Published in PLoS One on September 06, 2012
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med (2013) 3.65
The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 2.17
Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome (2013) 1.98
The role of the bacterial microbiome in lung disease. Expert Rev Respir Med (2013) 1.62
Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One (2013) 1.46
The development of lower respiratory tract microbiome in mice. Microbiome (2017) 1.39
Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med (2014) 1.36
Application of a neutral community model to assess structuring of the human lung microbiome. MBio (2015) 1.25
Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med (2015) 1.01
The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. Am J Respir Crit Care Med (2014) 1.00
Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant (2014) 0.98
The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol (2015) 0.97
Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol (2014) 0.96
Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs. Ann Am Thorac Soc (2014) 0.95
16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles. Microbiome (2014) 0.93
Inflammation and immune response in COPD: where do we stand? Mediators Inflamm (2013) 0.92
A brave new world: the lung microbiota in an era of change. Ann Am Thorac Soc (2014) 0.86
Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease. PLoS One (2016) 0.84
Sputum microbiota associated with new, recurrent and treatment failure tuberculosis. PLoS One (2013) 0.84
The bacterial microbiota in inflammatory lung diseases. Clin Immunol (2015) 0.84
Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome (2016) 0.83
Bacterial Topography of the Healthy Human Lower Respiratory Tract. MBio (2017) 0.79
The microbiome of the human lower airways: a next generation sequencing perspective. World Allergy Organ J (2015) 0.79
The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection. Tuberculosis (Edinb) (2015) 0.79
Pseudomonas aeruginosa and Periodontal Pathogens in the Oral Cavity and Lungs of Cystic Fibrosis Patients: a Case-Control Study. J Clin Microbiol (2015) 0.78
Extracellular Vesicles, a Key Mediator to Link Environmental Microbiota to Airway Immunity. Allergy Asthma Immunol Res (2017) 0.77
Lungs, microbes and the developing neonate. Neonatology (2015) 0.77
Microbiome diversity in the sputum of patients with pulmonary tuberculosis. Eur J Clin Microbiol Infect Dis (2016) 0.77
Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways. J Allergy Clin Immunol (2015) 0.77
The pediatric microbiome and the lung. Curr Opin Pediatr (2015) 0.77
Microbiome in chronic obstructive pulmonary disease. Ann Transl Med (2017) 0.76
Variability of the Sheep Lung Microbiota. Appl Environ Microbiol (2016) 0.76
Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study. BMC Microbiol (2016) 0.75
Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats. PLoS One (2017) 0.75
Lung Microbiota and Its Impact on the Mucosal Immune Phenotype. Microbiol Spectr (2017) 0.75
Bacteria isolated from lung modulate asthma susceptibility in mice. ISME J (2017) 0.75
Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome (2017) 0.75
Transcriptional Classification and Functional Characterization of Human Airway Macrophage and Dendritic Cell Subsets. J Immunol (2016) 0.75
The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients. Exp Mol Med (2017) 0.75
'The Microbiome and the Pathophysiology of Asthma'. Respir Res (2016) 0.75
Dendritic cells in lung immunopathology. Semin Immunopathol (2016) 0.75
The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases. Virulence (2016) 0.75
The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science. Nurs Res (2017) 0.75
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
Defining the normal bacterial flora of the oral cavity. J Clin Microbiol (2005) 15.75
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25
Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29
Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol (1998) 10.53
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Disordered microbial communities in asthmatic airways. PLoS One (2010) 6.35
Global diversity in the human salivary microbiome. Genome Res (2009) 5.16
Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med (2011) 4.78
Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One (2011) 4.65
Estimating F-statistics. Annu Rev Genet (2002) 4.30
Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A (2007) 4.06
Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88
Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol (1997) 3.78
Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30
Pharyngeal aspiration in normal adults and patients with depressed consciousness. Am J Med (1978) 2.65
Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One (2010) 2.60
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio (2010) 2.53
Oropharyngeal decontamination decreases incidence of ventilator-associated pneumonia. A randomized, placebo-controlled, double-blind clinical trial. JAMA (1991) 2.32
Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One (2012) 2.16
Diagnostic accuracy of protected specimen brush and bronchoalveolar lavage in nosocomial pneumonia: impact of previous antimicrobial treatments. Crit Care Med (1998) 2.14
Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol (2007) 2.12
Quantitative aspiration during sleep in normal subjects. Chest (1997) 1.98
Airway inflammation and bronchial bacterial colonization in chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2006) 1.88
A COMPARISON OF TRANSTRACHEAL ASPIRATION WITH OTHER METHODS OF DETERMINING THE BACTERIAL FLORA OF THE LOWER RESPIRATORY TRACT. N Engl J Med (1963) 1.79
Bronchoalveolar lavage for diagnosing acute bacterial pneumonia. J Infect Dis (1987) 1.75
Quantitative bacterial cultures of bronchoalveolar lavage fluids and protected brush catheter specimens from normal subjects. Am Rev Respir Dis (1989) 1.70
Tropheryma whipplei in patients with pneumonia. Emerg Infect Dis (2010) 1.59
Oropharyngeal or gastric colonization and nosocomial pneumonia in adult intensive care unit patients. A prospective study based on genomic DNA analysis. Am J Respir Crit Care Med (1997) 1.57
Should fiberoptic bronchoscopy aspirates be cultured? Am Rev Respir Dis (1976) 1.24
Bacteriology of the lower respiratory tract as determined by fiber-optic bronchoscopy and transtracheal aspiration. J Infect Dis (1976) 1.23
Quantitative culture of bronchoalveolar lavage fluid for the diagnosis of bacterial pneumonia. Am J Med (1993) 1.12
Diagnostic fiberoptic bronchoscopy and protected brush culture in patients with community-acquired pneumonia. Chest (1990) 1.03
