{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T21:48:20Z","timestamp":1793828900950,"version":"4.6.1"},"reference-count":282,"publisher":"European Respiratory Society (ERS)","issue":"179","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["publications.ersnet.org"],"crossmark-restriction":true},"short-container-title":["Eur Respir Rev"],"accepted":{"date-parts":[[2025,8,30]]},"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:p>Despite recent advances, the underlying mechanisms of the development and progression of many chronic respiratory diseases remain to be elucidated. Factors such as heterogeneity and complexity of human diseases and difficulty interpreting large datasets hinder research into chronic respiratory diseases. Omics assesses the changes in specific biological entities, such as mRNA expression, epigenetics\/epigenomics, genomics, proteomics, metagenomics and metabolomics, and provides valuable insights into the roles of these processes in chronic respiratory diseases. High-throughput omics at bulk, single-cell and spatial levels empower the exploration of disease-related changes through untargeted data-driven statistical methods. Multi-omics is the exploration and integration of multiple biological processes, which compared to a single-omics, can provide a substantially greater and more holistic overview of the pathogenic mechanisms that underpin complex diseases. Multi-omics analysis can comprehensively characterise the mechanisms that drive chronic respiratory diseases, capturing unique biological signatures and cellular interactions at different omics levels. Use of these methods has begun to identify key factors and biomarkers in chronic respiratory diseases. Here, we review current omics approaches and highlight recent advances in respiratory research achieved using multi-omics and integrative methods. Our review provides a valuable resource for researchers and clinicians in this area.<\/jats:p>","DOI":"10.1183\/16000617.0286-2024","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T18:41:12Z","timestamp":1790966472000},"page":"240286","update-policy":"https:\/\/doi.org\/10.1183\/ers-crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Multi-omics to study chronic respiratory diseases and viral infections"],"prefix":"10.1183","volume":"35","author":[{"given":"Sobia","family":"Idrees","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tayyaba","family":"Sadaf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saima Firdous","family":"Rehman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt D.","family":"Johansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3591-2080","authenticated-orcid":false,"given":"Keshav Raj","family":"Paudel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0489-2638","authenticated-orcid":false,"given":"Gang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuting","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7464-7921","authenticated-orcid":false,"given":"Malte D.","family":"Luecken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elinor","family":"Hortle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashleigh S.","family":"Philp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurtis F.","family":"Budden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"O'Rourke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerard E.","family":"Kaiko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sionne E.M.","family":"Lucas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne L.","family":"Dickinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3950-9539","authenticated-orcid":false,"given":"Peter C.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph E.","family":"Powell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lai-Ying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel C.","family":"Chambers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamera","family":"Corte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9807-327X","authenticated-orcid":false,"given":"Gaetano","family":"Caramori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5240-7978","authenticated-orcid":false,"given":"Maor","family":"Sauler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5676-6126","authenticated-orcid":false,"given":"Peter A.","family":"Wark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janine","family":"Gote-Schniering","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8601-8206","authenticated-orcid":false,"given":"Mareike","family":"Lehmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M.","family":"Conlon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theodore S.","family":"Kapellos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1969-480X","authenticated-orcid":false,"given":"Ali \u00d6nder","family":"Yildirim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosa","family":"Faner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shyamali C.","family":"Dharmage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8113-0653","authenticated-orcid":false,"given":"Craig E.","family":"Wheelock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maarten","family":"van den Berge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3372-6521","authenticated-orcid":false,"given":"Martijn C.","family":"Nawijn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Polverino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabrielle T.","family":"Belz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0417-7607","authenticated-orcid":false,"given":"Sanjay H.","family":"Chotirmall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3559-9431","authenticated-orcid":false,"given":"Leopoldo N.","family":"Segal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alen","family":"Faiz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip M.","family":"Hansbro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"81","published-online":{"date-parts":[[2026,1,14]]},"reference":[{"key":"2026100211390068000_35.179.240286.1","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-017-0631-9"},{"key":"2026100211390068000_35.179.240286.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3356"},{"key":"2026100211390068000_35.179.240286.3","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1513\/pats.201010-065MS","article-title":"Aspen Lung Conference 2010: systems biology of lung diseases \u2013 progress in the omics era","volume":"8","author":"Sheppard","year":"2011","journal-title":"Proc Am Thorac Soc"},{"key":"2026100211390068000_35.179.240286.4","doi-asserted-by":"publisher","DOI":"10.1183\/16000617.0022-2018"},{"key":"2026100211390068000_35.179.240286.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2016.04.038"},{"key":"2026100211390068000_35.179.240286.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.tips.2016.10.012"},{"key":"2026100211390068000_35.179.240286.7","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1111\/cts.12446","article-title":"Personalized medicine in Europe","volume":"10","author":"Nimmesgern","year":"2017","journal-title":"Clin Transl Sci"},{"key":"2026100211390068000_35.179.240286.8","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/S2213-2600(18)30296-0","article-title":"Precision medicine in COPD exacerbations","volume":"6","author":"Agusti","year":"2018","journal-title":"Lancet Respir Med"},{"key":"2026100211390068000_35.179.240286.9","doi-asserted-by":"publisher","DOI":"10.1152\/japplphysiol.01310.2010"},{"key":"2026100211390068000_35.179.240286.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.08.026"},{"key":"2026100211390068000_35.179.240286.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37961-4"},{"key":"2026100211390068000_35.179.240286.12","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1165\/rcmb.2021-0403OC","article-title":"Chronic obstructive pulmonary disease is associated with epigenome-wide differential methylation in BAL lung cells","volume":"66","author":"Eriksson Str\u00f6m","year":"2022","journal-title":"Am J Respir Cell Mol Biol"},{"key":"2026100211390068000_35.179.240286.13","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/s13148-021-01208-0","article-title":"Genome-wide methylation and expression analyses reveal the epigenetic landscape of immune-related diseases for tobacco smoking","volume":"13","author":"Mao","year":"2021","journal-title":"Clin Epigenetics"},{"key":"2026100211390068000_35.179.240286.14","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1139\/gen-2024-0019","article-title":"Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel","volume":"67","author":"Nkongolo","year":"2024","journal-title":"Genome"},{"key":"2026100211390068000_35.179.240286.15","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5533506"},{"key":"2026100211390068000_35.179.240286.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.01.003"},{"key":"2026100211390068000_35.179.240286.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-023-00580-2"},{"key":"2026100211390068000_35.179.240286.18","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.03406-2020"},{"key":"2026100211390068000_35.179.240286.19","doi-asserted-by":"publisher","DOI":"10.1038\/4434"},{"key":"2026100211390068000_35.179.240286.20","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/978-1-4939-3136-1_8","article-title":"Microarray technology and its applications for detecting plasma microRNA biomarkers in digestive tract cancers","volume":"1368","author":"Konishi","year":"2016","journal-title":"Methods Mol Biol"},{"key":"2026100211390068000_35.179.240286.21","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1749"},{"key":"2026100211390068000_35.179.240286.22","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401422101"},{"key":"2026100211390068000_35.179.240286.23","doi-asserted-by":"publisher","DOI":"10.1152\/physiolgenomics.00167.2009"},{"key":"2026100211390068000_35.179.240286.24","doi-asserted-by":"publisher","DOI":"10.1038\/nm1556"},{"key":"2026100211390068000_35.179.240286.25","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00104-2021"},{"key":"2026100211390068000_35.179.240286.26","first-page":"117","article-title":"Screening of genes related to lung cancer caused by smoking with RNA-seq","volume":"18","author":"Zhou","year":"2014","journal-title":"Eur Rev Med Pharmacol Sci"},{"key":"2026100211390068000_35.179.240286.27","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00115412"},{"key":"2026100211390068000_35.179.240286.28","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1164\/rccm.202108-1901OC","article-title":"Increased SARS-CoV-2 infection, protease, and inflammatory responses in chronic obstructive pulmonary disease primary bronchial epithelial cells defined with single-cell RNA sequencing","volume":"206","author":"Johansen","year":"2022","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.29","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4380"},{"key":"2026100211390068000_35.179.240286.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-023-02327-2"},{"key":"2026100211390068000_35.179.240286.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107872"},{"key":"2026100211390068000_35.179.240286.32","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2020.08.001"},{"key":"2026100211390068000_35.179.240286.33","doi-asserted-by":"publisher","DOI":"10.15252\/embj.20105114"},{"key":"2026100211390068000_35.179.240286.34","doi-asserted-by":"publisher","DOI":"10.1164\/RCCM.201712-2410OC\/SUPPL_FILE\/DISCLOSURES.PDF"},{"key":"2026100211390068000_35.179.240286.35","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aba1983"},{"key":"2026100211390068000_35.179.240286.36","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.978824"},{"key":"2026100211390068000_35.179.240286.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0394-6"},{"key":"2026100211390068000_35.179.240286.38","doi-asserted-by":"publisher","DOI":"10.1161\/circulationaha.120.052318"},{"key":"2026100211390068000_35.179.240286.39","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.02441-2018"},{"key":"2026100211390068000_35.179.240286.40","doi-asserted-by":"publisher","DOI":"10.1038\/S41591-020-0901-9"},{"key":"2026100211390068000_35.179.240286.41","doi-asserted-by":"publisher","DOI":"10.1042\/etls20210074"},{"key":"2026100211390068000_35.179.240286.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0292-x"},{"key":"2026100211390068000_35.179.240286.43","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0667-5"},{"key":"2026100211390068000_35.179.240286.44","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0071-9"},{"key":"2026100211390068000_35.179.240286.45","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2012.11.053"},{"key":"2026100211390068000_35.179.240286.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.11.026"},{"key":"2026100211390068000_35.179.240286.47","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"2026100211390068000_35.179.240286.48","doi-asserted-by":"publisher","DOI":"10.4331\/wjbc.v12.i5.57"},{"key":"2026100211390068000_35.179.240286.49","doi-asserted-by":"publisher","DOI":"10.1373\/clinchem.2009.137158"},{"key":"2026100211390068000_35.179.240286.50","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/s43586-022-00175-x","article-title":"Liquid chromatography-tandem mass spectrometry for clinical diagnostics","volume":"2","author":"Thomas","year":"2022","journal-title":"Nat Rev Methods Primers"},{"key":"2026100211390068000_35.179.240286.51","doi-asserted-by":"publisher","DOI":"10.3343\/alm.2018.38.2.110"},{"key":"2026100211390068000_35.179.240286.52","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2288-12-40","article-title":"Determination of inflammatory biomarkers in patients with COPD: a comparison of different assays","volume":"12","author":"L\u00f3pez-Campos","year":"2012","journal-title":"BMC Med Res Methodol"},{"key":"2026100211390068000_35.179.240286.53","doi-asserted-by":"publisher","DOI":"10.1111\/resp.14111"},{"key":"2026100211390068000_35.179.240286.