Published in Genome Biol on January 01, 2014
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Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Inflamm Bowel Dis (2015) 0.91
Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome (2016) 0.83
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Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation. Microb Biotechnol (2016) 0.78
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Regulation of inflammation by microbiota interactions with the host. Nat Immunol (2017) 0.75
Fungal dysbiosis: immunity and interactions at mucosal barriers. Nat Rev Immunol (2017) 0.75
The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients. BMC Microbiol (2017) 0.75
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
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
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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
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Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
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The Registry of the International Society for Heart and Lung Transplantation: Twenty-eighth Adult Lung and Heart-Lung Transplant Report--2011. J Heart Lung Transplant (2011) 2.36
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Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environ Microbiol (2011) 1.84
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One (2013) 1.64
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Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One (2012) 1.51
Achromobacter xylosoxidans in cystic fibrosis: prevalence and clinical relevance. J Cyst Fibros (2006) 1.44
Characterization of some strains from human clinical sources which resemble "Leptotrichia sanguinegens": description of Sneathia sanguinegens sp. nov., gen. nov. Syst Appl Microbiol (2001) 1.43
Pseudomonas aeruginosa: host defence in lung diseases. Respirology (2010) 1.39
Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun (2012) 1.36
Aspergillus colonization of the lung allograft is a risk factor for bronchiolitis obliterans syndrome. Am J Transplant (2009) 1.34
Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response. Cell Microbiol (2013) 1.24
Presence of mutans streptococci and Candida spp. in dental plaque/dentine of carious teeth and early childhood caries. Arch Oral Biol (2006) 1.20
A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol (2012) 1.17
Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study. Transplantation (2009) 1.17
Bacterial and fungal colonization of burn wounds. Mem Inst Oswaldo Cruz (2005) 1.15
Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog (2014) 1.13
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One (2013) 1.11
Pulmonary infections in HIV-infected patients: an update in the 21st century. Eur Respir J (2011) 1.09
Streptococcus mutans, Candida albicans, and the human mouth: a sticky situation. PLoS Pathog (2013) 1.09
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Pneumonia due to methicillin-resistant Staphylococcus aureus: clinical features, diagnosis and management. Curr Opin Pulm Med (2009) 1.01
Effect of Streptococcus salivarius K12 on the in vitro growth of Candida albicans and its protective effect in an oral candidiasis model. Appl Environ Microbiol (2012) 0.99
Clinical and microbiological diagnosis of oral candidiasis. J Clin Exp Dent (2013) 0.99
Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients. BMC Microbiol (2012) 0.97
Impact of graft colonization with gram-negative bacteria after lung transplantation on the development of bronchiolitis obliterans syndrome in recipients with cystic fibrosis. Respir Med (2008) 0.94
Chlamydia pneumoniae serology in donors and recipients and the risk of bronchiolitis obliterans syndrome after lung transplantation. Transplantation (2005) 0.88
Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection. J Clin Microbiol (2013) 0.87
Assessing oropharyngeal dysphagia after lung transplantation: altered swallowing mechanisms and increased morbidity. J Heart Lung Transplant (2007) 0.86
Targeting allograft injury and inflammation in the management of post-lung transplant bronchiolitis obliterans syndrome. Am J Transplant (2009) 0.84
Reduced salivary flow and colonization by mutans streptococci in children with Down syndrome. Clinics (Sao Paulo) (2012) 0.82
De novo or persistent pseudomonal airway colonization after lung transplantation: importance for bronchiolitis obliterans syndrome? Transplantation (2008) 0.81
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
Long-term proton pump inhibitor therapy and risk of hip fracture. JAMA (2006) 9.53
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
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
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
The association between hepatitis C infection and survival after orthotopic liver transplantation. Gastroenterology (2002) 4.98
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
Optimization and validation of an 8-color intracellular cytokine staining (ICS) assay to quantify antigen-specific T cells induced by vaccination. J Immunol Methods (2007) 4.69
Intravenous delivery of a multi-mechanistic cancer-targeted oncolytic poxvirus in humans. Nature (2011) 4.61
Serum lactate is associated with mortality in severe sepsis independent of organ failure and shock. Crit Care Med (2009) 4.56
Standardization of cytokine flow cytometry assays. BMC Immunol (2005) 4.55
Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections. Blood (2008) 4.34
