{"entity": "researcher", "timestamp": "2026-08-20T20:43:09.451Z", "family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1"}}, "publications": [{"entity": "publication", "iuid": "ac0652984bb2418391760e337cc32f0b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac0652984bb2418391760e337cc32f0b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac0652984bb2418391760e337cc32f0b"}}, "title": "Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction.", "authors": [{"family": "Dahlberg", "given": "Simon K", "initials": "SK", "orcid": "0009-0004-1327-5721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6292b48f802f4fd3a81e84628af9cf43.json"}}, {"family": "Bonet", "given": "David Fern\u00e1ndez", "initials": "DF", "orcid": "0000-0001-5402-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}, {"family": "Hoffecker", "given": "Ian T", "initials": "IT", "orcid": "0000-0001-6941-4576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1a249b0d0d34c6e827dc2b15eb33a9f.json"}}], "type": "journal article", "published": "2025-10-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9652", "issn-l": "2041-1723"}, "abstract": "Spatial transcriptomics technologies aim to spatially map gene expression in tissues and typically use oligonucleotide array surfaces that have undergone spatial indexing. These arrays are used to capture nucleic acids diffusing from adjacently placed tissues, allowing subsequent sequencing to reveal both gene and position. Slide-tags is a recently developed method by Russell et al. that inverts this principle. Instead of capturing molecules released from the tissue, probes are detached from a pre-decoded bead array and diffused into tissues, tagging nuclei with spatial barcodes. In this work we reanalyze this data and discover a latent, spatially informative cell-bead network formed incidentally from barcode diffusion and the biophysical properties of the tissue. This allows us to treat Slide-tags as a network-based imaging-by-sequencing approach. By optimizing spatial constraints encoded in the cell-bead network structure, we can achieve unassisted tissue reconstruction, a fundamental shift from classical spatial technologies based on pre-indexed arrays.", "doi": "10.1038/s41467-025-65295-w", "pmid": "41173855", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12579210"}, {"db": "pii", "key": "10.1038/s41467-025-65295-w"}], "notes": [], "created": "2026-08-20T08:54:08.092Z", "modified": "2026-08-20T08:54:08.319Z"}, {"entity": "publication", "iuid": "21ac2787e8714170a235347a214b134a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/21ac2787e8714170a235347a214b134a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/21ac2787e8714170a235347a214b134a"}}, "title": "Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies", "authors": [{"family": "Williams", "given": "Eleanor C", "initials": "EC", "orcid": "0000-0002-8023-9550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dca992134b6f45e9b6e547394eff3be0.json"}}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "Lindvall", "given": "Martina Olsson", "initials": "MO"}, {"family": "Hamm", "given": "Gregory", "initials": "G"}, {"family": "Oag", "given": "Steven", "initials": "S"}, {"family": "Majumder", "given": "Muntasir Mamun", "initials": "MM"}, {"family": "Denholm", "given": "James", "initials": "J"}, {"family": "Hamidinekoo", "given": "Azam", "initials": "A"}, {"family": "Morlanes", "given": "Javier Escudero", "initials": "JE"}, {"family": "Vicari", "given": "Marco", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Setyo", "given": "Laura", "initials": "L"}, {"family": "Zakirov", "given": "Aleksandr", "initials": "A"}, {"family": "Hornberg", "given": "Jorrit J", "initials": "JJ"}, {"family": "Stamou", "given": "Marianna", "initials": "M"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Ollerstam", "given": "Anna", "initials": "A"}, {"family": "Tan", "given": "Jennifer", "initials": "J"}, {"family": "Mohorianu", "given": "Irina", "initials": "I"}], "type": "posted-content", "published": "2025-03-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.26.640381", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:01:12.056Z", "modified": "2026-08-20T11:01:12.126Z"}, {"entity": "publication", "iuid": "36ba338548a9481180f086c6f3e98627", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36ba338548a9481180f086c6f3e98627.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36ba338548a9481180f086c6f3e98627"}}, "title": "Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis.", "authors": [{"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "Olsson Lindvall", "given": "Martina", "initials": "M"}, {"family": "H\u00fchn", "given": "Michael", "initials": "M"}, {"family": "Ptasinski", "given": "Victoria", "initials": "V", "orcid": "0000-0002-2186-6634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ae48d0488b14f49b65dc864136e5c7b.json"}}, {"family": "Setyo", "given": "Laura", "initials": "L"}, {"family": "Keith", "given": "Benjamin P", "initials": "BP"}, {"family": "Collin", "given": "Astrid", "initials": "A"}, {"family": "Oag", "given": "Steven", "initials": "S"}, {"family": "Volckaert", "given": "Thomas", "initials": "T"}, {"family": "Borde", "given": "Annika", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92fe93e1a4d74881b321eb1d5862ad13.json"}}, {"family": "Belfield", "given": "Graham", "initials": "G"}, {"family": "Jackson", "given": "Sonya", "initials": "S"}, {"family": "Ollerstam", "given": "Anna", "initials": "A"}, {"family": "Stamou", "given": "Marianna", "initials": "M", "orcid": "0000-0003-0496-3229", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d449336f5cb4528abc778ef17390961.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}, {"family": "Hornberg", "given": "Jorrit J", "initials": "JJ"}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "56", "issue": "8", "pages": "1725-1736", "issn-l": "1061-4036"}, "abstract": "Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. Here we generated spatially resolved transcriptome maps of human IPF (n = 4) and bleomycin-induced mouse pulmonary fibrosis (n = 6) to address these limitations. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by transforming growth factor beta signaling alongside predicted regulators, such as TP53 and APOE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.", "doi": "10.1038/s41588-024-01819-2", "pmid": "38951642", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11319205"}, {"db": "pii", "key": "10.1038/s41588-024-01819-2"}], "notes": [], "created": "2026-08-20T09:00:11.224Z", "modified": "2026-08-20T09:00:11.414Z"}, {"entity": "publication", "iuid": "f1be6983d54e47c39eb7c5e6d67c564d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1be6983d54e47c39eb7c5e6d67c564d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1be6983d54e47c39eb7c5e6d67c564d"}}, "title": "Spatial transcriptomics Visium data for mouse bleomycin model of lung fibrosis", "authors": [{"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "Lindvall", "given": "Martina Olsson", "initials": "MO", "orcid": "0000-0002-8609-5607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffa26721bc4b424d8544aa3f0570c3d4.json"}}, {"family": "H\u00fchn", "given": "Michael", "initials": "M"}, {"family": "Ptasinski", "given": "Victoria", "initials": "V"}, {"family": "Setyo", "given": "Laura", "initials": "L"}, {"family": "Keith", "given": "Benjamin", "initials": "B"}, {"family": "Collin", "given": "Astrid", "initials": "A"}, {"family": "Oag", "given": "Steven", "initials": "S"}, {"family": "Volckaert", "given": "Thomas", "initials": "T"}, {"family": "Borde", "given": "Annika", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Lindgren", "given": "Julia", "initials": "J"}, {"family": "Belfield", "given": "Graham", "initials": "G"}, {"family": "Jackson", "given": "Sonya", "initials": "S"}, {"family": "Ollerstam", "given": "Anna", "initials": "A"}, {"family": "Stamou", "given": "Marianna", "initials": "M"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}, {"family": "Hornberg", "given": "Jorrit J", "initials": "JJ"}], "type": "dataset", "published": "2024-05-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.6019/s-bsst1409", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:48:00.199Z", "modified": "2026-08-20T13:48:00.262Z"}, {"entity": "publication", "iuid": "c3e177c65cc745ac9759e39cfda5681b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c3e177c65cc745ac9759e39cfda5681b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c3e177c65cc745ac9759e39cfda5681b"}}, "title": "Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.", "authors": [{"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2023-10-03", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "39", "issue": "10", "issn-l": "1367-4803"}, "abstract": "Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation.\n\nThe R package semla is available on GitHub (https://github.com/ludvigla/semla), under the MIT License, and deposited on Zenodo (https://doi.org/10.5281/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https://ludvigla.github.io/semla/.", "doi": "10.1093/bioinformatics/btad626", "pmid": "37846051", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10597621"}, {"db": "pii", "key": "7319366"}], "notes": [], "created": "2026-08-20T09:39:40.270Z", "modified": "2026-08-20T09:39:40.352Z"}]}