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2011.07.053"},{"key":"2026100211390068000_35.179.240286.55","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00021.2016"},{"key":"2026100211390068000_35.179.240286.56","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1164\/rccm.202108-1943OC","article-title":"Endotyping chronic obstructive pulmonary disease, bronchiectasis, and the \u201cchronic obstructive pulmonary disease-bronchiectasis association\u201d","volume":"206","author":"Huang","year":"2022","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.57","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2020-215114"},{"key":"2026100211390068000_35.179.240286.58","doi-asserted-by":"crossref","first-page":"104262","DOI":"10.1016\/j.ebiom.2022.104262","article-title":"Unique and shared systemic biomarkers for emphysema in alpha-1 antitrypsin deficiency and chronic obstructive pulmonary disease","volume":"84","author":"Serban","year":"2022","journal-title":"EBioMedicine"},{"key":"2026100211390068000_35.179.240286.59","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2019-213200"},{"key":"2026100211390068000_35.179.240286.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01303-3"},{"key":"2026100211390068000_35.179.240286.61","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00035.2018"},{"key":"2026100211390068000_35.179.240286.62","doi-asserted-by":"publisher","DOI":"10.1007\/s11306-018-1367-3"},{"key":"2026100211390068000_35.179.240286.63","doi-asserted-by":"publisher","DOI":"10.1016\/J.COPBIO.2018.07.010"},{"key":"2026100211390068000_35.179.240286.64","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3597"},{"key":"2026100211390068000_35.179.240286.65","doi-asserted-by":"crossref","first-page":"101408","DOI":"10.1016\/j.xpro.2022.101408","article-title":"Targeted LC-MS\/MS-based metabolomics and lipidomics on limited hematopoietic stem cell numbers","volume":"3","author":"Sch\u00f6nberger","year":"2022","journal-title":"STAR Protoc"},{"key":"2026100211390068000_35.179.240286.66","doi-asserted-by":"crossref","first-page":"e1009105","DOI":"10.1371\/journal.pcbi.1009105","article-title":"Pathway analysis in metabolomics: recommendations for the use of over-representation analysis","volume":"17","author":"Wieder","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2026100211390068000_35.179.240286.67","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01714-5"},{"key":"2026100211390068000_35.179.240286.68","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202105-1268OC"},{"key":"2026100211390068000_35.179.240286.69","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01733-2021"},{"key":"2026100211390068000_35.179.240286.70","doi-asserted-by":"publisher","DOI":"10.1038\/nm.4176"},{"key":"2026100211390068000_35.179.240286.71","doi-asserted-by":"crossref","first-page":"21912","DOI":"10.1038\/s41598-020-78951-6","article-title":"Serum metabolites as biomarkers in systemic sclerosis-associated interstitial lung disease","volume":"10","author":"Meier","year":"2020","journal-title":"Sci Rep"},{"key":"2026100211390068000_35.179.240286.72","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s12931-018-0714-2","article-title":"Serum metabolic profiling identified a distinct metabolic signature in patients with idiopathic pulmonary fibrosis \u2013 a potential biomarker role for LysoPC","volume":"19","author":"Rindlisbacher","year":"2018","journal-title":"Respir Res"},{"key":"2026100211390068000_35.179.240286.73","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202008-3206OC"},{"key":"2026100211390068000_35.179.240286.74","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201410-1771OC"},{"key":"2026100211390068000_35.179.240286.75","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1016\/j.chest.2021.10.049","article-title":"Identification of sputum biomarkers predictive of pulmonary exacerbations in COPD","volume":"161","author":"Esther","year":"2022","journal-title":"Chest"},{"key":"2026100211390068000_35.179.240286.76","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1146\/annurev-biodatasci-011420-031537","article-title":"Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence","volume":"3","author":"Alexandrov","year":"2020","journal-title":"Annu Rev Biomed Data Sci"},{"key":"2026100211390068000_35.179.240286.77","doi-asserted-by":"publisher","DOI":"10.1186\/s13244-020-00887-2"},{"key":"2026100211390068000_35.179.240286.78","doi-asserted-by":"crossref","first-page":"602","DOI":"10.3390\/jpm11070602","article-title":"Radiomics in lung diseases imaging: state-of-the-art for clinicians","volume":"11","author":"Frix","year":"2021","journal-title":"J Pers Med"},{"key":"2026100211390068000_35.179.240286.79","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.acra.2012.04.020","article-title":"Automated texture-based quantification of centrilobular nodularity and centrilobular emphysema in chest CT images","volume":"19","author":"Ginsburg","year":"2012","journal-title":"Acad Radiol"},{"key":"2026100211390068000_35.179.240286.80","doi-asserted-by":"crossref","unstructured":"Lauer D , Magnin CY , Kolly LR , et al . Radioproteomics stratifies molecular response to antifibrotic treatment in pulmonary fibrosis. JCI Insight 2024; 9. doi: 10.1172\/jci.insight.181757","DOI":"10.1172\/jci.insight.181757"},{"key":"2026100211390068000_35.179.240286.81","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.04503-2020"},{"key":"2026100211390068000_35.179.240286.82","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.3390\/cancers15061634","article-title":"More than meets the eye: integration of radiomics with transcriptomics for reconstructing the tumor microenvironment and predicting response to therapy","volume":"15","author":"Logotheti","year":"2023","journal-title":"Cancers"},{"key":"2026100211390068000_35.179.240286.83","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0159066"},{"key":"2026100211390068000_35.179.240286.84","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01228-07"},{"key":"2026100211390068000_35.179.240286.85","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0029-9"},{"key":"2026100211390068000_35.179.240286.86","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01930-2017"},{"key":"2026100211390068000_35.179.240286.87","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-022-01075-1"},{"key":"2026100211390068000_35.179.240286.88","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.cels.2023.06.003","article-title":"BayesTME: an end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment","volume":"14","author":"Zhang","year":"2023","journal-title":"Cell Systems"},{"key":"2026100211390068000_35.179.240286.89","doi-asserted-by":"publisher","DOI":"10.1038\/S41592-020-01033-Y"},{"key":"2026100211390068000_35.179.240286.90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000675"},{"key":"2026100211390068000_35.179.240286.91","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01243-4"},{"key":"2026100211390068000_35.179.240286.92","doi-asserted-by":"crossref","first-page":"e157837","DOI":"10.1172\/jci.insight.157837","article-title":"Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury","volume":"8","author":"Cross","year":"2023","journal-title":"JCI Insight"},{"key":"2026100211390068000_35.179.240286.93","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/s12931-022-02067-w","article-title":"Digital quantification of p16-positive foci in fibrotic interstitial lung disease is associated with a phenotype of idiopathic pulmonary fibrosis with reduced survival","volume":"23","author":"Keow","year":"2022","journal-title":"Respir Res"},{"key":"2026100211390068000_35.179.240286.94","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-022-01064-x"},{"key":"2026100211390068000_35.179.240286.95","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2021.04.048"},{"key":"2026100211390068000_35.179.240286.96","doi-asserted-by":"crossref","first-page":"9381","DOI":"10.1038\/s41467-024-53752-x","article-title":"High-parametric protein maps reveal the spatial organization in early-developing human lung","volume":"15","author":"Sariyar","year":"2024","journal-title":"Nat Commun"},{"key":"2026100211390068000_35.179.240286.97","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3390\/proteomes10030033","article-title":"Viral biomarker detection and validation using MALDI mass spectrometry imaging (MSI)","volume":"10","author":"O'Rourke","year":"2022","journal-title":"Proteomes"},{"key":"2026100211390068000_35.179.240286.98","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-02007-6"},{"key":"2026100211390068000_35.179.240286.99","doi-asserted-by":"crossref","first-page":"e1900328","DOI":"10.1002\/pmic.201900328","article-title":"Spatial proteomics: a gateway to understanding cell biology","volume":"20","author":"Borner","year":"2020","journal-title":"Proteomics"},{"key":"2026100211390068000_35.179.240286.100","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1038\/s41467-022-28445-y","article-title":"SM-Omics is an automated platform for high-throughput spatial multi-omics","volume":"13","author":"Vickovic","year":"2022","journal-title":"Nat Commun"},{"key":"2026100211390068000_35.179.240286.101","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01676-0"},{"key":"2026100211390068000_35.179.240286.102","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01536-3"},{"key":"2026100211390068000_35.179.240286.103","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00475.2018"},{"key":"2026100211390068000_35.179.240286.104","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38437-1"},{"key":"2026100211390068000_35.179.240286.105","doi-asserted-by":"crossref","first-page":"17950","DOI":"10.1021\/acs.analchem.4c02350","article-title":"Development of a desorption electrospray ionization-multiple-reaction-monitoring mass spectrometry (DESI-MRM) workflow for spatially mapping oxylipins in pulmonary tissue","volume":"96","author":"Smith","year":"2024","journal-title":"Anal Chem"},{"key":"2026100211390068000_35.179.240286.106","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/elv040"},{"key":"2026100211390068000_35.179.240286.107","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbz085"},{"key":"2026100211390068000_35.179.240286.108","doi-asserted-by":"crossref","first-page":"e12014","DOI":"10.1002\/ccs3.12014","article-title":"Proteome-wide assessment of human interactome as a source of capturing domain-motif and domain-domain interactions","volume":"18","author":"Idrees","year":"2024","journal-title":"J Cell Commun Signal"},{"key":"2026100211390068000_35.179.240286.109","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1002\/1873-3468.14841","article-title":"Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods","volume":"598","author":"Idrees","year":"2024","journal-title":"FEBS Lett"},{"key":"2026100211390068000_35.179.240286.110","doi-asserted-by":"crossref","first-page":"630","DOI":"10.3390\/microorganisms12030630","article-title":"Exploring viral-host protein interactions as antiviral therapies: a computational perspective","volume":"12","author":"Idrees","year":"2024","journal-title":"Microorganisms"},{"key":"2026100211390068000_35.179.240286.111","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1204"},{"key":"2026100211390068000_35.179.240286.112","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1006"},{"key":"2026100211390068000_35.179.240286.113","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1131"},{"key":"2026100211390068000_35.179.240286.114","first-page":"1113","article-title":"How different viruses perturb host cellular machinery via short linear motifs","volume":"22","author":"Idrees","year":"2023","journal-title":"EXCLI J"},{"key":"2026100211390068000_35.179.240286.115","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/s41392-020-00315-3","article-title":"Recent advances in the development of protein-protein interactions modulators: mechanisms and clinical trials","volume":"5","author":"Lu","year":"2020","journal-title":"Signal Transduct Target Ther"},{"key":"2026100211390068000_35.179.240286.116","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2009.04.124"},{"key":"2026100211390068000_35.179.240286.117","doi-asserted-by":"publisher","DOI":"10.1021\/bi201428h"},{"key":"2026100211390068000_35.179.240286.118","doi-asserted-by":"publisher","DOI":"10.1016\/j.coisb.2021.03.007"},{"key":"2026100211390068000_35.179.240286.119","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559"},{"key":"2026100211390068000_35.179.240286.120","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac589"},{"key":"2026100211390068000_35.179.240286.121","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04179-4"},{"key":"2026100211390068000_35.179.240286.122","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26674-1"},{"key":"2026100211390068000_35.179.240286.123","doi-asserted-by":"publisher","DOI":"10.1101\/gr.136838.111"},{"key":"2026100211390068000_35.179.240286.124","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/s42003-021-02153-7","article-title":"Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment","volume":"4","author":"Rubin","year":"2021","journal-title":"Commun Biol"},{"key":"2026100211390068000_35.179.240286.125","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz446"},{"key":"2026100211390068000_35.179.240286.126","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3593"},{"key":"2026100211390068000_35.179.240286.127","doi-asserted-by":"crossref","first-page":"1077003","DOI":"10.3389\/fimmu.2023.1077003","article-title":"Single-cell protein activity analysis reveals a novel subpopulation of chondrocytes and the corresponding key master regulator proteins associated with anti-senescence and OA progression","volume":"14","author":"Guang","year":"2023","journal-title":"Front Immunol"},{"key":"2026100211390068000_35.179.240286.128","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-S1-S7"},{"key":"2026100211390068000_35.179.240286.129","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1949-z"},{"key":"2026100211390068000_35.179.240286.130","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463"},{"key":"2026100211390068000_35.179.240286.131","doi-asserted-by":"crossref","first-page":"15463","DOI":"10.1038\/s41598-021-94805-1","article-title":"AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators","volume":"11","author":"Meiler","year":"2021","journal-title":"Sci Rep"},{"key":"2026100211390068000_35.179.240286.132","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.441"},{"key":"2026100211390068000_35.179.240286.133","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1007\/s11831-022-09821-9","article-title":"A systematic review on biomarker identification for cancer diagnosis and prognosis in multi-omics: from computational needs to machine learning and deep learning","volume":"30","author":"Dhillon","year":"2023","journal-title":"Arch Comput Methods