High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis

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The Epidemiology and Prevention of Candida auris

(2019) Graham M. Snyder et al.   Current Infectious Disease Reports

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus

(2019) Sohn G. Kim et al.   NATURE

Incidence, Risk Factors, and Long-term Outcome of Acute Leukemia Patients With Early Candidemia After Allogeneic Stem Cell Transplantation: A Study by the Acute Leukemia and Infectious Diseases Working Parties of European Society for Blood and Marrow Transplantation

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Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant

(2018) Ying Taur et al.   Science Translational Medicine

Enlisting commensal microbes to resist antibiotic-resistant pathogens

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Precision identification of diverse bloodstream pathogens in the gut microbiome

(2018) Fiona B. Tamburini et al.   NATURE MEDICINE

Protective Factors in the Intestinal Microbiome Against Clostridium difficile Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation

(2017) Yeon Joo Lee et al.   JOURNAL OF INFECTIOUS DISEASES

The microbiome in hematopoietic stem cell transplant recipients and cancer patients: Opportunities for clinical advances that reduce infection

(2017) Andrew Y. Koh   PLoS Pathogens

TheRTA3Gene, Encoding a Putative Lipid Translocase, Influences the Susceptibility of Candida albicans to Fluconazole

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Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011–2014

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DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Intestinal microbiome changes and stem cell transplantation: Lessons learned

(2016) Ying Taur   Virulence

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

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

The ever-evolving landscape of candidaemia in patients with acute leukaemia: non-susceptibility to caspofungin and multidrug resistance are associated with increased mortality

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Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization

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The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Update on RefSeq microbial genomes resources

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The Candida Pathogenic Species Complex

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The Spectrum of Fungi That Infects Humans

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Unexpected Genomic Variability in Clinical and Environmental Strains of the Pathogenic Yeast Candida parapsilosis

(2013) Leszek P. Pryszcz et al.   Genome Biology and Evolution

Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

(2013) Heidi E.L. Lischer et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

FungiQuant: A broad-coverage fungal quantitative real-time PCR assay

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Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Sequence and Analysis of the Genome of the Pathogenic Yeast Candida orthopsilosis

(2012) Alessandro Riccombeni et al.   PLoS One

Differentiation of Candida parapsilosis, C. orthopsilosis, and C. metapsilosis by specific PCR amplification of the RPS0 intron

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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

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Candidemia in patients with hematologic malignancies in the era of new antifungal agents (2001-2007)

(2009) Nikolaos V. Sipsas et al.   CANCER

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Increasing incidence of Candida parapsilosis candidemia with caspofungin usage

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