Genome plasticity in Candida albicans is driven by long repeat sequences

Rapid Phenotypic and Genotypic Diversification After Exposure to the Oral Host Niche inCandida albicans

(2018) Anja Forche et al.   GENETICS

GC content elevates mutation and recombination rates in the yeastSaccharomyces cerevisiae

(2018) Denis A. Kiktev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Break-Induced Replication: The Where, The Why, and The How

(2018) J. Kramara et al.   TRENDS IN GENETICS

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

(2018) Jeanne Ropars et al.   Nature Communications

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

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

Functional diversification accompanies gene family expansion of MED2 homologs in Candida albicans

(2018) Matthew J. Dunn et al.   PLoS Genetics

Rapid Phenotypic and Genotypic Diversification After Exposure to the Oral Host Niche inCandida albicans

(2018) Anja Forche et al.   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

The Genome of the Human Pathogen Candida albicans Is Shaped by Mutation and Cryptic Sexual Recombination

(2018) Joshua M. Wang et al.   mBio

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

(2018) Sreejith Ramakrishnan et al.   PLoS Genetics

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

(2018) Stephanie Lauer et al.   PLOS BIOLOGY

The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source

(2017) Amber L. Scott et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmental change drives accelerated adaptation through stimulated copy number variation

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

TheCandidaGenome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data

(2016) Marek S. Skrzypek et al.   NUCLEIC ACIDS RESEARCH

Regulation of Single-Strand Annealing and its Role in Genome Maintenance

(2016) Ragini Bhargava et al.   TRENDS IN GENETICS

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

(2016) Laura S. Burrack et al.   PLoS Genetics

Candida albicans Agglutinin-Like Sequence (Als) Family Vignettes: A Review of Als Protein Structure and Function

(2016) Lois L. Hoyer et al.   Frontiers in Microbiology

Candida albicans repetitive elements display epigenetic diversity and plasticity

(2016) Verónica Freire-Benéitez et al.   Scientific Reports

Polyploidy can drive rapid adaptation in yeast

(2015) Anna M. Selmecki et al.   NATURE

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

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

(2015) Aleeza C. Gerstein et al.   mBio

Mechanisms of Gene Duplication and Amplification

(2015) Andrew B. Reams et al.   Cold Spring Harbor Perspectives in Biology

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

(2015) Anna B. Sunshine et al.   PLOS BIOLOGY

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

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

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

The evolution of drug resistance in clinical isolates of Candida albicans

(2015) Christopher B Ford et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

(2014) Ian A. Warren et al.   Genome Biology and Evolution

Genetic and phenotypic intra-species variation inCandida albicans

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

Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres

(2014) H.-J. Tsai et al.   mBio

Transcription and Recombination: When RNA Meets DNA

(2014) A. Aguilera et al.   Cold Spring Harbor Perspectives in Biology

Sources of DNA Double-Strand Breaks and Models of Recombinational DNA Repair

(2014) A. Mehta et al.   Cold Spring Harbor Perspectives in Biology

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

(2014) Darren A Abbey et al.   Genome Medicine

Causes of Genome Instability

(2013) Andrés Aguilera et al.   Annual Review of Genetics

Regulations of sugar transporters: insights from yeast

(2013) J. Horák   CURRENT GENETICS

Break-induced replication: functions and molecular mechanism

(2013) Anna Malkova et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Homozygous deletion of DIS3L2 exon 9 due to non-allelic homologous recombination between LINE-1s in a Japanese patient with Perlman syndrome

(2013) Ken Higashimoto et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

(2013) Meleah A. Hickman et al.   NATURE

Aneuploidy underlies a multicellular phenotypic switch

(2013) Z. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Break-Induced DNA Replication

(2013) R. P. Anand et al.   Cold Spring Harbor Perspectives in Biology

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

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

Mutations Arising During Repair of Chromosome Breaks

(2012) Anna Malkova et al.   Annual Review of Genetics

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

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

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

Functional divergence of gene duplicates through ectopic recombination

(2012) Joaquin F Christiaens et al.   EMBO REPORTS

The Three Clades of the Telomere-Associated TLO Gene Family of Candida albicans Have Different Splicing, Localization, and Expression Features

(2012) Matthew Z. Anderson et al.   EUKARYOTIC CELL

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

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

Mouse model of oropharyngeal candidiasis

(2012) Norma V Solis et al.   Nature Protocols

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Whole-genome sequencing of a laboratory-evolved yeast strain

(2010) Carlos L Araya et al.   BMC GENOMICS

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

(2010) Eva M. Strawbridge et al.   CURRENT GENETICS

Genomic Plasticity of the Human Fungal Pathogen Candida albicans

(2010) Anna Selmecki et al.   EUKARYOTIC CELL

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

(2010) V. M. Bruno et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast

(2010) Norman Pavelka et al.   NATURE

Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2

(2010) Ningxin Zhang et al.   PLoS One

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

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

(2010) Eva H. Stukenbrock et al.   PLoS Genetics

Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase

(2010) Amnon Koren et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

(2009) Marina Marcet-Houben et al.   BMC EVOLUTIONARY BIOLOGY

Aneuploid Chromosomes Are Highly Unstable during DNA Transformation ofCandida albicans

(2009) Kelly Bouchonville et al.   EUKARYOTIC CELL

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

(2009) A. Forche et al.   GENETICS

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

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

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

Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans

(2009) Carrie Ketel 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

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

(2008) Anna Selmecki et al.   MOLECULAR MICROBIOLOGY

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

Coding fungal tandem repeats as generators of fungal diversity

(2008) Emma Levdansky et al.   Fungal Biology Reviews