Microbiota Present in Cystic Fibrosis Lungs as Revealed by Whole Genome Sequencing

The Cystic Fibrosis Airway Microbiome

(2013) S. V. Lynch et al.   Cold Spring Harbor Perspectives in Medicine

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

Culturomics: a new approach to study the human microbiome

(2012) G. Greub   CLINICAL MICROBIOLOGY AND INFECTION

The microbiome as a human organ

(2012) F. Baquero et al.   CLINICAL MICROBIOLOGY AND INFECTION

Reducing bias in bacterial community analysis of lower respiratory infections

(2012) Geraint B Rogers et al.   ISME Journal

Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability

(2012) L. M. Filkins et al.   JOURNAL OF BACTERIOLOGY

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

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

ITS2 Database IV: Interactive taxon sampling for internal transcribed spacer 2 based phylogenies

(2012) Christian Koetschan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Airway Microbiota in Cystic Fibrosis: A Complex Fungal and Bacterial Community—Implications for Therapeutic Management

(2012) Laurence Delhaes et al.   PLoS One

Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature for Cystic Fibrosis

(2012) P. C. Blainey et al.   Science Translational Medicine

Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures

(2012) J. C. Madan et al.   mBio

Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

(2011) Emily S. Charlson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Bronchoalveolar lavage in children with cystic fibrosis: how many lobes should be sampled?

(2010) F. J. Gilchrist et al.   ARCHIVES OF DISEASE IN CHILDHOOD

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients

(2010) F. Bittar et al.   CLINICAL MICROBIOLOGY AND INFECTION

Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa

(2010) Vanja Klepac-Ceraj et al.   ENVIRONMENTAL MICROBIOLOGY

Pseudomonas aeruginosa and their small diffusible extracellular molecules inhibit Aspergillus fumigatus biofilm formation

(2010) Eilidh Mowat et al.   FEMS MICROBIOLOGY LETTERS

Medically important bacterial–fungal interactions

(2010) Anton Y. Peleg et al.   NATURE REVIEWS MICROBIOLOGY

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Development of an Oligonucleotide Array for Direct Detection of Fungi in Sputum Samples from Patients with Cystic Fibrosis

(2008) J.-P. Bouchara et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The role of respiratory viruses in cystic fibrosis

(2008) Dennis Wat et al.   Journal of Cystic Fibrosis

TheStreptococcus milleri group—An unrecognized cause of disease in cystic fibrosis: A case series and literature review

(2008) Michael D. Parkins et al.   PEDIATRIC PULMONOLOGY