Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Differential Retention of Gene Functions in a Secondary Metabolite Cluster

(2017) Hannah T. Reynolds et al.   MOLECULAR BIOLOGY AND EVOLUTION

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Balancing selection for aflatoxin in Aspergillus flavus is maintained through interference competition with, and fungivory by insects

(2017) Milton T. Drott et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

(2017) Abigail L. Lind et al.   PLOS BIOLOGY

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Disparate Independent Genetic Events Disrupt the Secondary Metabolism GeneperAin Certain Symbiotic Epichloë Species

(2015) Daniel Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

(2015) C. Alisha Quandt et al.   BMC GENOMICS

Phylogenomics and evolution of secondary metabolism in plant-associated fungi

(2015) Joseph W Spatafora et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity withinFusarium fujikuroi

(2015) Matteo Chiara et al.   Genome Biology and Evolution

Clustering of Two Genes Putatively Involved in Cyanate Detoxification Evolved Recently and Independently in Multiple Fungal Lineages

(2015) M. Holly Elmore et al.   Genome Biology and Evolution

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The long reach of telomeres: Figure 1.

(2014) Tom Misteli   GENES & DEVELOPMENT

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Alternaria host-selective toxins: determinant factors of plant disease

(2013) Kazuya Akimitsu et al.   JOURNAL OF GENERAL PLANT PATHOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Repeated loss of an anciently horizontally transferred gene cluster in Botrytis

(2013) Matthew A. Campbell et al.   MYCOLOGIA

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

(2013) Rosie E. Bradshaw et al.   NEW PHYTOLOGIST

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

(2013) Julia Schumacher et al.   PLoS One

Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds

(2013) K. L. McGary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Philipp Wiemann et al.   PLoS Pathogens

Terpendole E, a Kinesin Eg5 Inhibitor, Is a Key Biosynthetic Intermediate of Indole-Diterpenes in the Producing Fungus Chaunopycnis alba

(2012) Takayuki Motoyama et al.   CHEMISTRY & BIOLOGY

Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

(2012) Han Zhang et al.   PLoS One

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Effect of sexual recombination on population diversity in aflatoxin production byAspergillus flavusand evidence for cryptic heterokaryosis

(2011) RODRIGO A. OLARTE et al.   MOLECULAR ECOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species

(2011) Izumi Chuma et al.   PLoS Pathogens

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

(2011) Christian P Kubicek et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

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

Production of fumonisins B2 and B4 in Tolypocladium species

(2010) Jesper Mølgaard Mogensen et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Larvicidal activity of metabolites from the endophytic Podospora sp. against the malaria vector Anopheles gambiae

(2010) Josphat C. Matasyoh et al.   PARASITOLOGY RESEARCH

Fungal toxins affect the fitness and stable isotope fractionation of Collembola

(2010) Swantje Staaden et al.   SOIL BIOLOGY & BIOCHEMISTRY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Recombination and lineage-specific gene loss in the aflatoxin gene cluster ofAspergillus flavus

(2009) GEROMY G. MOORE et al.   MOLECULAR ECOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

Evolution of genome architecture

(2008) Eugene V. Koonin   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Immunosuppressive effect of cyclosporin A on insect humoral immune response

(2008) Marta J. Fiolka   JOURNAL OF INVERTEBRATE PATHOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY