Research graph
References from The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Local targets link to admitted publications; unresolved targets remain external evidence.
The lung microbiome in health and disease
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The human lung microbiome—a hidden link between microbes and human health and diseases
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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
10.1038/s41587-023-01688-w · 2023 · External reference
A multi-omic future for microbiome studies
10.1038/nmicrobiol.2016.49 · 2016 · External reference
10.1016/j.csbj.2021.11.029
10.1016/j.csbj.2021.11.029 · External reference
Radiomics in lung diseases imaging: state-of-the-art for clinicians
2021 · External reference
Sputum induction
2002 · External reference
Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples
10.1002/ppul.24037 · 2018 · External reference
10.1164/rccm.201104-0655oc
10.1164/rccm.201104-0655oc · External reference
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION nanopore sequencing confers species-level resolution
10.1186/s12866-021-02094-5 · 2021 · External reference
A refined view of airway microbiome in chronic obstructive pulmonary disease at species and strain-levels
10.3389/fmicb.2020.01758 · 2020 · External reference
Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study
10.1183/13993003.00766-2018 · 2018 · External reference
10.1038/nbt.3935
10.1038/nbt.3935 · External reference
Human and extracellular DNA depletion for metagenomic analysis of complex clinical infection samples yields optimized viable microbiome profiles
10.1016/j.celrep.2019.01.091 · 2019 · External reference
10.1186/s40168-018-0426-3
10.1186/s40168-018-0426-3 · External reference
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
10.1038/s41587-019-0156-5 · 2019 · External reference
Advances and challenges in metatranscriptomic analysis
10.3389/fgene.2019.00904 · 2019 · External reference
Transcriptionally active lung microbiome and its association with bacterial biomass and host inflammatory status
2018 · External reference
Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism
10.1183/13993003.03434-2020 · 2021 · External reference
Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome
2021 · External reference
Lower airway dysbiosis augments lung inflammatory injury in mild-to-moderate COPD
10.1164/rccm.202210-1865oc · 2023 · External reference
Metaproteomics: much more than measuring gene expression in microbial communities
10.1128/msystems.00115-19 · 2019 · External reference
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10.1007/s00248-006-9196-8 · External reference
10.1016/j.jbiotec.2017.06.1201
10.1016/j.jbiotec.2017.06.1201 · External reference
Pregnancy zone protein is associated with airway infection, neutrophil extracellular trap formation, and disease severity in bronchiectasis
10.1164/rccm.201812-2351oc · 2019 · External reference
Airway host-microbiome interactions in chronic obstructive pulmonary disease
10.1186/s12931-019-1085-z · 2019 · External reference
Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions
10.1038/s41564-022-01196-8 · 2022 · External reference
A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes
2022 · External reference
The sputum microbiome, airway inflammation and mortality in chronic obstructive pulmonary disease
2020 · External reference
10.1016/s2213-2600(20)30504-x
10.1016/s2213-2600(20)30504-x · External reference
Sputum proteomics in nontuberculous mycobacterial lung disease
10.1016/j.chest.2021.11.014 · 2022 · External reference
Understanding the host-microbe interactions using metabolic modeling
10.1186/s40168-020-00955-1 · 2021 · External reference
Neisseria species as pathobionts in bronchiectasis
2022 · External reference
Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease
10.1016/j.chom.2023.04.018 · 2023 · External reference
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
10.1186/s12859-019-3176-8 · 2019 · External reference
10.1002/imt2.10
10.1002/imt2.10 · External reference
10.1016/j.ccm.2016.11.001
10.1016/j.ccm.2016.11.001 · External reference
Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children
10.1038/s41467-019-10294-x · 2019 · External reference
Lung virome: new potential biomarkers for asthma severity and exacerbation
10.1016/j.jaci.2021.03.017 · 2021 · External reference
Integrative microbiomics in bronchiectasis exacerbations
10.1038/s41591-021-01289-7 · 2021 · External reference
10.1038/s41579-018-0041-0
10.1038/s41579-018-0041-0 · External reference
10.1038/s41564-019-0643-y
10.1038/s41564-019-0643-y · External reference
Extended bacteria culture-based clustering identifies a phenotype associating increased cough and enterobacterales in stable chronic obstructive pulmonary disease
