Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus

(2021) Jacob L. Steenwyk et al.   Microbiology Spectrum

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coinfinder: detecting significant associations and dissociations in pangenomes

(2020) Fiona Jane Whelan et al.   Microbial Genomics

Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis

(2020) Renato A. C. dos Santos et al.   Frontiers in Genetics

Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species

(2020) Jacob L. Steenwyk et al.   GENETICS

Effects of Agricultural Fungicide Use on Aspergillus fumigatus Abundance, Antifungal Susceptibility, and Population Structure

(2020) Amelia E. Barber et al.   mBio

Mutations in hmg1, Challenging the Paradigm of Clinical Triazole Resistance in Aspergillus fumigatus

(2019) Jeffrey M. Rybak et al.   mBio

Nutritional Heterogeneity Among Aspergillus fumigatus Strains Has Consequences for Virulence in a Strain- and Host-Dependent Manner

(2019) Laure Nicolas Annick Ries et al.   Frontiers in Microbiology

Revealing the Virulence Potential of Clinical and Environmental Aspergillus fumigatus Isolates Using Whole-Genome Sequencing

(2019) Fabiola Puértolas-Balint et al.   Frontiers in Microbiology

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Aspergillus fumigatus and Aspergillosis in 2019

(2019) Jean-Paul Latgé et al.   CLINICAL MICROBIOLOGY REVIEWS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Linking secondary metabolites to gene clusters through genome sequencing of six diverseAspergillusspecies

(2018) Inge Kjærbølling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Comparative Analysis of Aspergillus fumigatus Strains: The Reference Genome as a Matter of Concern

(2018) Rocio Garcia-Rubio et al.   Genes

Incidence and outcome of invasive fungal diseases after allogeneic hematopoietic stem cell transplantation: A Swiss transplant cohort study

(2018) Sabine Kuster et al.   Transplant Infectious Disease

Voriconazole Resistance and Mortality in Invasive Aspergillosis: A Multicenter Retrospective Cohort Study

(2018) Pieter P Lestrade et al.   CLINICAL INFECTIOUS DISEASES

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Secondary metabolite arsenal of an opportunistic pathogenic fungus

(2016) Elaine Bignell et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Heterogeneity among Isolates Reveals that Fitness in Low Oxygen Correlates with Aspergillus fumigatus Virulence

(2016) Caitlin H. Kowalski et al.   mBio

Characterization of Aspergillus fumigatus Isolates from Air and Surfaces of the International Space Station

(2016) Benjamin P. Knox et al.   mSphere

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Incidence and characteristics of invasive fungal diseases in allogeneic hematopoietic stem cell transplant recipients: a retrospective cohort study

(2015) Nicole Harrison et al.   BMC INFECTIOUS DISEASES

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Divergent Targets of Aspergillus fumigatus AcuK and AcuM Transcription Factors during GrowthIn Vitroversus Invasive Disease

(2014) Monsicha Pongpom et al.   INFECTION AND IMMUNITY

Genetic and virulence variation in an environmental population of the opportunistic pathogen Aspergillus fumigatus

(2014) F. Alshareef et al.   MICROBIOLOGY-SGM

The pH-Responsive PacC Transcription Factor of Aspergillus fumigatus Governs Epithelial Entry and Tissue Invasion during Pulmonary Aspergillosis

(2014) Margherita Bertuzzi et al.   PLoS Pathogens

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Strain Dependent Variation of Immune Responses to A. fumigatus: Definition of Pathogenic Species

(2013) Lisa Rizzetto et al.   PLoS One

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Molecular Epidemiology of Aspergillus fumigatus Isolates Harboring the TR34/L98H Azole Resistance Mechanism

(2012) S. M. T. Camps et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Targeted Disruption of Nonribosomal Peptide Synthetasepes3Augments the Virulence of Aspergillus fumigatus

(2011) Karen A. O'Hanlon et al.   INFECTION AND IMMUNITY

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2011) N. D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

SREBP Coordinates Iron and Ergosterol Homeostasis to Mediate Triazole Drug and Hypoxia Responses in the Human Fungal Pathogen Aspergillus fumigatus

(2011) Michael Blatzer et al.   PLoS Genetics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis

(2010) Ana Abad et al.   REVISTA IBEROAMERICANA DE MICOLOGIA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

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

Genes Differentially Expressed in Conidia and Hyphae of Aspergillus fumigatus upon Exposure to Human Neutrophils

(2008) Janyce A. Sugui et al.   PLoS One

Emergence of Azole Resistance in Aspergillus fumigatus and Spread of a Single Resistance Mechanism

(2008) Eveline Snelders et al.   PLOS MEDICINE

A Sterol-Regulatory Element Binding Protein Is Required for Cell Polarity, Hypoxia Adaptation, Azole Drug Resistance, and Virulence in Aspergillus fumigatus

(2008) Sven D. Willger et al.   PLoS Pathogens