CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

Diversity Measures in Environmental Sequences Are Highly Dependent on Alignment Quality—Data from ITS and New LSU Primers Targeting Basidiomycetes

(2012) Dirk Krüger et al.   PLoS One

Candida dubliniensis: An Appraisal of Its Clinical Significance as a Bloodstream Pathogen

(2012) Ziauddin Khan et al.   PLoS One

Characterization of the Fungal Microbiota (Mycobiome) in Healthy and Dandruff-Afflicted Human Scalps

(2012) Hee Kuk Park et al.   PLoS One

Unravelling Soil Fungal Communities from Different Mediterranean Land-Use Backgrounds

(2012) Alberto Orgiazzi et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

(2012) Serena Dollive et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects

(2011) Enshi Zhang et al.   MICROBIOLOGY AND IMMUNOLOGY

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

(2011) Teresita M. Porter et al.   NEW PHYTOLOGIST

Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

(2011) Mary E. Lucero et al.   PLoS One

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

(2011) Samuel V. Angiuoli et al.   PLoS One

Ergatis: a web interface and scalable software system for bioinformatics workflows

(2010) J. Orvis et al.   BIOINFORMATICS

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

(2010) James R White et al.   BMC BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

(2010) Shilin Chen et al.   PLoS One

Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

(2010) Mahmoud A. Ghannoum et al.   PLoS Pathogens

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

Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium

(2009) Taylor Mullineux et al.   FUNGAL GENETICS AND BIOLOGY

Windshield splatter analysis with the Galaxy metagenomic pipeline

(2009) S. Kosakovsky Pond et al.   GENOME RESEARCH

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

(2009) A. P. Jackson et al.   GENOME RESEARCH

Species-Specific Identification of a Wide Range of Clinically Relevant Fungal Pathogens by Use of Luminex xMAP Technology

(2009) C. Landlinger et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Internal Transcribed Spacer Region Sequence Heterogeneity inRhizopus microsporus: Implications for Molecular Diagnosis in Clinical Microbiology Laboratories

(2009) Patrick C. Y. Woo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The ITS2 Database III—sequences and structures for phylogeny

(2009) Christian Koetschan et al.   NUCLEIC ACIDS RESEARCH

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

(2008) Martin Ryberg et al.   BMC EVOLUTIONARY BIOLOGY

Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region

(2008) C. Landlinger et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES