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The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

https://doi.org/10.1101/676148
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Survival of Patients with Cystic Fibrosis Depending on Mutation Type and Nutritional Status
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Heterogeneous Host-Pathogen Encounters: Act Locally, Think Globally
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Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs
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Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung
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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
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Anaerobic metabolism and quorum sensing by Pseudomonas aeruginosa biofilms in chronically infected cystic fibrosis airways: rethinking antibiotic treatment strategies and drug targets
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Antibiotic resistance—the need for global solutions
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Probabilistic Quotient Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures. Application in 1 H NMR Metabonomics
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A model for predicting life expectancy of children with cystic fibrosis
inferredcites →https://doi.org/10.1038/ismej.2011.104openalex-snapshot
Spatial distribution of microbial communities in the cystic fibrosis lung
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Metabolite transfer with the fermentation product 2,3-butanediol enhances virulence by Pseudomonas aeruginosa
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Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome
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Evolution of metabolic divergence in Pseudomonas aeruginosa during long-term infection facilitates a proto-cooperative interspecies interaction
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Small-scale soft-bodied robot with multimodal locomotion
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Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung
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QIIME allows analysis of high-throughput community sequencing data
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3D molecular cartography using LC–MS facilitated by Optimus and 'ili software
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Ecological networking of cystic fibrosis lung infections
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Qiita: rapid, web-enabled microbiome meta-analysis
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Lung microbiota across age and disease stage in cystic fibrosis
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Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
inferredcites →https://doi.org/10.1073/pnas.1107435109openalex-snapshot
Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota
inferredcites →https://doi.org/10.1073/pnas.1203689109openalex-snapshot
Mass spectral molecular networking of living microbial colonies
inferredcites →https://doi.org/10.1073/pnas.1400586111openalex-snapshot
Bacterial fight-and-flight responses enhance virulence in a polymicrobial infection
inferredcites →https://doi.org/10.1073/pnas.1522149113openalex-snapshot
Biogeography of a human oral microbiome at the micron scale
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1101/538215openalex-snapshot
Systematic mapping of drug metabolism by the human gut microbiome
inferredcites →https://doi.org/10.1111/j.1469-0691.2010.03189.xopenalex-snapshot
The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples
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Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells
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Carbapenemase-Producing Enterobacteriaceae Recovered from the Environment of a Swine Farrow-to-Finish Operation in the United States
inferredcites →https://doi.org/10.1128/aem.01996-06openalex-snapshot
Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities
inferredcites →https://doi.org/10.1128/aem.71.12.8228-8235.2005openalex-snapshot
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
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Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
inferredcites →https://doi.org/10.1164/rccm.201312-2129ppopenalex-snapshot
The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography
inferredcites →https://doi.org/10.1186/1471-2105-11-395openalex-snapshot
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
inferredcites →https://doi.org/10.1186/2047-217x-2-16openalex-snapshot
EMPeror: a tool for visualizing high-throughput microbial community data
inferredcites →https://doi.org/10.1371/journal.pmed.1002184openalex-snapshot
Will 10 Million People Die a Year due to Antimicrobial Resistance by 2050?
inferredcites →https://doi.org/10.1371/journal.pone.0137165openalex-snapshot
Ultra-High-Resolution Computed Tomography of the Lung: Image Quality of a Prototype Scanner
inferredcites →https://doi.org/10.1513/annalsats.201408-395ocopenalex-snapshot
Burkholderia Species Infections in Patients with Cystic Fibrosis in British Columbia, Canada. 30 Years’ Experience
inferredcites →https://doi.org/10.1513/annalsats.201501-029ocopenalex-snapshot
Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography
inferredcites →https://doi.org/10.3399/bjgp14x682561openalex-snapshot
Antibiotic overuse: a key driver of antimicrobial resistance
inferredcites →https://doi.org/10.4049/jimmunol.1100647openalex-snapshot
Mass Spectrometric Characterization of Circulating and Functional Antigens Derived from Piperacillin in Patients with Cystic Fibrosis
inferredcites →https://doi.org/10.7189/jogh.06.010306openalex-snapshot
Global disease burden due to antibiotic resistance – state of the evidence
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