Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata

The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species

(2015) Ha X Dang et al.   BMC GENOMICS

Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS–PKS hybrid enzyme

(2015) Choong-Soo Yun et al.   Nature Communications

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins

(2014) Charley Staats et al.   BMC GENOMICS

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

(2014) Jonathan Grandaubert et al.   BMC GENOMICS

PAMLX: A Graphical User Interface for PAML

(2013) B. Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Assembler for de novo assembly of large genomes

(2013) Te-Chin Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer

(2012) Jinnan Hu et al.   BMC GENOMICS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Identification of a Polyketide Synthase Required for Alternariol (AOH) and Alternariol-9-Methyl Ether (AME) Formation in Alternaria alternata

(2012) Debjani Saha et al.   PLoS One

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

SMURF: Genomic mapping of fungal secondary metabolite clusters

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

Characterization of the programmed cell death induced by metabolic products of Alternaria alternata in tobacco BY-2 cells

(2010) Dan-Dan Cheng et al.   PHYSIOLOGIA PLANTARUM

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

Infernal 1.0: inference of RNA alignments

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

Horizontal Chromosome Transfer, a Mechanism for the Evolution and Differentiation of a Plant-Pathogenic Fungus

(2009) Yasunori Akagi et al.   EUKARYOTIC CELL

Alternaria alternataAT Toxin Induces Programmed Cell Death in Tobacco

(2009) Elena T. Yakimova et al.   JOURNAL OF PHYTOPATHOLOGY

Functional Analysis of a Multicopy Host-Selective ACT-Toxin Biosynthesis Gene in the Tangerine Pathotype of Alternaria alternata Using RNA Silencing

(2008) Y. Miyamoto et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

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

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