-5, kinesin-1 and myosin-17 cooperate in secretion of fungal chitin synthase

(2011) Martin Schuster et al.   EMBO JOURNAL

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

(2011) Adam Monier et al.   ENVIRONMENTAL MICROBIOLOGY

Effect of Tween 80 on the growth, lipid accumulation and fatty acid composition of Thraustochytrium aureum ATCC 34304

(2011) Yousuke Taoka et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolutionary phylogeny of the oomycete “fungi”

(2011) Gordon W. Beakes et al.   PROTOPLASMA

Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana

(2011) Eric Kemen et al.   PLOS BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

(2010) Sylvain Raffaele et al.   BMC GENOMICS

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

(2010) Byung H Park et al.   GLYCOBIOLOGY

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

(2010) J. Mark Cock et al.   NATURE

TheChlorella variabilisNC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

(2010) Guillaume Blanc et al.   PLANT CELL

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

(2010) M. F. Seidl et al.   PLANT PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

(2010) C André Lévesque et al.   GENOME BIOLOGY

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

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

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

(2009) John W Stiller et al.   BMC GENOMICS

Chitin in Diatoms and Its Association with the Cell Wall

(2009) Colleen A. Durkin et al.   EUKARYOTIC CELL

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

(2009) A. Monier et al.   GENOME RESEARCH

Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans

(2009) P. R. J. Birch et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Evolution of phototaxis

(2009) G. Jekely   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Multiple Horizontal Gene Transfer Events and Domain Fusions Have Created Novel Regulatory and Metabolic Networks in the Oomycete Genome

(2009) Paul Francis Morris et al.   PLoS One

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

(2009) John W Whitaker et al.   GENOME BIOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses

(2008) Nicolas Delaroque et al.   BMC EVOLUTIONARY BIOLOGY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding

(2008) Clement K.M. Tsui et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

RXLR-Mediated Entry of Phytophthora sojae Effector Avr1b into Soybean Cells Does Not Require Pathogen-Encoded Machinery

(2008) D. Dou et al.   PLANT CELL

Conserved C-Terminal Motifs Required for Avirulence and Suppression of Cell Death by Phytophthora sojae effector Avr1b

(2008) D. Dou et al.   PLANT CELL

Transcriptome of Aphanomyces euteiches: New Oomycete Putative Pathogenicity Factors and Metabolic Pathways

(2008) Elodie Gaulin et al.   PLoS One

Regulation of polarised growth in fungi

(2008) Peter E. Sudbery   Fungal Biology Reviews

Evolution of the cutinase gene family: Evidence for lateral gene transfer of a candidate Phytophthora virulence factor

(2007) Lassaad Belbahri et al.   GENE