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

Drug resistance and tolerance in fungi

(2020) Judith Berman et al.   NATURE REVIEWS MICROBIOLOGY

Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity

(2020) Antonis Rokas et al.   PLoS Pathogens

Uncovering New Mutations Conferring Azole Resistance in the Aspergillus fumigatus cyp51A Gene

(2020) Peiying Chen et al.   Frontiers in Microbiology

Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans

(2020) Rafael Wesley Bastos et al.   mSphere

Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus

(2019) Matthew E. Mead et al.   mSphere

In vitro activity of olorofim (F901318) against clinical isolates of cryptic species of Aspergillus by EUCAST and CLSI methodologies

(2019) Olga Rivero-Menendez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium

(2019) Jacob L. Steenwyk et al.   mBio

Update and recent advances on azole resistance mechanisms in

(2019) Alba Pérez-Cantero et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

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

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

Fungal biofilm morphology impacts hypoxia fitness and disease progression

(2019) Caitlin H. Kowalski et al.   Nature Microbiology

Aspergillus fumigatus and Aspergillosis in 2019

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

Recent trends in the epidemiology, diagnosis, treatment, and mechanisms of resistance in clinical Aspergillus species: A general review with a special focus on the Middle Eastern and North African region

(2019) Ayate Zakaria et al.   Journal of Infection and Public Health

Investigation of Multiple Resistance Mechanisms in Voriconazole-Resistant Aspergillus flavus Clinical Isolates from a Chest Hospital Surveillance in Delhi, India

(2018) Cheshta Sharma et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Insight into the Significance of Aspergillus fumigatus cyp51A Polymorphisms

(2018) Rocio Garcia-Rubio et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The evolutionary origins of pesticide resistance

(2018) Nichola J. Hawkins et al.   BIOLOGICAL REVIEWS

The pathogenicity of Aspergillus fumigatus, drug resistance, and nanoparticle delivery

(2018) David A. Szalewski et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Executive summary of clinical practice guideline for the management of invasive diseases caused by Aspergillus : 2018 Update by the GEMICOMED-SEIMC/REIPI

(2018) Carolina Garcia-Vidal et al.   ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA

Aspergillus terreus: Novel lessons learned on amphotericin B resistance

(2018) Wilfried Posch et al.   MEDICAL MYCOLOGY

Paralogous Cyp51s mediate the differential sensitivity of Fusarium oxysporum to sterol demethylation inhibitors

(2018) Bangxian Zheng et al.   PEST MANAGEMENT SCIENCE

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

Worldwide emergence of resistance to antifungal drugs challenges human health and food security

(2018) Matthew C. Fisher et al.   SCIENCE

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside

(2018) Justin Beardsley et al.   Future Microbiology

Molecular bases of antifungal resistance in filamentous fungi

(2017) Cheshta Sharma et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Heterogeneity Confounds Establishment of “a” Model Microbial Strain

(2017) Nancy P. Keller   mBio

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

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

Practice Guidelines for the Diagnosis and Management of Aspergillosis: 2016 Update by the Infectious Diseases Society of America

(2016) Thomas F. Patterson et al.   CLINICAL INFECTIOUS DISEASES

Epidemiology and molecular mechanisms of antifungal resistance in CandidaandAspergillus

(2016) Sarah Santos Gonçalves et al.   MYCOSES

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

(2016) Caitlin H. Kowalski et al.   mBio

Aspergillus fumigatus Photobiology Illuminates the Marked Heterogeneity between Isolates

(2016) Kevin K. Fuller et al.   mBio

Epidemiological and Genomic Landscape of Azole Resistance Mechanisms in Aspergillus Fungi

(2016) Daisuke Hagiwara et al.   Frontiers in Microbiology

Aspergillus fumigatus-Related Species in Clinical Practice

(2016) Frédéric Lamoth   Frontiers in Microbiology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Chronic pulmonary aspergillosis: rationale and clinical guidelines for diagnosis and management

(2015) David W. Denning et al.   EUROPEAN RESPIRATORY JOURNAL

The molecular mechanism of azole resistance in Aspergillus fumigatus: from bedside to bench and back

(2015) Xiaolei Wei et al.   JOURNAL OF MICROBIOLOGY

Genome sequence comparison of Aspergillus fumigatus strains isolated from patients with pulmonary aspergilloma and chronic necrotizing pulmonary aspergillosis

(2015) Azusa Takahashi-Nakaguchi et al.   MEDICAL MYCOLOGY

Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing

(2015) Alireza Abdolrasouli et al.   mBio

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genetic and phenotypic intra-species variation inCandida albicans

(2014) Matthew P. Hirakawa et al.   GENOME RESEARCH

Genetic Relatedness versus Biological Compatibility between Aspergillus fumigatus and Related Species

(2014) J. A. Sugui et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Cryptic and Rare Aspergillus Species in Brazil: Prevalence in Clinical Samples and In Vitro Susceptibility to Triazoles

(2014) C. E. Negri et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Paralog Re-Emergence: A Novel, Historically Contingent Mechanism in the Evolution of Antimicrobial Resistance

(2014) Nichola J. Hawkins et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antifungal Susceptibility Profile of Cryptic Species of Aspergillus

(2014) Ana Alastruey-Izquierdo et al.   MYCOPATHOLOGIA

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Allergic bronchopulmonary aspergillosis: review of literature and proposal of new diagnostic and classification criteria

(2013) R. Agarwal et al.   CLINICAL AND EXPERIMENTAL ALLERGY

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

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

The T788G Mutation in thecyp51CGene Confers Voriconazole Resistance in Aspergillus flavus Causing Aspergillosis

(2012) Wei Liu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Overexpression of the sterol 14α-demethylase gene (MgCYP51) in Mycosphaerella graminicola isolates confers a novel azole fungicide sensitivity phenotype

(2012) Hans J Cools et al.   PEST MANAGEMENT SCIENCE

Hidden Killers: Human Fungal Infections

(2012) G. D. Brown et al.   Science Translational Medicine

Fatal outcome after heart transplantation caused byAspergillus lentulus

(2012) A. Zbinden et al.   Transplant Infectious Disease

A ‘missing’ family of classical orthogonal polynomials

(2011) Luc Vinet et al.   Journal of Physics A-Mathematical and Theoretical

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Methods for usingGalleria mellonellaas a model host to study fungal pathogenesis

(2011) Beth Burgwyn Fuchs et al.   Virulence

Differential Aspergillus lentulus Echinocandin Susceptibilities Are Fksp Independent

(2010) J. F. Staab et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Pathogenicity ofAspergillus fumigatusmutants assessed inGalleria mellonellamatches that in mice

(2010) J. L. Slater et al.   MEDICAL MYCOLOGY

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

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Molecular Identification of Aspergillus Species Collected for the Transplant-Associated Infection Surveillance Network

(2009) S. A. Balajee et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mutations in the fks1 Gene in Candida albicans, C. tropicalis, and C. krusei Correlate with Elevated Caspofungin MICs Uncovered in AM3 Medium Using the Method of the European Committee on Antibiotic Susceptibility Testing

(2008) M. Desnos-Ollivier et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A Naturally Occurring Proline-to-Alanine Amino Acid Change in Fks1p in Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis Accounts for Reduced Echinocandin Susceptibility

(2008) G. Garcia-Effron et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics