Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

Genetic Dissection of Sesquiterpene Biosynthesis byFusarium fujikuroi

(2013) Nelson L. Brock et al.   CHEMBIOCHEM

A Functional Bikaverin Biosynthesis Gene Cluster in Rare Strains of Botrytis cinerea Is Positively Controlled by VELVET

(2013) Julia Schumacher et al.   PLoS One

Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator

(2013) Razieh Karimi-Aghcheh et al.   G3-Genes Genomes 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

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

(2013) Bradford J. Condon et al.   PLoS Genetics

Identification and Regulation offusA, the Polyketide Synthase Gene Responsible for Fusarin Production in Fusarium fujikuroi

(2012) Violeta Díaz-Sánchez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosynthesis of Fusarubins Accounts for Pigmentation of Fusarium fujikuroi Perithecia

(2012) Lena Studt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data

(2012) T. Bald et al.   BIOINFORMATICS

A heptaketide naphthaldehyde produced by a polyketide synthase from Nectria haematococca

(2012) Takayoshi Awakawa et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

(2012) Sebastian Müller et al.   BMC GENOMICS

Centromeres of filamentous fungi

(2012) Kristina M. Smith et al.   CHROMOSOME RESEARCH

Segregation of secondary metabolite biosynthesis in hybrids of Fusarium fujikuroi and Fusarium proliferatum

(2012) L. Studt et al.   FUNGAL GENETICS AND BIOLOGY

Tools for Botrytis cinerea: New expression vectors make the gray mold fungus more accessible to cell biology approaches

(2012) Julia Schumacher   FUNGAL GENETICS AND BIOLOGY

Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioides

(2012) Daren W. Brown et al.   FUNGAL GENETICS AND BIOLOGY

Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster

(2012) Matthew A. Campbell et al.   Genome Biology and Evolution

Quick guide to polyketide synthase and nonribosomal synthetase genes in Fusarium

(2012) Frederik T. Hansen et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Structure Elucidation of New Fusarins Revealing Insights in the Rearrangement Mechanisms of the Fusarium Mycotoxin Fusarin C

(2012) Karin Kleigrewe et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

New Approach via Gene Knockout and Single-Step Chemical Reaction for the Synthesis of Isotopically Labeled Fusarin C as an Internal Standard for the Analysis of this Fusarium Mycotoxin in Food and Feed Samples

(2012) Karin Kleigrewe et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Overexpression of theAspergillus nidulanshistone 4 acetyltransferase EsaA increases activation of secondary metabolite production

(2012) Alexandra A. Soukup et al.   MOLECULAR MICROBIOLOGY

The velvet complex governs mycotoxin production and virulence ofFusarium oxysporumon plant and mammalian hosts

(2012) Manuel S. López-Berges et al.   MOLECULAR MICROBIOLOGY

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

The Sfp-Type 4′-Phosphopantetheinyl Transferase Ppt1 of Fusarium fujikuroi Controls Development, Secondary Metabolism and Pathogenicity

(2012) Philipp Wiemann et al.   PLoS One

First fungal genome sequence from Africa: A preliminary analysis

(2012) Brenda D. Wingfield et al.   SOUTH AFRICAN JOURNAL OF SCIENCE

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

(2012) D. A. Martinez et al.   mBio

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows

(2011) Michael Specht et al.   BIOINFORMATICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Fusarium verticillioides chitin synthases CHS5 and CHS7 are required for normal growth and pathogenicity

(2011) Troy M. Larson et al.   CURRENT GENETICS

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

(2011) Daren W. Brown et al.   Fungal Biology

A New High-Performance Liquid Chromatography–Tandem Mass Spectrometry Method Based on Dispersive Solid Phase Extraction for the Determination of the Mycotoxin Fusarin C in Corn Ears and Processed Corn Samples

(2011) Karin Kleigrewe et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Heterochromatin Is Required for Normal Distribution of Neurospora crassa CenH3

(2011) K. M. Smith et al.   MOLECULAR AND CELLULAR BIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation

(2011) H.-W. Nutzmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome

(2011) Michael Specht et al.   PROTEOMICS

Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer

(2011) Anastasia Kalli et al.   PROTEOMICS

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

(2011) Christian P Kubicek et al.   GENOME BIOLOGY

Large scale purification of B-type fumonisins using centrifugal partition chromatography (CPC)

(2011) Florian Hübner et al.   Mycotoxin Research

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

Regulation of secondary metabolism by chromatin structure and epigenetic codes

(2010) Joseph Strauss et al.   FUNGAL GENETICS AND BIOLOGY

H2B- and H3-Specific Histone Deacetylases Are Required for DNA Methylation in Neurospora crassa

