Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

Multiple colony antifungal susceptibility testing detects polyresistance in clinical Candida cultures: an ECMM Excellence centers study

(2022) Miriam Alisa Knoll et al.   CLINICAL MICROBIOLOGY AND INFECTION

Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets

(2022) Nicolas Helmstetter et al.   GENETICS

Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia

(2022) Shaoji Cheng et al.   mBio

Genomic Assembly of Clinical Candida glabrata (Nakaseomyces glabrata) Isolates Reveals within-Species Structural Plasticity and Association with In Vitro Antifungal Susceptibility

(2022) Irene Stefanini et al.   Microbiology Spectrum

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole

(2021) Sofía Siscar-Lewin et al.   mBio

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin

(2020) Wei Zhou et al.   CELL

Functional information from clinically-derived drug resistant forms of the Candida glabrata Pdr1 transcription factor

(2020) Lucia Simonicova et al.   PLoS Genetics

Mitochondria-Mediated Azole Drug Resistance and Fungal Pathogenicity: Opportunities for Therapeutic Development

(2020) Jinxing Song et al.   Microorganisms

Molecular mechanisms of azole resistance in Candida bloodstream isolates

(2019) Jocelyn Qi-Min Teo et al.   BMC INFECTIOUS DISEASES

Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations

(2019) Laia Carreté et al.   Frontiers in Microbiology

Within-Host Genomic Diversity of Candida albicans in Healthy Carriers

(2019) Emilie Sitterlé et al.   Scientific Reports

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

(2018) Laia Carreté et al.   CURRENT BIOLOGY

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

(2018) Anja Forche et al.   GENETICS

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

(2018) Anja Forche et al.   GENETICS

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Jjj1 Is a Negative Regulator of Pdr1-Mediated Fluconazole Resistance in Candida glabrata

(2018) Sarah G. Whaley et al.   mSphere

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

A Candida auris Outbreak and Its Control in an Intensive Care Setting

(2018) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Changes in Prevalence of Health Care–Associated Infections in U.S. Hospitals

(2018) Shelley S. Magill et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

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

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

Invasive Candidiasis

(2015) Bart Jan Kullberg et al.   NEW ENGLAND JOURNAL OF MEDICINE

The evolution of drug resistance in clinical isolates of Candida albicans

(2015) Christopher B Ford et al.   eLife

Targeted Versus Universal Antifungal Prophylaxis Among Liver Transplant Recipients

(2014) G. A. Eschenauer et al.   AMERICAN JOURNAL OF TRANSPLANTATION

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome structure and dynamics of the yeast pathogenCandida glabrata

(2014) Khadija M. Ahmad et al.   FEMS YEAST RESEARCH

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

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

Caspofungin MICs Correlate with Treatment Outcomes among Patients with Candida glabrata Invasive Candidiasis and Prior Echinocandin Exposure

(2013) Ryan K. Shields et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick

(2013) Piet W. J. de Groot et al.   EUKARYOTIC CELL

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

(2013) Meleah A. Hickman et al.   NATURE

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of Mitochondrial Functions Associated with Azole Resistance in Candida glabrata Results in Enhanced Virulence in Mice

(2011) Sélène Ferrari et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mitochondria and Fungal Pathogenesis: Drug Tolerance, Virulence, and Potential for Antifungal Therapy

(2011) Miguel Shingu-Vazquez 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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

MixedCandida albicansstrain populations in colonized and infected mucosal tissues

(2008) Mette D. Jacobsen et al.   FEMS YEAST RESEARCH