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

Mind the gap; seven reasons to close fragmented genome assemblies

(2016) Bart P.H.J. Thomma et al.   FUNGAL GENETICS AND BIOLOGY

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

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

(2015) Alison C Testa et al.   BMC GENOMICS

Overview of genomic and bioinformatic resources for Zymoseptoria tritici

(2015) Alison Testa et al.   FUNGAL GENETICS AND BIOLOGY

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

(2015) Braham Dhillon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

(2014) Ian Reid et al.   BMC BIOINFORMATICS

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

(2014) Lyndel W Meinhardt et al.   BMC GENOMICS

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

Database resources of the National Center for Biotechnology Information

(2014)   NUCLEIC ACIDS RESEARCH

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

(2014) Xiao Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

(2014) Yong Zhang et al.   Nature Communications

The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte

(2014) Xi-Hui Xu et al.   Scientific Reports

Early insights into the genome sequence of Uromyces fabae

(2014) Tobias Link et al.   Frontiers in Plant Science

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

(2013) Frank O. Aylward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Compositional patterns in the genomes of unicellular eukaryotes

(2013) Maria Costantini et al.   BMC GENOMICS

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation

(2013) Guoqing Pan et al.   BMC GENOMICS

Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus

(2013) Xiao Hu et al.   CHINESE SCIENCE BULLETIN

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System

(2013) Cassandra Collins et al.   JOURNAL OF PROTEOME RESEARCH

Evolution of fungal sexual reproduction

(2013) Joseph Heitman et al.   MYCOLOGIA

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Multiple Interkingdom Horizontal Gene Transfers in Pyrenophora and Closely Related Species and Their Contributions to Phytopathogenic Lifestyles

(2013) Bao-Fa Sun et al.   PLoS One

Genomic Insights into the Atopic Eczema-Associated Skin Commensal Yeast Malassezia sympodialis

(2013) A. Gioti et al.   mBio

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

(2013) Tejashwari Meerupati et al.   PLoS 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

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

(2013) Christopher L. Schardl et al.   PLoS Genetics

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

The pointy end of the stick: managing biological invasions

(2013) Marnie Campbell   Management of Biological Invasions

The Genomics of Obligate (and Nonobligate) Biotrophs

(2012) Pietro D. Spanu   Annual Review of Phytopathology

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution

(2012) Sheng Zhu et al.   BMC GENOMICS

Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina

(2012) Md Islam et al.   BMC GENOMICS

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

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

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

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Genomic tillage and the harvest of fungal phytopathogens

(2012) Richard Oliver   NEW PHYTOLOGIST

Sex in Cheese: Evidence for Sexuality in the Fungus Penicillium roqueforti

(2012) Jeanne Ropars et al.   PLoS One

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

(2012) Pierre J. G. M. de Wit et al.   PLoS Genetics

Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

(2012) Donald M. Gardiner et al.   PLoS Pathogens

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous FungusNeurospora tetrasperma

(2011) Christopher E. Ellison et al.   GENETICS

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

(2011) Randy M Berka et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

(2011) Christopher A. Desjardins et al.   PLoS Genetics

Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine

(2011) Peng Zheng et al.   GENOME BIOLOGY

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

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

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm

(2010) Eran Elhaik et al.   NUCLEIC ACIDS RESEARCH

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

Comparative Testing of DNA Segmentation Algorithms Using Benchmark Simulations

(2009) Eran Elhaik et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi

(2009) Donna E. Akiyoshi et al.   PLoS Pathogens

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

(2008) James K Hane et al.   BMC BIOINFORMATICS

Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

(2008) Wei-Jen Chung et al.   CURRENT BIOLOGY