Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana

(2017) Megan C. McDonald et al.   MOLECULAR PLANT PATHOLOGY

A functionally conserved Zn2 Cys6 binuclear cluster transcription factor class regulates necrotrophic effector gene expression and host-specific virulence of two major Pleosporales fungal pathogens of wheat

(2017) Kasia Rybak et al.   MOLECULAR PLANT PATHOLOGY

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

Proposal for a unified nomenclature for target-site mutations associated with resistance to fungicides

(2016) Wesley Mair et al.   PEST MANAGEMENT SCIENCE

Evaluation of a Multilocus Indel DNA Region for the Detection of the Wheat Tan Spot PathogenPyrenophora tritici-repentis

(2016) Pao Theen See et al.   PLANT DISEASE

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

(2016) Robert A. Syme et al.   PLoS One

Genetic relationships between race-nonspecific and race-specific interactions in the wheat–Pyrenophora tritici-repentis pathosystem

(2016) Gayan K. Kariyawasam et al.   THEORETICAL AND APPLIED GENETICS

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

(2015) Jennifer M. Shelton et al.   BMC GENOMICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The impact of Septoria tritici Blotch disease on wheat: An EU perspective

(2015) Helen Fones et al.   FUNGAL GENETICS AND BIOLOGY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

(2015) Karine de Guillen et al.   PLoS Pathogens

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Necrotrophic Effector Epistasis in the Pyrenophora tritici-repentis-Wheat Interaction

(2015) Viola A. Manning et al.   PLoS One

Leaf yellowing of the wheat cultivar Mace in the absence of yellow spot disease

(2014) C. S. Moffat et al.   AUSTRALASIAN PLANT PATHOLOGY

andi: Fast and accurate estimation of evolutionary distances between closely related genomes

(2014) Bernhard Haubold et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

High Variability of Mitochondrial Gene Order among Fungi

(2014) Gabriela Aguileta et al.   Genome Biology and Evolution

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

gKaKs: the pipeline for genome-level Ka/Ks calculation

(2013) Chengjun Zhang et al.   BIOINFORMATICS

Global population structure and migration patterns suggest significant population differentiation among isolates of Pyrenophora tritici-repentis

(2013) S. Gurung et al.   FUNGAL GENETICS AND BIOLOGY

The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences

(2013) Cyril Férandon et al.   FUNGAL GENETICS AND BIOLOGY

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Peppy: Proteogenomic Search Software

(2013) Brian A. Risk et al.   JOURNAL OF PROTEOME RESEARCH

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

Resequencing and Comparative Genomics of Stagonospora nodorum : Sectional Gene Absence and Effector Discovery

(2013) Robert Andrew Syme et al.   G3-Genes Genomes Genetics

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Evolution of three Pyrenophora cereal pathogens: Recent divergence, speciation and evolution of non-coding DNA

(2012) Simon R. Ellwood et al.   FUNGAL GENETICS AND BIOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Frequent Gain and Loss of Introns in Fungal Cytochrome b Genes

(2012) Liang-Fen Yin et al.   PLoS One

A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

(2012) Simon R Ellwood et al.   GENOME BIOLOGY

Simple sequence repeats and diversity of globally distributed populations ofPyrenophora tritici-repentis

(2011) R. Aboukhaddour et al.   CANADIAN JOURNAL OF PLANT PATHOLOGY

Entry of oomycete and fungal effectors into plant and animal host cells

(2011) Shiv D. Kale et al.   CELLULAR MICROBIOLOGY

Evolutionary Dynamics of the mS952 Intron: A Novel Mitochondrial Group II Intron Encoding a LAGLIDADG Homing Endonuclease Gene

(2011) Sahra-Taylor Mullineux et al.   JOURNAL OF MOLECULAR EVOLUTION

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

(2011) James K Hane et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

(2010) James K Hane et al.   BMC GENOMICS

External Lipid PI3P Mediates Entry of Eukaryotic Pathogen Effectors into Plant and Animal Host Cells

(2010) Shiv D. Kale et al.   CELL

Proteinaceous necrotrophic effectors in fungal virulence

(2010) Kar-Chun Tan et al.   FUNCTIONAL PLANT BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Repeated genomic transfers from echovirus 30 to echovirus 6 lineages indicate co-divergence between co-circulating populations of the two human enterovirus serotypes

(2010) J.-L. Bailly et al.   INFECTION GENETICS AND EVOLUTION

Estimating disease losses to the Australian wheat industry

(2009) Gordon M. Murray et al.   AUSTRALASIAN PLANT PATHOLOGY

Ubiquity of ToxA and absence of ToxB in Australian populations ofPyrenophora tritici-repentis

(2009) Eva A. Antoni et al.   AUSTRALASIAN PLANT PATHOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Lateral Transfer of Genes and Gene Fragments in Prokaryotes

(2009) Cheong Xin Chan et al.   Genome Biology and Evolution

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Influence of water activity and temperature on growth and mycotoxin production by isolates of Pyrenophora tritici-repentis from wheat

(2009) Noureddine Bouras et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Are Protein Domains Modules of Lateral Genetic Transfer?

(2009) Cheong Xin Chan et al.   PLoS One

GenomeVx: simple web-based creation of editable circular chromosome maps

(2008) G. C. Conant et al.   BIOINFORMATICS

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

(2008) James K Hane et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

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

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

Genome characterization ofPyrenophora tritici-repentisisolates reveals high plasticity and independent chromosomal location ofToxAandToxB

(2008) R. ABOUKHADDOUR et al.   MOLECULAR PLANT PATHOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY