Related references
Note: Only part of the references are listed.A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme
Katharina Eitzen et al.
ELIFE (2021)
Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus
Michael Habig et al.
NATURE COMMUNICATIONS (2021)
A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
Ursula Oggenfuss et al.
ELIFE (2021)
Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen
Simone Fouche et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Target the core: durable plant resistance against filamentous plant pathogens through effector recognition
Jasper R. L. Depotter et al.
PEST MANAGEMENT SCIENCE (2020)
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model
David E. Torres et al.
Fungal Biology Reviews (2020)
SignalP 5.0 improves signal peptide predictions using deep neural networks
Jose Juan Almagro Armenteros et al.
NATURE BIOTECHNOLOGY (2019)
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
Yang Liao et al.
NUCLEIC ACIDS RESEARCH (2019)
Molecular Interactions Between Smut Fungi and Their Host Plants
Weiliang Zuo et al.
Annual Review of Phytopathology (2019)
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
Kaining Hu et al.
BMC BIOINFORMATICS (2019)
Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation
Jasper R. L. Depotter et al.
MOLECULAR ECOLOGY (2019)
An evolutionary framework for host shifts - jumping ships for survival
Marco Thines
NEW PHYTOLOGIST (2019)
Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses
Ga-Eun Lee et al.
VIRUSES-BASEL (2019)
The need for speed: compartmentalized genome evolution in filamentous phytopathogens
Lamprinos Frantzeskakis et al.
MOLECULAR PLANT PATHOLOGY (2019)
The Pfam protein families database in 2019
Sara El-Gebali et al.
NUCLEIC ACIDS RESEARCH (2019)
Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
Lamprinos Frantzeskakis et al.
BMC GENOMICS (2018)
A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
Jeremy Berthelier et al.
BMC GENOMICS (2018)
Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum
Gabriel Schweizer et al.
GENOME BIOLOGY AND EVOLUTION (2018)
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Han Zhang et al.
NUCLEIC ACIDS RESEARCH (2018)
RNAi is a critical determinant of centromere evolution in closely related fungi
Vikas Yadav et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp tritici Reveals High Interhaplotype Diversity
Benjamin Schwessinger et al.
MBIO (2018)
Ustilago species causing leaf-stripe smut revisited
Julia Kruse et al.
IMA FUNGUS (2018)
Mining the effector repertoire of the biotrophic fungal pathogen Ustilago hordei during host and non-host infection
Bilal Okmen et al.
MOLECULAR PLANT PATHOLOGY (2018)
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
Juan Manuel Crescente et al.
BMC BIOINFORMATICS (2018)
A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni
Remco Stam et al.
GENOME BIOLOGY AND EVOLUTION (2018)
Ten things you should know about transposable elements
Guillaume Bourque et al.
GENOME BIOLOGY (2018)
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci
Christina A. Cuomo et al.
G3-GENES GENOMES GENETICS (2017)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher et al.
NATURE (2017)
Evolution and genome architecture in fungal plant pathogens
Mareike Moeller et al.
NATURE REVIEWS MICROBIOLOGY (2017)
Life, death and rebirth of avirulence effectors in a fungal pathogen of Brassica crops, Leptosphaeria maculans
Thierry Rouxel et al.
NEW PHYTOLOGIST (2017)
Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response
Vivien Horvath et al.
TRENDS IN GENETICS (2017)
SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets
Hongliang Mao et al.
BIOINFORMATICS (2017)
Retroviral DNA Integration
Paul Lesbats et al.
CHEMICAL REVIEWS (2016)
Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
Nikolaos Vakirlis et al.
GENOME RESEARCH (2016)
Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
Luigi Faino et al.
GENOME RESEARCH (2016)
DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses
Thomas Wicker et al.
NATURE COMMUNICATIONS (2016)
A complete toolset for the study of Ustilago bromivora and Brachypodium sp as a fungal-temperate grass pathosystem
Franziska Rabe et al.
ELIFE (2016)
Understanding Plant Immunity as a Surveillance System to Detect Invasion
David E. Cook et al.
ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 53 (2015)
FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
Ka-Kit Lam et al.