Eng"},{"key":"2026100211390068000_35.179.240286.134","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-162"},{"key":"2026100211390068000_35.179.240286.135","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.118.301595"},{"key":"2026100211390068000_35.179.240286.136","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2022.854752"},{"key":"2026100211390068000_35.179.240286.137","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts163"},{"key":"2026100211390068000_35.179.240286.138","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-11"},{"key":"2026100211390068000_35.179.240286.139","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv244"},{"key":"2026100211390068000_35.179.240286.140","doi-asserted-by":"publisher","DOI":"10.1038\/s41416-024-02587-w"},{"key":"2026100211390068000_35.179.240286.141","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1093\/bioinformatics\/btz124","article-title":"Using association signal annotations to boost similarity network fusion","volume":"35","author":"Ruan","year":"2019","journal-title":"Bioinformatics"},{"key":"2026100211390068000_35.179.240286.142","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002227"},{"key":"2026100211390068000_35.179.240286.143","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s12561-016-9176-6","article-title":"A Bayesian approach for learning gene networks underlying disease severity in COPD","volume":"10","author":"Shaddox","year":"2018","journal-title":"Stat Biosci"},{"key":"2026100211390068000_35.179.240286.144","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq182"},{"key":"2026100211390068000_35.179.240286.145","doi-asserted-by":"crossref","first-page":"bbab024","DOI":"10.1093\/bib\/bbab024","article-title":"Advances in bulk and single-cell multi-omics approaches for systems biology and precision medicine","volume":"22","author":"Li","year":"2021","journal-title":"Brief Bioinform"},{"key":"2026100211390068000_35.179.240286.146","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1208949110"},{"key":"2026100211390068000_35.179.240286.147","doi-asserted-by":"publisher","DOI":"10.1038\/nature13385"},{"key":"2026100211390068000_35.179.240286.148","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2003-4-9-117"},{"key":"2026100211390068000_35.179.240286.149","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.03.014"},{"key":"2026100211390068000_35.179.240286.150","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188746"},{"key":"2026100211390068000_35.179.240286.151","doi-asserted-by":"crossref","first-page":"1496392","DOI":"10.3389\/falgy.2024.1496392","article-title":"Unraveling heterogeneity and treatment of asthma through integrating multi-omics data","volume":"5","author":"Zhang","year":"2024","journal-title":"Front Allergy"},{"key":"2026100211390068000_35.179.240286.152","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-022-02293-2"},{"key":"2026100211390068000_35.179.240286.153","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00895-7"},{"key":"2026100211390068000_35.179.240286.154","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab403"},{"key":"2026100211390068000_35.179.240286.155","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/s41540-025-00489-y","article-title":"Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series","volume":"11","author":"Mei","year":"2025","journal-title":"NPJ Syst Biol Appl"},{"key":"2026100211390068000_35.179.240286.156","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20178124"},{"key":"2026100211390068000_35.179.240286.157","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02015-1"},{"key":"2026100211390068000_35.179.240286.158","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1932-8"},{"key":"2026100211390068000_35.179.240286.159","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2020.02.013"},{"key":"2026100211390068000_35.179.240286.160","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0284563"},{"key":"2026100211390068000_35.179.240286.161","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2018.06.001"},{"key":"2026100211390068000_35.179.240286.162","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2310"},{"key":"2026100211390068000_35.179.240286.163","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1681"},{"key":"2026100211390068000_35.179.240286.164","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-023-00599-5"},{"key":"2026100211390068000_35.179.240286.165","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05688-9"},{"key":"2026100211390068000_35.179.240286.166","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01938-4"},{"key":"2026100211390068000_35.179.240286.167","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1269-0"},{"key":"2026100211390068000_35.179.240286.168","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab594"},{"key":"2026100211390068000_35.179.240286.169","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa443"},{"key":"2026100211390068000_35.179.240286.170","doi-asserted-by":"publisher","DOI":"10.1038\/S41587-023-01767-Y"},{"key":"2026100211390068000_35.179.240286.171","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02116-x"},{"key":"2026100211390068000_35.179.240286.172","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s13073-024-01350-3","article-title":"Machine learning integrative approaches to advance computational immunology","volume":"16","author":"Curion","year":"2024","journal-title":"Genome Med"},{"key":"2026100211390068000_35.179.240286.173","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43629-w"},{"key":"2026100211390068000_35.179.240286.174","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbz166"},{"key":"2026100211390068000_35.179.240286.175","doi-asserted-by":"publisher","DOI":"10.1093\/BIB\/BBAC430"},{"key":"2026100211390068000_35.179.240286.176","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0355-5"},{"key":"2026100211390068000_35.179.240286.177","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-021-00370-8"},{"key":"2026100211390068000_35.179.240286.178","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01139-4"},{"key":"2026100211390068000_35.179.240286.179","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00830-w"},{"key":"2026100211390068000_35.179.240286.180","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02362-7"},{"key":"2026100211390068000_35.179.240286.181","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAB043"},{"key":"2026100211390068000_35.179.240286.182","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01273-7"},{"key":"2026100211390068000_35.179.240286.183","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1038\/s41592-024-02316-4","article-title":"Deciphering spatial domains from spatial multi-omics with SpatialGlue","volume":"21","author":"Long","year":"2024","journal-title":"Nat Methods"},{"key":"2026100211390068000_35.179.240286.184","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0631-4"},{"key":"2026100211390068000_35.179.240286.185","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2019.05.006"},{"key":"2026100211390068000_35.179.240286.186","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-024-02193-4"},{"key":"2026100211390068000_35.179.240286.187","doi-asserted-by":"crossref","unstructured":"Schaar AC , Tejada-Lapuerta A , Palla G , et al. Nicheformer: a foundation model for single-cell and spatial omics. bioRxiv 2024; preprint [10.1101\/2024.04.15.589472].","DOI":"10.2139\/ssrn.4803291"},{"key":"2026100211390068000_35.179.240286.188","doi-asserted-by":"publisher","DOI":"10.1111\/febs.15572"},{"key":"2026100211390068000_35.179.240286.189","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4636"},{"key":"2026100211390068000_35.179.240286.190","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2022111272"},{"key":"2026100211390068000_35.179.240286.191","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202112-2704PP"},{"key":"2026100211390068000_35.179.240286.192","doi-asserted-by":"publisher","DOI":"10.1148\/radiol.2015141579"},{"key":"2026100211390068000_35.179.240286.193","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/s12931-025-03250-5","article-title":"Multi-omics characterization of early chronic obstructive pulmonary disease","volume":"26","author":"Li","year":"2025","journal-title":"Respir Res"},{"key":"2026100211390068000_35.179.240286.194","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1038\/s41564-022-01196-8","article-title":"Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions","volume":"7","author":"Yan","year":"2022","journal-title":"Nat Microbiol"},{"key":"2026100211390068000_35.179.240286.195","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19701-0"},{"key":"2026100211390068000_35.179.240286.196","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2023-330521"},{"key":"2026100211390068000_35.179.240286.197","doi-asserted-by":"crossref","first-page":"2102603","DOI":"10.1183\/13993003.02603-2021","article-title":"A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes","volume":"59","author":"Abdel-Aziz","year":"2022","journal-title":"Eur Respir J"},{"key":"2026100211390068000_35.179.240286.198","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1016\/j.jaci.2024.07.012","article-title":"Multiomics analysis identified IL-4-induced IL1RL1high eosinophils characterized by prominent cysteinyl leukotriene metabolism","volume":"154","author":"Sunata","year":"2024","journal-title":"J Allergy Clin Immunol"},{"key":"2026100211390068000_35.179.240286.199","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/S2213-2600(17)30387-9","article-title":"Genetic variants associated with susceptibility to idiopathic pulmonary fibrosis in people of European ancestry: a genome-wide association study","volume":"5","author":"Allen","year":"2017","journal-title":"Lancet Respir Med"},{"key":"2026100211390068000_35.179.240286.200","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1186\/s12967-025-06368-8","article-title":"Genetic insights into idiopathic pulmonary fibrosis: a multi-omics approach to identify potential therapeutic targets","volume":"23","author":"Wen","year":"2025","journal-title":"J Transl Med"},{"key":"2026100211390068000_35.179.240286.201","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-024-05398-y"},{"key":"2026100211390068000_35.179.240286.202","doi-asserted-by":"crossref","first-page":"2188","DOI":"10.3390\/jcm10102188","article-title":"Targeting the complement cascade in the pathophysiology of COVID-19 disease","volume":"10","author":"Ng","year":"2021","journal-title":"J Clin Med"},{"key":"2026100211390068000_35.179.240286.203","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1080\/21505594.2022.2092941","article-title":"The role of multi-omics in the diagnosis of COVID-19 and the prediction of new therapeutic targets","volume":"13","author":"Ma","year":"2022","journal-title":"Virulence"},{"key":"2026100211390068000_35.179.240286.204","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.10.037"},{"key":"2026100211390068000_35.179.240286.205","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2020.104051"},{"key":"2026100211390068000_35.179.240286.206","doi-asserted-by":"crossref","first-page":"100636","DOI":"10.1016\/j.xgen.2024.100636","article-title":"Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic risk to childhood-onset asthma","volume":"4","author":"Djeddi","year":"2024","journal-title":"Cell Genom"},{"key":"2026100211390068000_35.179.240286.207","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1016\/j.jaci.2020.11.002","article-title":"Integrated-omics endotyping of infants with rhinovirus bronchiolitis and risk of childhood asthma","volume":"147","author":"Raita","year":"2021","journal-title":"J Allergy Clin Immunol"},{"key":"2026100211390068000_35.179.240286.208","doi-asserted-by":"crossref","first-page":"106329","DOI":"10.1016\/j.isci.2023.106329","article-title":"Multi-omics analysis reveals underlying host responses in pediatric respiratory syncytial virus pneumonia","volume":"26","author":"Huang","year":"2023","journal-title":"iScience"},{"key":"2026100211390068000_35.179.240286.209","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23859-6"},{"key":"2026100211390068000_35.179.240286.210","doi-asserted-by":"crossref","first-page":"e16194","DOI":"10.7717\/peerj.16194","article-title":"Multi-omics data integration reveals the complexity and diversity of host factors associated with influenza virus infection","volume":"11","author":"Zhu","year":"2023","journal-title":"PeerJ"},{"key":"2026100211390068000_35.179.240286.211","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34487-z"},{"key":"2026100211390068000_35.179.240286.212","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1038\/s41564-021-00964-2","article-title":"Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy","volume":"6","author":"Martin-Sancho","year":"2021","journal-title":"Nat Microbiol"},{"key":"2026100211390068000_35.179.240286.213","doi-asserted-by":"crossref","first-page":"e1011020","DOI":"10.1371\/journal.ppat.1011020","article-title":"A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness","volume":"18","author":"Platt","year":"2022","journal-title":"PLoS Pathog"},{"key":"2026100211390068000_35.179.240286.214","doi-asserted-by":"crossref","first-page":"1011254","DOI":"10.3389\/fcimb.2022.1011254","article-title":"Multi-omics association analysis reveals interactions between the oropharyngeal microbiome and the metabolome in pediatric patients with influenza A virus pneumonia","volume":"12","author":"Hu","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"2026100211390068000_35.179.240286.215","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.jaci.2022.04.032","article-title":"Airway and parenchymal transcriptomics in a novel model of asthma and COPD overlap","volume":"150","author":"Tu","year":"2022","journal-title":"J Allergy Clin Immunol"},{"key":"2026100211390068000_35.179.240286.216","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/resp.14480","article-title":"Omics technologies to study virus infection and chronic lung diseases","volume":"28","author":"Hansbro","year":"2023","journal-title":"Respirology"},{"key":"2026100211390068000_35.179.240286.217","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1164\/rccm.202210-1865OC","article-title":"Lower airway dysbiosis augments lung inflammatory injury in mild-to-moderate chronic obstructive pulmonary disease","volume":"208","author":"Sulaiman","year":"2023","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.218","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112525"},{"key":"2026100211390068000_35.179.240286.219","doi-asserted-by":"crossref","first-page":"7349","DOI":"10.1038\/s41467-023-42913-z","article-title":"TLR7 