10.3389/fmicb.2021.781797 · 2021 · External reference
Characterization of lung and oral microbiomes in lung cancer patients using culturomics and 16S rRNA gene sequencing
2023 · External reference
Chest CT signs in pulmonary disease: a pictorial review
10.1016/j.chest.2016.12.033 · 2017 · External reference
Radiomics: from qualitative to quantitative imaging
10.1259/bjr.20190948 · 2020 · External reference
Non-small cell lung cancer radiogenomics map identifies relationships between molecular and imaging phenotypes with prognostic implications
10.1148/radiol.2017161845 · 2018 · External reference
Respiratory microbiota and radiomics features in the stable COPD patients
10.1186/s12931-023-02434-1 · 2023 · External reference
10.1186/s13059-015-0637-x
10.1186/s13059-015-0637-x · External reference
WGCNA: an R package for weighted correlation network analysis
10.1186/1471-2105-9-559 · 2008 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
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10.1093/nar/27.1.29 · External reference
10.1093/nar/gkt1178
10.1093/nar/gkt1178 · External reference
10.1128/aac.00419-13
10.1128/aac.00419-13 · External reference
10.1093/nar/gki008
10.1093/nar/gki008 · External reference
mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements
10.1128/aem.00991-22 · 2022 · External reference
Environmental fungal sensitisation associates with poorer clinical outcomes in COPD
2020 · External reference
10.1093/nar/gkq1018
10.1093/nar/gkq1018 · External reference
10.1093/nar/gkaa1024
10.1093/nar/gkaa1024 · External reference
10.1073/pnas.0506580102
10.1073/pnas.0506580102 · External reference
GSVA: gene set variation analysis for microarray and RNA-seq data
10.1186/1471-2105-14-7 · 2013 · External reference
10.1038/s41586-019-1237-9
10.1038/s41586-019-1237-9 · External reference
The MetaCyc Database
10.1093/nar/30.1.59 · 2002 · External reference
10.1093/nar/gkv1277
10.1093/nar/gkv1277 · External reference
10.1093/bioinformatics/btac232
10.1093/bioinformatics/btac232 · External reference
AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments
10.1371/journal.pcbi.1009826 · 2022 · External reference
CustOmics: a versatile deep-learning based strategy for multi-omics integration
10.1371/journal.pcbi.1010921 · 2023 · External reference
10.1371/journal.pcbi.1005752
10.1371/journal.pcbi.1005752 · External reference
Similarity network fusion for the integration of multi-omics and microbiomes in respiratory disease
10.1183/13993003.01016-2021 · 2021 · External reference
Integration of multi-omics datasets enables molecular classification of COPD
2018 · External reference
10.5114/aoms.2012.30280
10.5114/aoms.2012.30280 · External reference
Lung Microbiome in Asthma: Current Perspectives
10.3390/jcm8111967 · 2019 · External reference
10.1016/j.immuni.2020.01.007
10.1016/j.immuni.2020.01.007 · External reference
10.1371/journal.pone.0008578
10.1371/journal.pone.0008578 · External reference
Multi-omics profiling approach to asthma: an evolving paradigm
10.3390/jpm12010066 · 2022 · External reference
Microbiome research and multi-omics integration for personalized medicine in asthma
10.3390/jpm11121299 · 2021 · External reference
Integration of metagenomics-metabolomics reveals specific signatures and functions of airway microbiota in mite-sensitized childhood asthma
10.1111/all.14438 · 2020 · External reference
Associations between fungal and bacterial microbiota of airways and asthma endotypes
10.1016/j.jaci.2019.06.025 · 2019 · External reference
A multiomics approach to identify genes associated with childhood asthma risk and morbidity
10.1165/rcmb.2017-0002oc · 2017 · External reference
10.1186/s13073-021-00967-y
10.1186/s13073-021-00967-y · External reference
Integrative study of the upper and lower airway microbiome and transcriptome in asthma
10.1172/jci.insight.133707 · 2020 · External reference
Integrated omics endotyping of infants with respiratory syncytial virus bronchiolitis and risk of childhood asthma
10.1038/s41467-021-23859-6 · 2021 · External reference
Benchmarking omics-based prediction of asthma development in children
10.1186/s12931-023-02368-8 · 2023 · External reference
Chronic obstructive pulmonary disease: current burden and future projections
10.1183/09031936.06.00025805 · 2006 · External reference
Chronic obstructive pulmonary emphysema; a disease of smokers
10.7326/0003-4819-45-2-268 · 1956 · External reference
10.1183/13993003.01406-2015
10.1183/13993003.01406-2015 · External reference
Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study
10.1136/thoraxjnl-2017-210741 · 2018 · External reference
10.1164/rccm.202009-3448oc
10.1164/rccm.202009-3448oc · External reference
10.1164/rccm.201504-0779oc
10.1164/rccm.201504-0779oc · External reference
