Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs

Drug resistance and tolerance in fungi

(2020) Judith Berman et al.   NATURE REVIEWS MICROBIOLOGY

Linking the organization of DNA replication with genome maintenance

(2019) Balveer Singh et al.   CURRENT GENETICS

Twenty Years of the SENTRY Antifungal Surveillance Program: Results for Candida Species From 1997–2016

(2019) Michael A Pfaller et al.   Open Forum Infectious Diseases

Rapid and extensive karyotype diversification in haploid clinical Candida auris isolates

(2019) Gustavo Bravo Ruiz et al.   CURRENT GENETICS

Aneuploidy Enables Cross-Adaptation to Unrelated Drugs

(2019) Feng Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype

(2019) Anja Forche et al.   PLoS Genetics

A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans

(2019) Cedric A. Brimacombe et al.   PLOS BIOLOGY

Genome plasticity in Candida albicans is driven by long repeat sequences

(2019) Robert T Todd et al.   eLife

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Transcription-induced formation of extrachromosomal DNA during yeast ageing

(2019) Ryan M. Hull et al.   PLOS BIOLOGY

The Rim Pathway Mediates Antifungal Tolerance in Candida albicans through Newly Identified Rim101 Transcriptional Targets, Including Hsp90 and Ipt1

(2018) Cécile Garnaud et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli

(2018) Prabh Basra et al.   Genome Biology and Evolution

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells

(2018) Teressa Paulsen et al.   TRENDS IN GENETICS

Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia

(2018) Alexander Rosenberg et al.   Nature Communications

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

(2018) Jeanne Ropars et al.   Nature Communications

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

(2018) Henrik Devitt Møller et al.   Nature Communications

Adaptation by copy number variation in monopartite viruses

(2018) Avraham Bayer et al.   Current Opinion in Virology

Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs

(2018) Harley O’Connor Mount et al.   PLoS Genetics

Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen

(2018) Iuliana V. Ene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-strand annealing between inverted DNA repeats: Pathway choice, participating proteins, and genome destabilizing consequences

(2018) Sreejith Ramakrishnan et al.   PLoS Genetics

Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death

(2018) Haley Hieronymus et al.   eLife

Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species

(2018) José F. Muñoz et al.   Nature Communications

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

(2018) Stephanie Lauer et al.   PLOS BIOLOGY

Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

(2017) Aleeza C. Gerstein et al.   EVOLUTION

The Hsp90 Chaperone Network Modulates Candida Virulence Traits

(2017) Teresa R. O’Meara et al.   TRENDS IN MICROBIOLOGY

Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells

(2017) Sunyoung Hwang et al.   Cell Reports

Environmental change drives accelerated adaptation through stimulated copy number variation

(2017) Ryan M. Hull et al.   PLOS BIOLOGY

Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro

(2017) Guirong Qiao et al.   Frontiers in Plant Science

Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors

(2017) Michael Marotta et al.   Scientific Reports

Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma

(2016) Caixia Cheng et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Simultaneous Emergence of Multidrug-ResistantCandida aurison 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses

(2016) Shawn R. Lockhart et al.   CLINICAL INFECTIOUS DISEASES

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

(2016) Kelsey R. Cone et al.   JOURNAL OF VIROLOGY

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

(2016) Faiyaz Notta et al.   NATURE

Heteroresistance to Fluconazole Is a Continuously Distributed Phenotype among Candida glabrata Clinical Strains Associated with In Vivo Persistence

(2016) Ronen Ben-Ami et al.   mBio

Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria

(2016) Alvaro San Millan et al.   Nature Ecology & Evolution

Chromothripsis and Kataegis Induced by Telomere Crisis

(2015) John Maciejowski et al.   CELL

Defining the frontiers between antifungal resistance, tolerance and the concept of persistence

(2015) Eric Delarze et al.   DRUG RESISTANCE UPDATES

Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions

(2015) Virginia Lopez et al.   GENES & DEVELOPMENT

Physical limits on kinesin-5–mediated chromosome congression in the smallest mitotic spindles

(2015) Kelsey M. McCoy et al.   MOLECULAR BIOLOGY OF THE CELL

Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification

(2015) Sarah K. Deng et al.   MOLECULAR CELL

Non-invasive detection of genome-wide somatic copy number alterations by liquid biopsies

(2015) Ellen Heitzer et al.   Molecular Oncology

Polyploidy can drive rapid adaptation in yeast

(2015) Anna M. Selmecki et al.   NATURE

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Extrachromosomal circular DNA is common in yeast

(2015) Henrik D. Møller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyploid Titan Cells Produce Haploid and Aneuploid Progeny To Promote Stress Adaptation