promotes smoke-induced experimental lung damage through the activity of mast cell tryptase","volume":"14","author":"Liu","year":"2023","journal-title":"Nat Commun"},{"key":"2026100211390068000_35.179.240286.220","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01431-2021"},{"key":"2026100211390068000_35.179.240286.221","doi-asserted-by":"crossref","first-page":"e70018","DOI":"10.1002\/mco2.70018","article-title":"Influence of gut and lung dysbiosis on lung cancer progression and their modulation as promising therapeutic targets: a comprehensive review","volume":"5","author":"Thapa","year":"2024","journal-title":"MedComm"},{"key":"2026100211390068000_35.179.240286.222","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.3390\/pharmaceutics13122008","article-title":"Recent advances in chronotherapy targeting respiratory diseases","volume":"13","author":"Paudel","year":"2021","journal-title":"Pharmaceutics"},{"key":"2026100211390068000_35.179.240286.223","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1164\/rccm.201912-2420LE","article-title":"Lung DNA methylation in chronic obstructive pulmonary disease: relationship with smoking status and airflow limitation severity","volume":"203","author":"Casas-Recasens","year":"2021","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.224","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28809-4"},{"key":"2026100211390068000_35.179.240286.225","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00658-2020"},{"key":"2026100211390068000_35.179.240286.226","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/S2213-2600(18)30510-1","article-title":"Functional effects of the microbiota in chronic respiratory disease","volume":"7","author":"Budden","year":"2019","journal-title":"Lancet Respir Med"},{"key":"2026100211390068000_35.179.240286.227","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2016.142"},{"key":"2026100211390068000_35.179.240286.228","doi-asserted-by":"crossref","first-page":"e133","DOI":"10.1038\/cti.2017.6","article-title":"Microbiome effects on immunity, health and disease in the lung","volume":"6","author":"Shukla","year":"2017","journal-title":"Clin Transl Immunology"},{"key":"2026100211390068000_35.179.240286.229","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1002\/JLB.3MR0720-472RR","article-title":"The role of the microbiome and the NLRP3 inflammasome in the gut and lung","volume":"108","author":"Donovan","year":"2020","journal-title":"J Leukoc Biol"},{"key":"2026100211390068000_35.179.240286.230","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1164\/rccm.202110-2241OC","article-title":"Lung microbiota and metabolites collectively associate with clinical outcomes in milder stage chronic obstructive pulmonary disease","volume":"206","author":"Madapoosi","year":"2022","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.231","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12931-023-02349-x","article-title":"Proteomics and metabolomics profiling reveal panels of circulating diagnostic biomarkers and molecular subtypes in stable COPD","volume":"24","author":"Zhang","year":"2023","journal-title":"Respir Res"},{"key":"2026100211390068000_35.179.240286.232","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/j.chom.2023.04.018","article-title":"Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease","volume":"31","author":"Liang","year":"2023","journal-title":"Cell Host Microbe"},{"key":"2026100211390068000_35.179.240286.233","doi-asserted-by":"publisher","DOI":"10.1111\/all.14548"},{"key":"2026100211390068000_35.179.240286.234","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1164\/rccm.202301-0067OC","article-title":"Blood-based transcriptomic and proteomic biomarkers of emphysema","volume":"209","author":"Suryadevara","year":"2024","journal-title":"Am J Respir Crit Care Med"},{"key":"2026100211390068000_35.179.240286.235","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202303-0507LE"},{"key":"2026100211390068000_35.179.240286.236","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202301-0085OC"},{"key":"2026100211390068000_35.179.240286.237","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00060014"},{"key":"2026100211390068000_35.179.240286.238","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.pulmoe.2022.09.002","article-title":"Preclinical interstitial lung disease in relatives of familial pulmonary fibrosis patients","volume":"29","author":"Lucas","year":"2023","journal-title":"Pulmonology"},{"key":"2026100211390068000_35.179.240286.239","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aba1972"},{"key":"2026100211390068000_35.179.240286.240","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-020-0542-8"},{"key":"2026100211390068000_35.179.240286.241","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2020.06.020"},{"key":"2026100211390068000_35.179.240286.242","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44467-6"},{"key":"2026100211390068000_35.179.240286.243","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00451.2020"},{"key":"2026100211390068000_35.179.240286.244","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1165\/rcmb.2020-0546OC","article-title":"Molecular signatures of idiopathic pulmonary fibrosis","volume":"65","author":"Konigsberg","year":"2021","journal-title":"Am J Respir Cell Mol Biol"},{"key":"2026100211390068000_35.179.240286.245","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1007\/s00018-021-04094-0","article-title":"Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis","volume":"79","author":"Zheng","year":"2022","journal-title":"Cell Mol Life Sci"},{"key":"2026100211390068000_35.179.240286.246","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/s12931-023-02435-0","article-title":"Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression","volume":"24","author":"Ruan","year":"2023","journal-title":"Respir Res"},{"key":"2026100211390068000_35.179.240286.247","doi-asserted-by":"publisher","DOI":"10.15252\/emmm.202012871"},{"key":"2026100211390068000_35.179.240286.248","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1093\/qjmed\/hcad206","article-title":"Integrative analysis reveals the recurrent genetic etiologies in idiopathic pulmonary fibrosis","volume":"116","author":"Guo","year":"2023","journal-title":"QJM"},{"key":"2026100211390068000_35.179.240286.249","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/s41587-024-02143-0","article-title":"A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models","volume":"43","author":"Ren","year":"2025","journal-title":"Nat Biotechnol"},{"key":"2026100211390068000_35.179.240286.250","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1016\/j.ijbiomac.2021.10.144","article-title":"COVID-19: a review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks","volume":"193","author":"Murugan","year":"2021","journal-title":"Int J Biol Macromol"},{"key":"2026100211390068000_35.179.240286.251","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1038\/s41598-023-28816-5","article-title":"Integrated multiomics analysis to infer COVID-19 biological insights","volume":"13","author":"Sameh","year":"2023","journal-title":"Sci