Lung microbiota and metabolites collectively associate with clinical outcomes in milder stage chronic obstructive pulmonary disease
10.1164/rccm.202110-2241oc · 2022 · External reference
Bronchiectasis
10.1038/s41572-018-0042-3 · 2018 · External reference
10.1016/s0140-6736(18)31767-7
10.1016/s0140-6736(18)31767-7 · External reference
10.1164/rccm.202205-0893oc
10.1164/rccm.202205-0893oc · External reference
10.1164/rccm.201607-1408oc
10.1164/rccm.201607-1408oc · External reference
10.1164/rccm.201607-1525oc
10.1164/rccm.201607-1525oc · External reference
Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis
10.1164/rccm.201809-1650oc · 2019 · External reference
10.1056/nejmoa2002032
10.1056/nejmoa2002032 · External reference
Unresolved reference
2021 · External reference
Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome
2021 · External reference
Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients
10.1038/s41421-021-00257-2 · 2021 · External reference
Dynamics of the upper respiratory tract microbiota and its association with mortality in COVID-19
10.1164/rccm.202103-0814oc · 2021 · External reference
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
10.1038/s41467-021-26500-8 · 2021 · External reference
A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation
10.1038/s41467-021-22344-4 · 2021 · External reference
Multi-omics profiling predicts allograft function after lung transplantation
10.1183/13993003.03292-2020 · 2022 · External reference
10.1038/s41579-022-00821-x
10.1038/s41579-022-00821-x · External reference
Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-Years for 29 Cancer Groups, 1990 to 2017: A Systematic Analysis for the Global Burden of Disease Study
10.1001/jamaoncol.2019.2996 · 2019 · External reference
Interaction between the microbiome and TP53 in human lung cancer
10.1186/s13059-018-1501-6 · 2018 · External reference
10.1158/2159-8290.cd-20-0263
10.1158/2159-8290.cd-20-0263 · External reference
10.1038/s41586-022-04427-4
10.1038/s41586-022-04427-4 · External reference
The lung microbiota affects pulmonary inflammation and oxidative stress induced by pm(2.5) exposure
10.1021/acs.est.1c08888 · 2022 · External reference
10.1186/s40168-018-0541-1
10.1186/s40168-018-0541-1 · External reference
10.1126/science.aao5774
10.1126/science.aao5774 · External reference
10.1038/nature18646
10.1038/nature18646 · External reference
Single sample pathway analysis in metabolomics: performance evaluation and application
10.1186/s12859-022-05005-1 · 2022 · External reference
Comprehensive analysis of immune-related gene signature based on ssGSEA algorithms in the prognosis and immune landscape of hepatocellular carcinoma
10.3389/fgene.2022.1064432 · 2022 · External reference
Transcriptomic gene signatures associated with persistent airflow limitation in patients with severe asthma
10.1183/13993003.02298-2016 · 2017 · External reference
T-helper cell type 2 (Th2) and non-Th2 molecular phenotypes of asthma using sputum transcriptomics in U-BIOPRED
2017 · External reference
Differential proteomic patterns of plasma extracellular vesicles show potential to discriminate β-thalassemia subtypes
10.1016/j.isci.2023.106048 · 2023 · External reference
10.1371/journal.pcbi.1009442
10.1371/journal.pcbi.1009442 · External reference
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10.1371/journal.pcbi.1004226
10.1371/journal.pcbi.1004226 · External reference
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10.1371/journal.pcbi.1002687 · External reference
The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans
2023 · External reference
10.18637/jss.v028.i05
10.18637/jss.v028.i05 · External reference
Classification and Regression by randomForest
2002 · External reference
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification
10.1038/s41467-021-23774-w · 2021 · External reference
AutoGGN: a gene graph network AutoML tool for multi-omics research
2021 · External reference
10.1038/s41587-022-01520-x
10.1038/s41587-022-01520-x · External reference
AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments
10.1371/journal.pcbi.1009826 · 2022 · External reference
Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE
10.1186/s12864-019-6285-x · 2019 · External reference
Unresolved reference
External reference
Association of sputum microbiome with clinical outcome of initial antibiotic treatment in hospitalized patients with acute exacerbations of COPD
10.1016/j.phrs.2020.105095 · 2020 · External reference
10.1016/j.jaci.2016.08.055
10.1016/j.jaci.2016.08.055 · External reference
Sputum microbiome is associated with 1-year mortality following COPD hospitalizations
2018 · External reference
Integration of multi-omics datasets enables molecular classification of COPD
2018 · External reference
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10.1038/s41396-020-0727-y · External reference
