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Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Rapid Worldwide Emergence of Pathogenic Fungi
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Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance
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Resistance of Candida to azoles and echinocandins worldwide
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Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans
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Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata
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When experimental selection for virulence leads to loss of virulence
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Understand the genomic diversity and evolution of fungal pathogen Candida glabrata by genome-wide analysis of genetic variations
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Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis
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A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
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Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
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Emerging fungal threats to animal, plant and ecosystem health
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Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
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Candida blankii : an emergent opportunistic yeast with reduced susceptibility to antifungals
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Gene flow contributes to diversification of the major fungal pathogen Candida albicans
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Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species
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LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris
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Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection
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Highly accurate protein structure prediction with AlphaFold
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Transposable elements contribute to fungal genes and impact fungal lifestyle
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Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata
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Epistatic genetic interactions govern morphogenesis during sexual reproduction and infection in a global human fungal pathogen
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Echinocandin Resistance in Candida
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Recent trends in molecular diagnostics of yeast infections: from PCR to NGS
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The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata
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The fitness costs and benefits of trisomy of each Candida albicans chromosome
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Fungal infections in animals: a patchwork of different situations
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Aneuploidy Enables Cross-Adaptation to Unrelated Drugs
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The FoldX web server: an online force field
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Regulation of anti-sense transcription by Mot1p and NC2 via removal of TATA-binding protein (TBP) from the 3′-end of genes
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Sources of PCR-induced distortions in high-throughput sequencing data sets
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Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi
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Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi
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Hogwash: three methods for genome-wide association studies in bacteria
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Scaling accurate genetic variant discovery to tens of thousands of samples
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PerSVade: Personalized Structural Variation detection in your species of interest
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The Spectrum of Fungi That Infects Humans
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Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
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Fungal evolution: major ecological adaptations and evolutionary transitions
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Cg PDR 1 gain‐of‐function mutations lead to azole‐resistance and increased adhesion in clinical Candida glabrata strains
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Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium
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Worldwide emergence of resistance to antifungal drugs challenges human health and food security
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Experimental evolution of a fungal pathogen into a gut symbiont
inferredcites →https://doi.org/10.1128/aac.00651-17openalex-snapshot
Loss of C-5 Sterol Desaturase Activity Results in Increased Resistance to Azole and Echinocandin Antifungals in a Clinical Isolate of Candida parapsilosis
inferredcites →https://doi.org/10.1128/aac.01466-20openalex-snapshot
Experimental Evolution Identifies Adaptive Aneuploidy as a Mechanism of Fluconazole Resistance in Candida auris
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Comparative Genomics of Serial Candida glabrata Isolates and the Rapid Acquisition of Echinocandin Resistance during Therapy
inferredcites →https://doi.org/10.1128/mbio.02512-19openalex-snapshot
Comparative Genomics for the Elucidation of Multidrug Resistance in Candida lusitaniae
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Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance
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Global burden of chronic pulmonary aspergillosis complicating sarcoidosis
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Y MAP : a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens
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CLOVE: classification of genomic fusions into structural variation events
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Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris
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Locating rearrangement events in a phylogeny based on highly fragmented assemblies
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Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum
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Correction to: Comparative transcriptomics reveals PrrABmediated control of metabolic, respiration, energy-generating, and dormancy pathways in Mycobacterium smegmatis
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Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates
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Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans
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The Ensembl Variant Effect Predictor
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Structural variant calling: the long and the short of it
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GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
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PerSVade: personalized structural variant detection in any species of interest
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Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia
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Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing
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Clade II Candida auris possess genomic structural variations related to an ancestral strain
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Gain of Function Mutations in CgPDR1 of Candida glabrata Not Only Mediate Antifungal Resistance but Also Enhance Virulence
inferredcites →https://doi.org/10.1371/journal.ppat.1002718openalex-snapshot
Global Analysis of the Evolution and Mechanism of Echinocandin Resistance in Candida glabrata
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Finding the needle in a haystack: Mapping antifungal drug resistance in fungal pathogen by genomic approaches
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Evolution inCandida albicansPopulations During a Single Passage Through a Mouse Host
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Microevolution of the pathogenic yeasts Candida albicans and Candida glabrata during antifungal therapy and host infection
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Fungal Diseases in the 21st Century: The Near and Far Horizons
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Genome-Wide Association for Itraconazole Sensitivity in Non-resistant Clinical Isolates of Aspergillus fumigatus
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Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis
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Genomics and Virulence of Fonsecaea pugnacius, Agent of Disseminated Chromoblastomycosis
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Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types
inferredcites →https://doi.org/10.3389/fmicb.2019.00112openalex-snapshot
Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations
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Comparative Genomic Data Provide New Insight on the Evolution of Pathogenicity in Sporothrix Species
inferredcites →https://doi.org/10.3389/fphar.2018.01338openalex-snapshot
A Review on the Synthesis and Bioactivity Aspects of Beauvericin, a Fusarium Mycotoxin
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Mutagenesis of Puccinia graminis f. sp. tritici and Selection of Gain-of-Virulence Mutants
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Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium
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Genomic Instability in Fungal Plant Pathogens
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Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens
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Global and Multi-National Prevalence of Fungal Diseases—Estimate Precision
inferredcites →https://doi.org/10.3390/pathogens10060701openalex-snapshot
Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
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Genome plasticity in Candida albicans is driven by long repeat sequences
inferredcites →https://doi.org/10.7554/elife.58349openalex-snapshot
Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Interconnected worlds: a comprehensive review of fungal defenses, antimicrobial resistance, and their evolutionary dynamics
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Genomic Innovation and Virulence Evolution in the Emerging Human Fungal Pathogen Candida auris
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Fungal plasticity drives adaptation and survival across pathogenic and free-living contexts
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Bioinformatics in Antifungal Design: Strategies To Overcome Resistance from a Proteomic Perspective
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Nothing makes sense in drug resistance except in the light of evolution
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Unraveling Traditional Chinese Medicine with single-cell RNA sequencing: Current applications and future frontiers
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Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap
inferred← citeshttps://doi.org/10.1038/s41564-023-01547-zopenalex-snapshot
Recent gene selection and drug resistance underscore clinical adaptation across Candida species
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Unlocking the potential of experimental evolution to study drug resistance in pathogenic fungi
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Drug-resistance genes and antifungal susceptibility of Trichophyton verrucosum variants isolated from bovine skin lesions and farm environments
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The Impact of the Fungal Priority Pathogens List on Medical Mycology: A Northern European Perspective
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Persistence and spread of fluconazole-resistant Candida parapsilosis clinical isolates associated with increased ERG11 copies in Qatar
inferred← citeshttps://doi.org/10.1099/mic.0.001447openalex-snapshot
Genetic modification of Candida maltosa, a non-pathogenic CTG species, reveals EFG1 function
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CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis
inferred← citeshttps://doi.org/10.1128/mmbr.00029-23openalex-snapshot
Threats from the Candida parapsilosis complex: the surge of multidrug resistance and a hotbed for new emerging pathogens
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Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes
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inferred← citeshttps://doi.org/10.3389/fmicb.2023.1134755openalex-snapshot
The challenges of the genome-based identification of antifungal resistance in the clinical routine
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Raman Metabolomics of Candida auris Clades: Profiling and Barcode Identification
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In Vivo Microevolutionary Analysis of a Fatal Case of Rhinofacial and Disseminated Mycosis Due to Azole-Drug-Resistant Candida Species
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Identification of Virulence Factors in Isolates of Candida haemulonii, Candida albicans and Clavispora lusitaniae with Low Susceptibility and Resistance to Fluconazole and Amphotericin B
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