Rep"},{"key":"2026100211390068000_35.179.240286.252","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1038\/s41564-021-00961-5","article-title":"Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome","volume":"6","author":"Sulaiman","year":"2021","journal-title":"Nat Microbiol"},{"key":"2026100211390068000_35.179.240286.253","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3390\/ijms18010020","article-title":"Reverse genetics approaches for the development of influenza vaccines","volume":"18","author":"Nogales","year":"2016","journal-title":"Int J Mol Sci"},{"key":"2026100211390068000_35.179.240286.254","doi-asserted-by":"crossref","first-page":"e632","DOI":"10.1016\/S2589-7500(22)00112-1","article-title":"Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study","volume":"4","author":"Byeon","year":"2022","journal-title":"Lancet Digit Health"},{"key":"2026100211390068000_35.179.240286.255","doi-asserted-by":"crossref","first-page":"1273662","DOI":"10.3389\/fmed.2023.1273662","article-title":"Editorial: Omics in respiratory virus infectious diseases: integrating multi-omics to reveal data characteristics and mechanisms for the diagnosis and treatment of disease","volume":"10","author":"Wang","year":"2023","journal-title":"Front Med"},{"key":"2026100211390068000_35.179.240286.256","doi-asserted-by":"publisher","DOI":"10.15761\/PCCM.1000139"},{"key":"2026100211390068000_35.179.240286.257","doi-asserted-by":"publisher","DOI":"10.1007\/s11882-016-0661-2"},{"key":"2026100211390068000_35.179.240286.258","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00919-w"},{"key":"2026100211390068000_35.179.240286.259","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/s13167-024-00395-z","article-title":"Multiomics as instrument to promote 3P medical approaches for the overall management of respiratory syncytial viral infections","volume":"16","author":"Bajinka","year":"2025","journal-title":"EPMA J"},{"key":"2026100211390068000_35.179.240286.260","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMp1714916"},{"key":"2026100211390068000_35.179.240286.261","doi-asserted-by":"crossref","first-page":"S120","DOI":"10.1016\/j.cmi.2015.12.005","article-title":"Universal influenza vaccines: a realistic option?","volume":"22","author":"de Vries","year":"2016","journal-title":"Clin Microbiol Infect"},{"key":"2026100211390068000_35.179.240286.262","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s41232-021-00173-8","article-title":"Multi-omics approach to precision medicine for immune-mediated diseases","volume":"41","author":"Ota","year":"2021","journal-title":"Inflamm Regen"},{"key":"2026100211390068000_35.179.240286.263","doi-asserted-by":"crossref","first-page":"7347","DOI":"10.3390\/ijms25137347","article-title":"Exploring molecular mechanisms and biomarkers in COPD: an overview of current advancements and perspectives","volume":"25","author":"Li","year":"2024","journal-title":"Int J Mol Sci"},{"key":"2026100211390068000_35.179.240286.264","doi-asserted-by":"publisher","DOI":"10.3389\/fnagi.2022.1065904"},{"key":"2026100211390068000_35.179.240286.265","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab061"},{"key":"2026100211390068000_35.179.240286.266","doi-asserted-by":"crossref","first-page":"kyad009","DOI":"10.1093\/discim\/kyad009","article-title":"Comparative phenotype of circulating versus tissue immune cells in human lung and blood compartments during health and disease","volume":"2","author":"Colombo","year":"2023","journal-title":"Discov Immunol"},{"key":"2026100211390068000_35.179.240286.267","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aav7223"},{"key":"2026100211390068000_35.179.240286.268","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00183214"},{"key":"2026100211390068000_35.179.240286.269","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2882-8"},{"key":"2026100211390068000_35.179.240286.270","doi-asserted-by":"crossref","first-page":"eabj9949","DOI":"10.1126\/sciadv.abj9949","article-title":"A transcriptomics-guided drug target discovery strategy identifies receptor ligands for lung regeneration","volume":"8","author":"Wu","year":"2022","journal-title":"Sci Adv"},{"key":"2026100211390068000_35.179.240286.271","doi-asserted-by":"crossref","first-page":"4026","DOI":"10.1111\/bph.15581","article-title":"A drug screen with approved compounds identifies amlexanox as a novel Wnt\/\u03b2-catenin activator inducing lung epithelial organoid formation","volume":"178","author":"Costa","year":"2021","journal-title":"Br J Pharmacol"},{"key":"2026100211390068000_35.179.240286.272","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00084.2017"},{"key":"2026100211390068000_35.179.240286.273","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-018-0876-y"},{"key":"2026100211390068000_35.179.240286.274","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adh0908"},{"key":"2026100211390068000_35.179.240286.275","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1215-1"},{"key":"2026100211390068000_35.179.240286.276","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1935-5"},{"key":"2026100211390068000_35.179.240286.277","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/elac017"},{"key":"2026100211390068000_35.179.240286.278","doi-asserted-by":"crossref","first-page":"719978","DOI":"10.3389\/fmolb.2021.719978","article-title":"Editorial: AI and multi-omics for rare diseases: challenges, advances and perspectives","volume":"8","author":"Bottini","year":"2021","journal-title":"Front Mol Biosci"},{"key":"2026100211390068000_35.179.240286.279","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2015.12.013"},{"key":"2026100211390068000_35.179.240286.280","doi-asserted-by":"crossref","first-page":"lsaa010","DOI":"10.1093\/jlb\/lsaa010","article-title":"Data protection and ethics requirements for multisite research with health data: a comparative examination of legislative governance frameworks and the role of data protection technologies","volume":"7","author":"Scheibner","year":"2020","journal-title":"J Law Biosci"},{"key":"2026100211390068000_35.179.240286.281","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03583-3"},{"key":"2026100211390068000_35.179.240286.282","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1093\/femsmc\/xtae010","article-title":"The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma","volume":"5","author":"Wilson","year":"2024","journal-title":"FEMS Microbes"}],"container-title":["European Respiratory Review"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1183\/16000617.0286-2024","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T18:41:25Z","timestamp":1790966485000},"score":1,"resource":{"primary":{"URL":"https:\/\/publications.ersnet.org\/lookup\/doi\/10.1183\/16000617.0286-2024"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":282,"journal-issue":{"issue":"179","published-online":{"date-parts":[[2026,1,14]]},"published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1183\/16000617.0286-2024"],"URL":"https:\/\/doi.org\/10.1183\/16000617.0286-2024","relation":{},"ISSN":["0905-9180","1600-0617"],"issn-type":[{"value":"0905-9180","type":"print"},{"value":"1600-0617","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]}}}