{"entity": "researcher", "timestamp": "2026-06-15T17:21:14.042Z", "family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396"}}, "publications": [{"entity": "publication", "iuid": "1fd41f8b0eca4b1287a6862547fe91fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fd41f8b0eca4b1287a6862547fe91fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fd41f8b0eca4b1287a6862547fe91fd"}}, "title": "The spatial landscape of gene expression isoforms in tissue sections.", "authors": [{"family": "Lebrigand", "given": "Kevin", "initials": "K", "orcid": "0000-0001-5604-7893", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb4fc2f3bb0848e2afe92c96c326617f.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}, {"family": "Barbry", "given": "Pascal", "initials": "P", "orcid": "0000-0001-9632-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7a905ca05b34448a12858cea60ba1c6.json"}}, {"family": "Waldmann", "given": "Rainer", "initials": "R", "orcid": "0000-0002-4599-2926", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3ba1e7c02664cb49caee4007cfc7e61.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "51", "issue": "8", "pages": "e47"}, "abstract": "In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.", "doi": "10.1093/nar/gkad169", "pmid": "36928528", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Spatial omics": null}, "xrefs": [{"db": "pmc", "key": "PMC10164556"}, {"db": "pii", "key": "7079641"}], "notes": [], "created": "2023-10-04T12:11:14.358Z", "modified": "2023-10-19T10:03:46.014Z"}, {"entity": "publication", "iuid": "6b272f66ea784595a9d1db9edde67b67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b272f66ea784595a9d1db9edde67b67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b272f66ea784595a9d1db9edde67b67"}}, "title": "Spatially resolved clonal copy number alterations in benign and malignant tissue.", "authors": [{"family": "Erickson", "given": "Andrew", "initials": "A"}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a238f7adbc242398a46fd24190a2811.json"}}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Kvastad", "given": "Linda", "initials": "L"}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Alonso Galicia", "given": "Leire", "initials": "L", "orcid": "0000-0001-8437-1332", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a941bba10fa44d4a5ac841ed50f060f.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Rajakumar", "given": "Timothy", "initials": "T"}, {"family": "Doultsinos", "given": "Dimitrios", "initials": "D", "orcid": "0000-0003-0873-9873", "researcher": {"href": "https://publications.scilifelab.se/researcher/91375a3b6b634771ada73458e9f2f2b1.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Ji", "given": "Andrew L", "initials": "AL", "orcid": "0000-0001-9688-5680", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba3c3c39f53a471cbd699bf4a8d64b23.json"}}, {"family": "Khavari", "given": "Paul A", "initials": "PA", "orcid": "0000-0003-0098-4989", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2aea38b6ba9430cbcfdc23b3190a2ec.json"}}, {"family": "Tarish", "given": "Firaz", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Maaskola", "given": "Jonas", "initials": "J", "orcid": "0000-0002-6665-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/a615b8e0928f45b083b4d4c8692af424.json"}}, {"family": "Colling", "given": "Richard", "initials": "R", "orcid": "0000-0001-6344-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/e817042b24944db1b2fcf74aee34f4e3.json"}}, {"family": "Mirtti", "given": "Tuomas", "initials": "T"}, {"family": "Hamdy", "given": "Freddie C", "initials": "FC"}, {"family": "Woodcock", "given": "Dan J", "initials": "DJ", "orcid": "0000-0003-0576-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e7fdc16acf4d3c98337e934a1f3433.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Mills", "given": "Ian G", "initials": "IG", "orcid": "0000-0001-5347-5083", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f24c9f52d047e4bf5c697768bd568e.json"}}, {"family": "Lamb", "given": "Alastair D", "initials": "AD"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "608", "issue": "7922", "pages": "360-367"}, "abstract": "Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.", "doi": "10.1038/s41586-022-05023-2", "pmid": "35948708", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Spatial omics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9365699"}, {"db": "pii", "key": "10.1038/s41586-022-05023-2"}], "notes": [], "created": "2022-08-19T08:38:11.036Z", "modified": "2023-10-16T11:27:00.695Z"}, {"entity": "publication", "iuid": "601f2cafa2194c0b9554d477b9dacdb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/601f2cafa2194c0b9554d477b9dacdb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/601f2cafa2194c0b9554d477b9dacdb2"}}, "title": "Developmental origins of cell heterogeneity in the human lung", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M", "orcid": "0000-0002-3042-6278", "researcher": {"href": "https://publications.scilifelab.se/researcher/6348d0901b3e44cd80bde25cecd0205b.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/af0596d61a794c188112ba7b256efac6.json"}}, {"family": "Abalo", "given": "Xesus", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d", "orcid": "0000-0002-4350-2524", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89be535ddfa4c6ab46201fb383f4a2b.json"}}, {"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X"}, {"family": "Hu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-1869-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/49a35358ad6e4b5eaec60d97504102ae.json"}}, {"family": "Sariyar", "given": "Sanem", "initials": "S"}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM", "orcid": "0000-0003-2722-1965", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa27c4c76374453ba3ffe7eafff4b9a.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-8277-8999", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac0b87b8e4548158ac5ea20a08f7a28.json"}}, {"family": "Firsova", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-6948-7281", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b05fc1689e4d6c9ec0ecd513905a36.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "posted-content", "published": "2022-01-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.01.11.475631", "pmid": null, "labels": {"In Situ Sequencing": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-28T09:49:49.063Z", "modified": "2025-12-18T20:03:09.998Z"}]}