Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

nQuire: a statistical framework for ploidy estimation using next generation sequencing

(2018) Clemens L. Weiß et al.   BMC BIOINFORMATICS

OUP accepted manuscript

(2018)   MEDICAL MYCOLOGY

Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names

(2018) Alexander P. Douglass et al.   PLoS Pathogens

Virulence factors and determination of antifungal susceptibilities of Candida species isolated from palm wine and sorghum beer

(2018) Laurence A.N. Egue et al.   MICROBIAL PATHOGENESIS

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Predisposing factors and outcome of uncommon yeast species-related fungaemia based on an exhaustive surveillance programme (2002–14)

(2017) Stéphane Bretagne et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multidrug-Resistant Candida: Epidemiology, Molecular Mechanisms, and Treatment

(2017) Maiken Cavling Arendrup et al.   JOURNAL OF INFECTIOUS DISEASES

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

The inheritance of mitochondrial DNA in interspecific Saccharomyces hybrids and their properties in winemaking

(2017) Alexandra Verspohl et al.   YEAST

Hybridization and emergence of virulence in opportunistic human yeast pathogens

(2017) Verónica Mixão et al.   YEAST

Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5

(2017) Christina A. Cuomo et al.   G3-Genes Genomes Genetics

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

(2016) Daniel Mapleson et al.   BIOINFORMATICS

NOVOPlasty:de novoassembly of organelle genomes from whole genome data

(2016) Nicolas Dierckxsens et al.   NUCLEIC ACIDS RESEARCH

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

(2016) Markus S. Schröder et al.   PLoS Genetics

Candida inconspicua and Candida norvegensis: New Insights into Identification in Relation to Sexual Reproduction and Genome Organization

(2015) J. Guitard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

(2015) Leszek P. Pryszcz et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Invasive infections due toCandida norvegensisandCandida inconspicua: report of 12 cases and review of the literature

(2013) Juliette Guitard et al.   MEDICAL MYCOLOGY

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

Epidemiology and outcomes of candidemia in 3648 patients: data from the Prospective Antifungal Therapy (PATH Alliance®) registry, 2004–2008

(2012) Michael Pfaller et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

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

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

Candida species: current epidemiology, pathogenicity, biofilm formation, natural antifungal products and new therapeutic options

(2012) J. C. O. Sardi et al.   JOURNAL OF MEDICAL MICROBIOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hidden Killers: Human Fungal Infections

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

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods

(2010) E. Cendejas-Bueno et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: a 10.5-Year Analysis of Susceptibilities of Candida Species to Fluconazole and Voriconazole as Determined by CLSI Standardized Disk Diffusion

(2010) M. A. Pfaller et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The changing face of epidemiology of invasive fungal disease in Europe

(2009) Cornelia Lass-Flörl   MYCOSES

Phylogenetic relationships among species ofPichia, IssatchenkiaandWilliopsisdetermined from multigene sequence analysis, and the proposal ofBarnettozymagen. nov.,Lindneragen. nov. andWickerhamomycesgen. nov.

(2008) Cletus P. Kurtzman et al.   FEMS YEAST RESEARCH

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

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY