Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

(2023) Katherine M. Kennedy et al.   NATURE

World Health Organization (WHO) Standard Methods for Pneumococcal Carriage Studies

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Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants

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inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

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GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

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The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study

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Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

(2020) Fiona J. Whelan et al.   Nature Microbiology

Metagenomic Characterization of the Respiratory Microbiome: A Pièce de Résistance

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Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae

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The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults

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Polyclonality, Shared Strains, and Convergent Evolution in Chronic CF S. aureus Airway Infection

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Understanding complex dynamics of behavioral, neurochemical and transcriptomic changes induced by prolonged chronic unpredictable stress in zebrafish

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Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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Bacterial colonization of handheld devices in a tertiary care setting: a hygiene intervention study

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Minimap2: pairwise alignment for nucleotide sequences

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Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations

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Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

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Concordance between upper and lower airway microbiota in infants with cystic fibrosis

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Microbial strain-level population structure and genetic diversity from metagenomes

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metaSPAdes: a new versatile metagenomic assembler

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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

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Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis

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MultiQC: summarize analysis results for multiple tools and samples in a single report

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Development of the respiratory tract microbiota in cystic fibrosis

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Comparative Genomic Analyses of theMoraxella catarrhalisSerosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution

(2016) Joshua P. Earl et al.   Genome Biology and Evolution

Commensal–Pathogen Interactions along the Human Nasal Passages

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The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study

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Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants

(2016) Insa Korten et al.   mSphere

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease

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Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Microbial communities in the respiratory tract of patients with interstitial lung disease

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Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

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Disordered Microbial Communities in Asthmatic Airways

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The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

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