Pegylated Interferon alfa-2a monotherapy results in suppression of HIV type 1 replication and decreased cell-associated HIV DNA integration. J Infect Dis (2012) 4.24
Gene transfer in humans using a conditionally replicating lentiviral vector. Proc Natl Acad Sci U S A (2006) 4.23
Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science (2012) 4.20
Overestimates of survival after HAART: implications for global scale-up efforts. PLoS One (2008) 4.20
Variants of DENND1B associated with asthma in children. N Engl J Med (2009) 4.18
Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88
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
Initiation of tumor necrosis factor-α antagonists and the risk of hospitalization for infection in patients with autoimmune diseases. JAMA (2011) 3.58
Insulin therapy and colorectal cancer risk among type 2 diabetes mellitus patients. Gastroenterology (2004) 3.57
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
Clinical risk factors for primary graft dysfunction after lung transplantation. Am J Respir Crit Care Med (2013) 3.38
The human gut virome: inter-individual variation and dynamic response to diet. Genome Res (2011) 3.32
Echocardiographic assessment of pulmonary hypertension in patients with advanced lung disease. Am J Respir Crit Care Med (2002) 3.32
Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med (2012) 3.29
Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine. N Engl J Med (2013) 3.24
Factors associated with nonadherence to early goal-directed therapy in the ED. Chest (2010) 3.23
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
RELMbeta/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract. Proc Natl Acad Sci U S A (2004) 3.05
The Registry of the International Society for Heart and Lung Transplantation: Twenty-eighth Adult Heart Transplant Report--2011. J Heart Lung Transplant (2011) 3.01
Efficacy of anti-tumor necrosis factor therapy in patients with ulcerative colitis. Am J Gastroenterol (2002) 3.01
Perforin expression directly ex vivo by HIV-specific CD8 T-cells is a correlate of HIV elite control. PLoS Pathog (2010) 2.99
A multibiomarker-based outcome risk stratification model for adult septic shock*. Crit Care Med (2014) 2.94
Inflammasome-regulated cytokines are critical mediators of acute lung injury. Am J Respir Crit Care Med (2012) 2.92
Registry of the International Society for Heart and Lung Transplantation: Twenty-sixth Official Adult Heart Transplant Report-2009. J Heart Lung Transplant (2009) 2.85
The Registry of the International Society for Heart and Lung Transplantation: 29th official adult heart transplant report--2012. J Heart Lung Transplant (2012) 2.83
Pharmacy refill adherence compared with CD4 count changes for monitoring HIV-infected adults on antiretroviral therapy. PLoS Med (2008) 2.82
Use of therapeutic hypothermia after in-hospital cardiac arrest. Crit Care Med (2013) 2.81
Neutrophil extracellular traps are pathogenic in primary graft dysfunction after lung transplantation. Am J Respir Crit Care Med (2015) 2.80
Mortality associated with medical therapy versus elective colectomy in ulcerative colitis: a cohort study. Ann Intern Med (2014) 2.73
The adult respiratory distress syndrome cognitive outcomes study: long-term neuropsychological function in survivors of acute lung injury. Am J Respir Crit Care Med (2012) 2.72
Racial differences pertaining to a belief about lung cancer surgery: results of a multicenter survey. Ann Intern Med (2003) 2.71
HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog (2011) 2.68
Functional polymorphisms in the transcription factor NRF2 in humans increase the risk of acute lung injury. FASEB J (2007) 2.65
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
Survival differences following lung transplantation among US transplant centers. JAMA (2010) 2.57
Diagnostic accuracy of CD4 cell count increase for virologic response after initiating highly active antiretroviral therapy. AIDS (2006) 2.57
Rosiglitazone for active ulcerative colitis: a randomized placebo-controlled trial. Gastroenterology (2007) 2.55
Registry of the International Society for Heart and Lung Transplantation: twenty-fourth official adult lung and heart-lung transplantation report-2007. J Heart Lung Transplant (2007) 2.55
Association of RBC transfusion with mortality in patients with acute lung injury. Chest (2007) 2.55
The Registry of the International Society for Heart and Lung Transplantation: Thirtieth Official Adult Heart Transplant Report--2013; focus theme: age. J Heart Lung Transplant (2013) 2.55
Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A (2013) 2.53
Association between vaccination for herpes zoster and risk of herpes zoster infection among older patients with selected immune-mediated diseases. JAMA (2012) 2.51
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
Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One (2007) 2.48
The Registry of the International Society for Heart and Lung Transplantation: Thirtieth Adult Lung and Heart-Lung Transplant Report--2013; focus theme: age. J Heart Lung Transplant (2013) 2.46
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
IL-7 is a potent and proviral strain-specific inducer of latent HIV-1 cellular reservoirs of infected individuals on virally suppressive HAART. J Clin Invest (2005) 2.41
Use of abdominopelvic computed tomography in emergency departments and rates of urgent diagnoses in Crohn's disease. Clin Gastroenterol Hepatol (2011) 2.40
The risk of mortality in patients with psoriasis: results from a population-based study. Arch Dermatol (2007) 2.32
Incidence and mortality of colorectal adenocarcinoma in persons with inflammatory bowel disease from 1998 to 2010. Gastroenterology (2012) 2.26