Research map: DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation

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  1. Fast gapped-read alignment with Bowtie 2 · Ben Langmead · 2012 · 62901 citations · Cited by this paper
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  11. Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis · Seng H. Cheng · 1990 · 1816 citations · Cited by this paper
  12. Nanopore-targeted sequencing: A new and effective technique for the diagnosis of non-tuberculous mycobacteria pulmonary disease · 2025 · Related
  13. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients · Eric E. Smith · 2006 · 1369 citations · Cited by this paper
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  15. Pseudomonas aeruginosa: all roads lead to resistance · Elena B. M. Breidenstein · 2011 · 1327 citations · Cited by this paper
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  17. rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development · Steven F. Stoddard · 2014 · 1187 citations · Cited by this paper
  18. Revisiting the natural history of Jorge Lobo’s disease: a mycological enigma spanning unresolved taxonomy, uncertain transmission, and inadequate therapy · 2026 · Related
  19. Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets · Robert Schmieder · 2011 · 786 citations · Cited by this paper
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  21. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection · Themoula Charalampous · 2019 · 755 citations · Cited by this paper
  22. Pseudomonas aeruginosa Evolutionary Adaptation and Diversification in Cystic Fibrosis Chronic Lung Infections · Craig Winstanley · 2016 · 731 citations · Cited by this paper
  23. The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage · Forest L. Rohwer · 2002 · 620 citations · Cited by this paper
  24. Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis · Elio Rossi · 2020 · 539 citations · Cited by this paper
  25. US Cystic Fibrosis Foundation and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous mycobacteria in individuals with cystic fibrosis · Andres R. Floto · 2015 · 480 citations · Cited by this paper
  26. Neutrophil Elastase Activity Is Associated with Exacerbations and Lung Function Decline in Bronchiectasis · James Duncan Chalmers · 2017 · 428 citations · Cited by this paper
  27. Improving saliva shotgun metagenomics by chemical host DNA depletion · Clarisse A. Marotz · 2018 · 386 citations · Cited by this paper
  28. Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures · Juliette C. Madan · 2012 · 359 citations · Cited by this paper
  29. Insights into Antibiotic Resistance Through Metagenomic Approaches · Robert Schmieder · 2011 · 312 citations · Cited by this paper
  30. A Phase 3 Open-Label Study of Elexacaftor/Tezacaftor/Ivacaftor in Children 6 through 11 Years of Age with Cystic Fibrosis and at Least One F508del Allele · Edith T. Zemanick · 2021 · 310 citations · Cited by this paper
  31. Lung function and microbiota diversity in cystic fibrosis · Leah Cuthbertson · 2020 · 277 citations · Cited by this paper
  32. The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants · Antonio Oliver · 2002 · 269 citations · Cited by this paper
  33. Characterization of Unusual Bacteria Isolated from Respiratory Secretions of Cystic Fibrosis Patients and Description of Inquilinus limosus gen. nov., sp. nov · Tom Coenye · 2002 · 260 citations · Cited by this paper
  34. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing · Mohammad Rubayet Hasan · 2016 · 260 citations · Cited by this paper
  35. Pulmonary exacerbations are associated with subsequent FEV1 decline in both adults and children with cystic fibrosis · Don B. Sanders · 2010 · 254 citations · Cited by this paper
  36. Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples · SAMUEL J. MARTIN · 2022 · 246 citations · Cited by this paper
  37. Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling · Geraint B. Rogers · 2003 · 238 citations · Cited by this paper
  38. The origin of DNA associated with mucus glycoproteins in cystic fibrosis sputum · Michael I. Lethem · 1990 · 221 citations · Cited by this paper
  39. Pharmacologic improvement of CFTR function rapidly decreases sputum pathogen density, but lung infections generally persist · David P. Nichols · 2023 · 220 citations · Cited by this paper

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