Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum

Effector Specialization in a Lineage of the Irish Potato Famine Pathogen

(2014) S. Dong et al.   SCIENCE

A review of the Ustilago-Sporisorium-Macalpinomyces complex

(2013) A.R. McTaggart et al.   PERSOONIA

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

Metabolic priming by a secreted fungal effector

(2011) Armin Djamei et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Eric Kemen et al.   PLOS BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

The molecular phylogeny of the white blister rust genus Pustula reveals a case of underestimated biodiversity with several undescribed species on ornamentals and crop plants

(2010) Sebastian Ploch et al.   Fungal Biology

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

SUPERFAMILY 1.75 including a domain-centric gene ontology method

(2010) D. A. de Lima Morais et al.   NUCLEIC ACIDS RESEARCH

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

(2010) J. Schirawski et al.   SCIENCE

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

(2010) S. Raffaele et al.   SCIENCE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Brian J. Haas et al.   NATURE

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Pep1, a Secreted Effector Protein of Ustilago maydis, Is Required for Successful Invasion of Plant Cells

(2009) Gunther Doehlemann et al.   PLoS Pathogens

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction

(2008) Qian Liu et al.   BIOINFORMATICS

Entering and breaking: virulence effector proteins of oomycete plant pathogens

(2008) Brett M. Tyler   CELLULAR MICROBIOLOGY

Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance

(2008) Paul RJ Birch et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

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

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

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

(2008) T. Lima et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH