{"entity": "researcher", "timestamp": "2026-09-23T15:25:44.185Z", "family": "Gote-Schniering", "given": "Janine", "initials": "J", "orcid": "0000-0001-7869-4936", "affiliations": ["Department of Rheumatology and Immunology and Department of Pulmonary Medicine, Allergology and Clinical Immunology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.", "Lung Precision Medicine (LPM), Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9633364034714be8bb01be7d3e587664.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9633364034714be8bb01be7d3e587664"}}, "publications": [{"entity": "publication", "iuid": "66774d6a31d24a0a84619dc0b4f93ab3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66774d6a31d24a0a84619dc0b4f93ab3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66774d6a31d24a0a84619dc0b4f93ab3"}}, "title": "Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.", "authors": [{"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68b3baa22ffe41c0aa352075c6ea70b9.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mahbubani", "given": "Krishnaa T", "initials": "KT", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de56aac2975a4292b9e6d1eeb8b74d02.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3ffb6926be74c11928edb174a245718.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Alonso Galicia", "given": "Leire", "initials": "L"}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Balassa", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Kovacs", "given": "Ferenc", "initials": "F", "orcid": "0000-0003-4512-4448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15d35f638dcc4014afbc2a3ef5e22418.json"}}, {"family": "Horvath", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Yuexin", "initials": "Y"}, {"family": "Gote-Schniering", "given": "Janine", "initials": "J", "orcid": "0000-0001-7869-4936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9633364034714be8bb01be7d3e587664.json"}}, {"family": "Stoleriu", "given": "Mircea-Gabriel", "initials": "MG"}, {"family": "Behr", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Meyer", "given": "Kerstin B", "initials": "KB", "orcid": "0000-0001-5906-1498", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f03ec52d8b2f404ba869e0524f33b3d2.json"}}, {"family": "Timens", "given": "Wim", "initials": "W", "orcid": "0000-0002-4146-6363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c55e709b313044e8809ca651b283e93b.json"}}, {"family": "Schiller", "given": "Herbert B", "initials": "HB"}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/573854d96a9e4e21a3b96135c11c6efc.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC", "orcid": "0000-0003-3372-6521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7551a303e7294578aa0c99966ffec1a2.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9745", "issn-l": "2041-1723"}, "abstract": "Integration of scRNA-seq data from millions of cells revealed a high diversity of cell types in the healthy and diseased human lung. In a large and complex organ, constantly exposed to external agents, it is crucial to understand the influence of lung tissue topography or external factors on gene expression variability within cell types. Here, we apply three spatial transcriptomics approaches, to: (i) localize the majority of lung cell types, including rare epithelial cells within the tissue topography, (ii) describe consistent anatomical and regional gene expression variability within and across cell types, and (iii) reveal distinct cellular neighborhoods in specific anatomical regions and examine gene expression variations in them. We thus provide a spatially resolved tissue reference atlas in three representative regions of the healthy human lung. We further demonstrate its utility by defining previously unknown imbalances of epithelial cell type compositions in chronic obstructive pulmonary disease lungs. Our topographic atlas enables a precise description of characteristic regional cellular responses upon experimental perturbations or during disease progression.", "doi": "10.1038/s41467-025-65704-0", "pmid": "41193468", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12589588"}, {"db": "pii", "key": "10.1038/s41467-025-65704-0"}], "notes": [], "created": "2026-09-23T09:11:50.400Z", "modified": "2026-09-23T09:11:50.613Z"}, {"entity": "publication", "iuid": "1e656547b1714f97affea326cd463d44", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1e656547b1714f97affea326cd463d44.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1e656547b1714f97affea326cd463d44"}}, "title": "The discovAIR project: a roadmap towards the Human Lung Cell Atlas.", "authors": [{"family": "Luecken", "given": "Malte D", "initials": "MD"}, {"family": "Zaragosi", "given": "Laure-Emmanuelle", "initials": "LE", "orcid": "0000-0001-6747-7928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5973b289a0a84dddb87b3457ef554ace.json"}}, {"family": "Madissoon", "given": "Elo", "initials": "E"}, {"family": "Sikkema", "given": "Lisa", "initials": "L", "orcid": "0000-0001-9686-6295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/462d0024767146ebba699345e9deeb9e.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB"}, {"family": "De Domenico", "given": "Elena", "initials": "E"}, {"family": "K\u00fcmmerle", "given": "Louis", "initials": "L"}, {"family": "Saglam", "given": "Adem", "initials": "A"}, {"family": "Berg", "given": "Marijn", "initials": "M"}, {"family": "Gay", "given": "Aurore C A", "initials": "ACA"}, {"family": "Schniering", "given": "Janine", "initials": "J", "orcid": "0000-0001-7869-4936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9633364034714be8bb01be7d3e587664.json"}}, {"family": "Mayr", "given": "Christoph H", "initials": "CH"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A"}, {"family": "Teichmann", "given": "Sarah A", "initials": "SA"}, {"family": "van Eunen", "given": "Karen", "initials": "K"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e9a287e31a64ec1a4a3cfc3dab53c6c.json"}}, {"family": "Saeb-Parsy", "given": "Kourosh", "initials": "K"}, {"family": "Leroy", "given": "Sylvie", "initials": "S"}, {"family": "Powell", "given": "Pippa", "initials": "P"}, {"family": "Sarkans", "given": "Ugis", "initials": "U"}, {"family": "Timens", "given": "Wim", "initials": "W", "orcid": "0000-0002-4146-6363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c55e709b313044e8809ca651b283e93b.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "van den Berge", "given": "Maarten", "initials": "M"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Horv\u00e1th", "given": "Peter", "initials": "P"}, {"family": "Denning", "given": "Jessica", "initials": "J"}, {"family": "Papatheodorou", "given": "Irene", "initials": "I"}, {"family": "Schultze", "given": "Joachim L", "initials": "JL"}, {"family": "Schiller", "given": "Herbert B", "initials": "HB"}, {"family": "Barbry", "given": "Pascal", "initials": "P", "orcid": "0000-0001-9632-6483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b90888809ec4532b824408fff59aab9.json"}}, {"family": "Petoukhov", "given": "Ilya", "initials": "I"}, {"family": "Misharin", "given": "Alexander V", "initials": "AV"}, {"family": "Adcock", "given": "Ian M", "initials": "IM", "orcid": "0000-0003-2101-8843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b61bb5380bf419c8e5ce461e36b7f7c.json"}}, {"family": "von Papen", "given": "Michael", "initials": "M"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ"}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Meyer", "given": "Kerstin B", "initials": "KB"}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC", "orcid": "0000-0003-3372-6521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7551a303e7294578aa0c99966ffec1a2.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Eur. Respir. J.", "issn": "1399-3003", "volume": "60", "issue": "2", "issn-l": "0903-1936"}, "abstract": "The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell-cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.", "doi": "10.1183/13993003.02057-2021", "pmid": "35086829", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9386332"}, {"db": "pii", "key": "13993003.02057-2021"}], "notes": [], "created": "2026-09-23T10:12:25.272Z", "modified": "2026-09-23T10:50:46.742Z"}]}