BIOINFORMATICS (2015)
The two-speed genomes of filamentous pathogens: waltz with plants
Suomeng Dong et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2015)
Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported2489Mbp
Ana Paula Ramos et al.
MOLECULAR PLANT PATHOLOGY (2015)
Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina
Q. -M. Wang et al.
STUDIES IN MYCOLOGY (2015)
Repbase Update, a database of repetitive elements in eukaryotic genomes
Weidong Bao et al.
MOBILE DNA (2015)
Sex or no sex: Evolutionary adaptation occurs regardless
Michael F. Seidl et al.
BIOESSAYS (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
InterProScan 5: genome-scale protein function classification
Philip Jones et al.
BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum
Rahul Sharma et al.
GENOME BIOLOGY AND EVOLUTION (2014)
SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes
Guenola Drillon et al.
PLOS ONE (2014)
PASTEC: An Automatic Transposable Element Classification Tool
Claire Hoede et al.
PLOS ONE (2014)
An Immunity-Triggering Effector from the Barley Smut Fungus Ustilago hordei Resides in an Ustilaginaceae-Specific Cluster Bearing Signs of Transposable Element-Assisted Evolution
Shawkat Ali et al.
PLOS PATHOGENS (2014)
Genome size analyses of Pucciniales reveal the largest fungal genomes
Silvia Tavares et al.
FRONTIERS IN PLANT SCIENCE (2014)
Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs
Guenola Drillon et al.
JOURNAL OF LOGIC AND COMPUTATION (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis
Francois Lefebvre et al.
PLANT CELL (2013)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Daehwan Kim et al.
GENOME BIOLOGY (2013)
Genome Sequence of the Basidiomycetous Yeast Pseudozyma antarctica T-34, a Producer of the Glycolipid Biosurfactants Mannosylerythritol Lipids
Tomotake Morita et al.
GENOME ANNOUNCEMENTS (2013)
Do TE activity and counteracting genome defenses, RNAi and methylation, shape the sex lives of smut fungi?
John D. Laurie et al.
PLANT SIGNALING & BEHAVIOR (2013)
Retrotransposons
David J. Finnegan
CURRENT BIOLOGY (2012)
Host Specificity of Sporisorium reilianum Is Tightly Linked to Generation of the Phytoalexin Luteolinidin by Sorghum bicolor
Katja Zuther et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Genome evolution in filamentous plant pathogens: why bigger can be better
Sylvain Raffaele et al.
NATURE REVIEWS MICROBIOLOGY (2012)
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
Yanbin Yin et al.
NUCLEIC ACIDS RESEARCH (2012)
Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements
John D. Laurie et al.
PLANT CELL (2012)
The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens
Daniel Croll et al.
PLOS PATHOGENS (2012)
Ultra-fast sequence clustering from similarity networks with SiLiX
Vincent Miele et al.
BMC BIOINFORMATICS (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Basidiomycete Mating Type Genes and Pheromone Signaling
Marjatta Raudaskoski et al.
EUKARYOTIC CELL (2010)
Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison
Jan Schirawski et al.
SCIENCE (2010)
The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis
Nicolas Corradi et al.
NATURE COMMUNICATIONS (2010)
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
David Ellinghaus et al.
BMC BIOINFORMATICS (2008)
A unified classification system for eukaryotic transposable elements
Thomas Wicker et al.
NATURE REVIEWS GENETICS (2007)
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
Joerg Kaemper et al.
NATURE (2006)
Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals
Guus Bakkeren et al.
FUNGAL GENETICS AND BIOLOGY (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li et al.
BIOINFORMATICS (2006)
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
DG Hwang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Versatile and open software for comparing large genomes
S Kurtz et al.
GENOME BIOLOGY (2004)
The diversity of LTR retrotransposons
ER Havecker et al.
GENOME BIOLOGY (2004)
Human SNP variability and mutation rate are higher in regions of high recombination
MJ Lercher et al.
TRENDS IN GENETICS (2002)
Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi
MD Katinka et al.
NATURE (2001)
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
A Krogh et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Share Paper