(2015) Aleeza C. Gerstein et al.   mBio

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

(2015) Bonita J. Brewer et al.   PLoS Genetics

The evolution of drug resistance in clinical isolates of Candida albicans

(2015) Christopher B Ford et al.   eLife

Contribution of Clinically Derived Mutations inERG11to Azole Resistance in Candida albicans

(2014) Stephanie A. Flowers et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Tissue Penetration of Antifungal Agents

(2014) T. Felton et al.   CLINICAL MICROBIOLOGY REVIEWS

The fitness costs of antibiotic resistance mutations

(2014) Anita H. Melnyk et al.   Evolutionary Applications

Genetic and phenotypic intra-species variation inCandida albicans

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

Prognostic factors and historical trends in the epidemiology of candidemia in critically ill patients: an analysis of five multicenter studies sequentially conducted over a 9-year period

(2014) Arnaldo L. Colombo et al.   INTENSIVE CARE MEDICINE

High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms

(2014) M. Adler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mechanisms of Antifungal Drug Resistance

(2014) Leah E. Cowen et al.   Cold Spring Harbor Perspectives in Medicine

Antifungal Drug Development: Challenges, Unmet Clinical Needs, and New Approaches

(2014) T. Roemer et al.   Cold Spring Harbor Perspectives in Medicine

Structures of Naturally Evolved CUP1 Tandem Arrays in Yeast Indicate That These Arrays Are Generated by Unequal Nonhomologous Recombination

(2014) Ying Zhao et al.   G3-Genes Genomes Genetics

YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

(2014) Darren A Abbey et al.   Genome Medicine

A Tetraploid Intermediate Precedes Aneuploid Formation in Yeasts Exposed to Fluconazole

(2014) Benjamin D. Harrison et al.   PLOS BIOLOGY

DNA Repair Pathway Selection Caused by Defects in TEL1, SAE2, and De Novo Telomere Addition Generates Specific Chromosomal Rearrangement Signatures

(2014) Christopher D. Putnam et al.   PLoS Genetics

Large Inverted Duplications in the Human Genome Form via a Fold-Back Mechanism

(2014) Karen E. Hermetz et al.   PLoS Genetics

Azole Heteroresistance in Cryptococcus neoformans: Emergence of Resistant Clones with Chromosomal Disomy in the Mouse Brain during Fluconazole Treatment

(2013) Edward Sionov et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Gene Copy-Number Alterations: A Cost-Benefit Analysis

(2013) Yun-Chi Tang et al.   CELL

Mechanisms ofCandidabiofilm drug resistance

(2013) Heather T Taff et al.   Future Microbiology

The ‘obligate diploid’ Candida albicans forms mating-competent haploids

(2013) Meleah A. Hickman et al.   NATURE

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Hsp21 Potentiates Antifungal Drug Tolerance in Candida albicans

(2013) François L. Mayer et al.   PLoS One

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast

(2013) Gregory I. Lang et al.   G3-Genes Genomes Genetics

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

(2013) Celia Payen et al.   G3-Genes Genomes Genetics

Single-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination

(2013) Kenneth J. Finn et al.   PLoS Genetics

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

Long Interspersed Element–1 (LINE-1): Passenger or Driver in Human Neoplasms?

(2013) Nemanja Rodić et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

(2012) Nels C. Elde et al.   CELL

A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans

(2012) Clarissa J. Nobile et al.   CELL

Exciting Developments in the Immunology of Fungal Infections

(2012) Gordon D. Brown et al.   Cell Host & Microbe

Dicentric chromosomes: unique models to study centromere function and inactivation

(2012) Kaitlin M. Stimpson et al.   CHROMOSOME RESEARCH

Epigenetic Inactivation and Subsequent Heterochromatinization of a Centromere Stabilize Dicentric Chromosomes

(2012) Hiroshi Sato et al.   CURRENT BIOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Amplification of the CUP1 gene is associated with evolution of copper tolerance in Saccharomyces cerevisiae

(2012) G. M. Adamo et al.   MICROBIOLOGY-SGM

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

(2012) E. W. L. Chow et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination-restarted replication makes inverted chromosome fusions at inverted repeats

(2012) Ken’Ichi Mizuno et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Characterization of the Chromosome 4 Genes That Affect Fluconazole-Induced Disomy Formation in Cryptococcus neoformans

(2012) Popchai Ngamskulrungroj et al.   PLoS One

Chromosomal duplication is a transient evolutionary solution to stress

(2012) A. H. Yona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Antifungal Drug Resistance: Mechanisms, Epidemiology, and Consequences for Treatment