A pilot study of quantitative aspiration in patients with symptoms of obstructive sleep apnea: comparison to a historic control group. Laryngoscope (2004) 0.96
Pattern of distribution of Prevotella species/phylotypes associated with healthy gingiva and periodontal disease. Eur J Clin Microbiol Infect Dis (2012) 0.92
Colonization and infection of the respiratory tract: What do we know? Paediatr Child Health (2004) 0.89
Special precautions reduce oropharyngeal contamination in bronchoalveolar lavage for bacteriologic studies. Lung (1989) 0.82
Molecular analysis of diversity within the genus Pseudomonas in the lungs of cystic fibrosis patients. Diagn Microbiol Infect Dis (2009) 0.79
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
ABT-263: a potent and orally bioavailable Bcl-2 family inhibitor. Cancer Res (2008) 9.65
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med (2013) 9.44
Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Invest (2008) 9.42
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat Med (2013) 8.89
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell (2008) 8.41
Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol (2004) 8.27
Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med (2014) 7.64
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res (2007) 6.89
Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus. Nat Immunol (2011) 6.73
siRNA-directed inhibition of HIV-1 infection. Nat Med (2002) 6.36
Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics (2008) 6.01
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature (2011) 4.81
Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med (2011) 4.78
HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res (2007) 4.72
Gene transfer in humans using a conditionally replicating lentiviral vector. Proc Natl Acad Sci U S A (2006) 4.23
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell (2007) 4.22
Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science (2012) 4.20
Variants of DENND1B associated with asthma in children. N Engl J Med (2009) 4.18
Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics (2003) 4.15
Copy number variation at 1q21.1 associated with neuroblastoma. Nature (2009) 4.10
Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88
Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N Engl J Med (2008) 3.80
Global landscape of HIV-human protein complexes. Nature (2011) 3.70
Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog (2006) 3.67
Efficacy of gene therapy for X-linked severe combined immunodeficiency. N Engl J Med (2010) 3.54
Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles. J Virol (2002) 3.46
Proinflammatory cytokine expression profile in degenerated and herniated human intervertebral disc tissues. Arthritis Rheum (2010) 3.45
Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data. Bioinformatics (2005) 3.34
The human gut virome: inter-individual variation and dynamic response to diet. Genome Res (2011) 3.32
Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med (2012) 3.29
Influence of Bcl-2 family members on the cellular response of small-cell lung cancer cell lines to ABT-737. Cancer Res (2007) 3.24
Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature (2013) 3.21
Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol (2006) 3.21
Group SCAD regression analysis for microarray time course gene expression data. Bioinformatics (2007) 3.04
A Markov random field model for network-based analysis of genomic data. Bioinformatics (2007) 2.93
Antitumor activity of a small-molecule inhibitor of human silent information regulator 2 enzymes. Cancer Res (2006) 2.92
Microglia/macrophage polarization dynamics reveal novel mechanism of injury expansion after focal cerebral ischemia. Stroke (2012) 2.88
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics (2004) 2.73
Functional materials for rechargeable batteries. Adv Mater (2011) 2.71
HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog (2011) 2.68
DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res (2008) 2.64
Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One (2010) 2.60
Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A (2013) 2.53
Variable Selection in Nonparametric Varying-Coefficient Models for Analysis of Repeated Measurements. J Am Stat Assoc (2008) 2.50
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nat Med (2012) 2.49
Assessing the potential for AAV vector genotoxicity in a murine model. Blood (2010) 2.48
The Bruton tyrosine kinase inhibitor PCI-32765 ameliorates autoimmune arthritis by inhibition of multiple effector cells. Arthritis Res Ther (2011) 2.48
Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One (2007) 2.48
Liver transplantation for hepatocellular carcinoma: Hangzhou experiences. Transplantation (2008) 2.48
Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. Nat Genet (2009) 2.47
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol (2010) 2.45
Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol (2010) 2.43
Interactions between S4-S5 linker and S6 transmembrane domain modulate gating of HERG K+ channels. J Biol Chem (2002) 2.34
Novel synthesis of 1-aroyl-3-aryl-4-substituted imidazole-2-thiones. Org Lett (2003) 2.30
Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am J Hum Genet (2002) 2.29
Nonparametric pathway-based regression models for analysis of genomic data. Biostatistics (2006) 2.28
Critical role of calpain I in mitochondrial release of apoptosis-inducing factor in ischemic neuronal injury. J Neurosci (2007) 2.23
Acute kidney injury during warfarin therapy associated with obstructive tubular red blood cell casts: a report of 9 cases. Am J Kidney Dis (2009) 2.21
Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Nature (2010) 2.21
Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics (2012) 2.19
Enhanced oligodendrogenesis and recovery of neurological function by erythropoietin after neonatal hypoxic/ischemic brain injury. Stroke (2010) 2.18
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. J Clin Invest (2012) 2.18
The BMP-binding protein Crossveinless 2 is a short-range, concentration-dependent, biphasic modulator of BMP signaling in Drosophila. Dev Cell (2008) 2.17
Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell (2013) 2.17
Neuroprotective effects of leptin against ischemic injury induced by oxygen-glucose deprivation and transient cerebral ischemia. Stroke (2007) 2.15
In Vivo Delivery of a Bcl-xL Fusion Protein Containing the TAT Protein Transduction Domain Protects against Ischemic Brain Injury and Neuronal Apoptosis. J Neurosci (2002) 2.12
The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood (2011) 2.11