(2010) K. M. Smith et al.   GENETICS

Characterizing the Anaerobic Response ofChlamydomonas reinhardtiiby Quantitative Proteomics

(2010) Mia Terashima et al.   MOLECULAR & CELLULAR PROTEOMICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans

(2010) Yazmid Reyes-Dominguez et al.   MOLECULAR MICROBIOLOGY

Functional characterization and manipulation of the apicidin biosynthetic pathway inFusarium semitectum

(2010) Jian-Ming Jin et al.   MOLECULAR MICROBIOLOGY

Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism

(2010) Thorsten Schinko et al.   MOLECULAR MICROBIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

(2010) P. Wong et al.   NUCLEIC ACIDS RESEARCH

EpiChIP: gene-by-gene quantification of epigenetic modification levels

(2010) Daniel Hebenstreit et al.   NUCLEIC ACIDS RESEARCH

Gibberellin biosynthesis and gibberellin oxidase activities in Fusarium sacchari, Fusarium konzum and Fusarium subglutinans strains

(2010) Claudia Troncoso et al.   PHYTOCHEMISTRY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

(2010) Minou Nowrousian et al.   PLoS Genetics

qvality: non-parametric estimation of q-values and posterior error probabilities

(2009) Lukas Käll et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Biosynthesis of the cyclooligomer depsipeptide bassianolide, an insecticidal virulence factor of Beauveria bassiana

(2009) Yuquan Xu et al.   FUNGAL GENETICS AND BIOLOGY

A Gene Cluster Containing Two Fungal Polyketide Synthases Encodes the Biosynthetic Pathway for a Polyketide, Asperfuranone, inAspergillus nidulans

(2009) Yi-Ming Chiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biosynthesis of the red pigment bikaverin inFusarium fujikuroi: genes, their function and regulation

(2009) Philipp Wiemann et al.   MOLECULAR MICROBIOLOGY

Epigenome manipulation as a pathway to new natural product scaffolds and their congeners

(2009) Robert H. Cichewicz   NATURAL PRODUCT REPORTS

Chromatin-level regulation of biosynthetic gene clusters

(2009) Jin Woo Bok et al.   Nature Chemical Biology

SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

(2009) Thomas Rattei et al.   NUCLEIC ACIDS RESEARCH

Diversity, regulation, and evolution of the gibberellin biosynthetic pathway in fungi compared to plants and bacteria

(2009) Christiane Bömke et al.   PHYTOCHEMISTRY

Infection Dynamics ofFusarium mangiferae, Causal Agent of Mango Malformation Disease

(2009) E. Gamliel-Atinsky et al.   PHYTOPATHOLOGY

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

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

Isolation and Characterization of the Gibberellin Biosynthetic Gene Cluster in Sphaceloma manihoticola

(2008) C. Bomke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Loss of Gibberellin Production in Fusarium verticillioides (Gibberella fujikuroi MP-A) Is Due to a Deletion in the Gibberellic Acid Gene Cluster

(2008) C. Bomke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Regulation of Carotenogenesis and Secondary Metabolism by Nitrogen in Wild-Type Fusarium fujikuroi and Carotenoid-Overproducing Mutants

(2008) R. Rodriguez-Ortiz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Funybase: a Fungal phylogenomic database

(2008) Sylvain Marthey et al.   BMC BIOINFORMATICS

Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis

(2008) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

A fumonisin biosynthetic gene cluster in Fusarium oxysporum strain O-1890 and the genetic basis for B versus C fumonisin production

(2008) Robert H. Proctor et al.   FUNGAL GENETICS AND BIOLOGY

Production of gibberellic acids by an orchid-associated Fusarium proliferatum strain

(2008) Elena A. Tsavkelova et al.   FUNGAL GENETICS AND BIOLOGY

Role of AREA, a regulator of nitrogen metabolism, during colonization of maize kernels and fumonisin biosynthesis in Fusarium verticillioides

(2008) Hun Kim et al.   FUNGAL GENETICS AND BIOLOGY

DupMasker: A tool for annotating primate segmental duplications

(2008) Z. Jiang et al.   GENOME RESEARCH

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

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

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

PEDANT covers all complete RefSeq genomes

(2008) M. C. Walter et al.   NUCLEIC ACIDS RESEARCH

Epigenetic remodeling of the fungal secondary metabolome

(2008) Russell B. Williams et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

(2008) G. Aguileta et al.   SYSTEMATIC BIOLOGY

Transformation-Mediated Complementation of aFUMGene Cluster Deletion inFusarium verticillioidesRestores both Fumonisin Production and Pathogenicity on Maize Seedlings

(2007) Anthony E. Glenn et al.   MOLECULAR PLANT-MICROBE INTERACTIONS