(2011) Michael A. Pfaller   AMERICAN JOURNAL OF MEDICINE

Current perspectives on echinocandin class drugs

(2011) David S Perlin   Future Microbiology

Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

(2011) Jun Zhou et al.   Genome Biology and Evolution

Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing

(2011) Gregory I. Lang et al.   Genome Biology and Evolution

Cap2-HAP Complex Is a Critical Transcriptional Regulator That Has Dual but Contrasting Roles in Regulation of Iron Homeostasis inCandida albicans

(2011) Rana Pratap Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans

(2011) A. Forche et al.   mBio

Origin-Dependent Inverted-Repeat Amplification: A Replication-Based Model for Generating Palindromic Amplicons

(2011) Bonita J. Brewer et al.   PLoS Genetics

Variation in Candida spp. distribution and antifungal resistance rates among bloodstream infection isolates by patient age: report from the SENTRY Antimicrobial Surveillance Program (2008–2009)

(2010) Michael A. Pfaller et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Screening for amino acid substitutions in the Candida albicans Erg11 protein of azole-susceptible and azole-resistant clinical isolates: new substitutions and a review of the literature

(2010) Florent Morio et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Genomic Plasticity of the Human Fungal Pathogen Candida albicans

(2010) Anna Selmecki et al.   EUKARYOTIC CELL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Clinically significant micafungin resistance in Candida albicans involves modification of a glucan synthase catalytic subunit GSC1 (FKS1) allele followed by loss of heterozygosity

(2010) K. Niimi et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Expansion of Hexose Transporter Genes Was Associated with the Evolution of Aerobic Fermentation in Yeasts

(2010) Z. Lin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast

(2010) Norman Pavelka et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

(2010) D. Gresham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of DNA Replication Control Is a Potent Inducer of Gene Amplification

(2010) B. M. Green et al.   SCIENCE

Cryptococcus neoformans Overcomes Stress of Azole Drugs by Formation of Disomy in Specific Multiple Chromosomes

(2010) Edward Sionov et al.   PLoS Pathogens

Autism and other neuropsychiatric symptoms are prevalent in individuals withMeCP2duplication syndrome

(2009) Melissa B. Ramocki et al.   ANNALS OF NEUROLOGY

Heteroresistance to Fluconazole in Cryptococcus neoformans Is Intrinsic and Associated with Virulence

(2009) E. Sionov et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Effect of Candida glabrata FKS1 and FKS2 Mutations on Echinocandin Sensitivity and Kinetics of 1,3- -D-Glucan Synthase: Implication for the Existing Susceptibility Breakpoint

(2009) G. Garcia-Effron et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Independent Association between Rate of Clearance of Infection and Clinical Outcome of HIV‐Associated Cryptococcal Meningitis: Analysis of a Combined Cohort of 262 Patients

(2009) Tihana Bicanic et al.   CLINICAL INFECTIOUS DISEASES

Mechanistic Plasticity of Sexual Reproduction and Meiosis in the Candida Pathogenic Species Complex

(2009) Jennifer L. Reedy et al.   CURRENT BIOLOGY

Aneuploid Chromosomes Are Highly Unstable during DNA Transformation ofCandida albicans

(2009) Kelly Bouchonville et al.   EUKARYOTIC CELL

Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium

(2009) Song Sun et al.   GENETICS

Evolution in Candida albicans Populations During a Single Passage Through a Mouse Host

(2009) A. Forche et al.   GENETICS

Transcriptional Analysis of the Candida albicans Cell Cycle

(2009) Pierre Côte et al.   MOLECULAR BIOLOGY OF THE CELL

Homothallic and heterothallic mating in the opportunistic pathogen Candida albicans

(2009) Kevin Alby et al.   NATURE

Formation of new chromosomes as a virulence mechanism in yeastCandida glabrata

(2009) Silvia Poláková et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Double-strand DNA breaks recruit the centromeric histone CENP-A

(2009) S. G. Zeitlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copy number variations and cancer

(2009) Adam Shlien et al.   Genome Medicine

A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

(2009) P. J. Hastings et al.   PLoS Genetics

Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance

(2009) Anna M. Selmecki et al.   PLoS Genetics

Gain-of-Function Mutations in the Transcription Factor MRR1 Are Responsible for Overexpression of the MDR1 Efflux Pump in Fluconazole-Resistant Candida dubliniensis Strains

(2008) S. Schubert et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mutations in the multi-drug resistance regulatorMRR1, followed by loss of heterozygosity, are the main cause ofMDR1overexpression in fluconazole-resistantCandida albicansstrains

(2008) Nico Dunkel et al.   MOLECULAR MICROBIOLOGY

An isochromosome confers drug resistance in vivo by amplification of two genes, ERG11 and TAC1

(2008) Anna Selmecki et al.   MOLECULAR MICROBIOLOGY

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch et al.   PLOS BIOLOGY

The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains

(2008) Anja Forche et al.   PLOS BIOLOGY

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics