Comparative Genomics of Taphrina Fungi Causing Varying Degrees of Tumorous Deformity in Plants

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

(2013) Zhongtao Zhao 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

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

(2013) O. H. Cisse et al.   mBio

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

(2012) Marco Falda et al.   BMC BIOINFORMATICS

MITOS: Improved de novo metazoan mitochondrial genome annotation

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

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

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

(2012) Cole Trapnell et al.   Nature Protocols

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Aneuploidy and Drug Resistance in Pathogenic Fungi

(2012) Kyung J. Kwon-Chung et al.   PLoS Pathogens

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Two-Component Systems and Their Co-Option for Eukaryotic Signal Transduction

(2011) G. Eric Schaller et al.   CURRENT BIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

PomBase: a comprehensive online resource for fission yeast

(2011) V. Wood et al.   NUCLEIC ACIDS RESEARCH

The main auxin biosynthesis pathway in Arabidopsis

(2011) K. Mashiguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Two-Component Mediated Peroxide Sensing and Signal Transduction in Fission Yeast

(2010) Janet Quinn et al.   ANTIOXIDANTS & REDOX SIGNALING

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Overwintering of Taphrina wiesneri within cherry shoots monitored with species-specific PCR

(2010) Masabumi Komatsu et al.   JOURNAL OF GENERAL PLANT PATHOLOGY

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

(2010) J. Schirawski et al.   SCIENCE

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

PAT proteins, an ancient family of lipid droplet proteins that regulate cellular lipid stores

(2009) Perry E. Bickel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fungal meiosis and parasexual reproduction—lessons from pathogenic yeast

(2009) Racquel K Sherwood et al.   CURRENT OPINION IN MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

General Rules for Optimal Codon Choice

(2009) Ruth Hershberg et al.   PLoS Genetics

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Dimorphism in fungal plant pathogens

(2008) Marina Nadal et al.   FEMS MICROBIOLOGY LETTERS

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

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

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

(2008) Y. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Indole-3-acetic acid (IAA) biosynthesis in the smut fungus Ustilago maydis and its relevance for increased IAA levels in infected tissue and host tumour formation

(2008) GAVIN REINEKE et al.   MOLECULAR PLANT PATHOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time

(2008) Denghui Xing et al.   PLANT JOURNAL