Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

(2013) Zhongtao Zhao et al.   BMC GENOMICS

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

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

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

Single-nucleotide polymorphism discovery inLeptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing

(2013) Dario I. Ojeda et al.   Molecular Ecology Resources

Genetic and Genomic Analysis of Rhizoctonia solani Interactions with Arabidopsis; Evidence of Resistance Mediated through NADPH Oxidases

(2013) Rhonda C. Foley et al.   PLoS One

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts

(2013) S. Hacquard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ploidy variation as an adaptive mechanism in human pathogenic fungi

(2013) Carl A. Morrow et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The evolution and pathogenic mechanisms of the rice sheath blight pathogen

(2013) Aiping Zheng et al.   Nature Communications

Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi

(2013) Tejashwari Meerupati et al.   PLoS Genetics

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi

(2012) Felix Horns et al.   Genome Biology and Evolution

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

(2012) Daniel Wibberg et al.   JOURNAL OF BIOTECHNOLOGY

Current models of the mode of action of Bacillus thuringiensis insecticidal crystal proteins: A critical review

(2012) Vincent Vachon et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors

(2012) D. K. Lakshman et al.   MYCOLOGIA

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

(2012) J. D. Laurie et al.   PLANT CELL

The Curious Chemical Biology of Cytosine: Deamination, Methylation,and Oxidation as Modulators of Genomic Potential

(2011) Christopher S. Nabel et al.   ACS Chemical Biology

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems

(2011) Renee Rioux et al.   CURRENT GENETICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Oomycete and fungal effector entry, a microbial Trojan horse

(2011) Shiv D. Kale   NEW PHYTOLOGIST

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

LTR Retrotransposons in Fungi

(2011) Anna Muszewska et al.   PLoS One

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

(2011) James K Hane et al.   GENOME BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

Recent developments in effector biology of filamentous plant pathogens

(2010) Ricardo Oliva et al.   CELLULAR MICROBIOLOGY

Maize genotype susceptibility to Rhizoctonia solani and its effect on sugar beet crop rotations

(2010) C. Kluth et al.   CROP PROTECTION

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Susceptibility of intercrops to infection with Rhizoctonia solani AG 2-2 IIIB and influence on subsequently cultivated sugar beet

(2010) C. Kluth et al.   PLANT PATHOLOGY

The B-3 Ethylene Response Factor MtERF1-1 Mediates Resistance to a Subset of Root Pathogens in Medicago truncatula without Adversely Affecting Symbiosis with Rhizobia

(2010) J. P. Anderson et al.   PLANT PHYSIOLOGY

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

(2010) J. Schirawski et al.   SCIENCE

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

(2010) Angela P. Van de Wouw et al.   PLoS Pathogens

Estimating disease losses to the Australian wheat industry

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

Estimating disease losses to the Australian barley industry

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Factors affecting protoplast formation by Rhizoctonia solani

(2009) Tung-Hsen Liu et al.   New Biotechnology

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System

(2009) Konstantinos Mavromatis et al.   PLoS One

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

(2008) Jorge MC Mondego et al.   BMC GENOMICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY