{"entity": "researcher", "timestamp": "2026-06-07T20:52:37.587Z", "family": "L\u00f6tstedt", "given": "B", "initials": "B", "orcid": "0000-0003-3545-5489", "affiliations": ["Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.", "Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.", "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b"}}, "publications": [{"entity": "publication", "iuid": "ae2005392bb1435d82f88df1dfd6bbe4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2005392bb1435d82f88df1dfd6bbe4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2005392bb1435d82f88df1dfd6bbe4"}}, "title": "Tissue and cellular spatiotemporal dynamics in colon aging", "authors": [{"family": "Daly", "given": "Aidan C", "initials": "AC"}, {"family": "Cambuli", "given": "Francesco", "initials": "F"}, {"family": "\u00c4ij\u00f6", "given": "Tarmo", "initials": "T", "orcid": "0000-0002-3008-4634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1b52cf5dea442c6bbee87f3507cadb4.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B", "orcid": "0000-0003-3545-5489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}}, {"family": "Marjanovic", "given": "Nemanja Despot", "initials": "ND"}, {"family": "Fernandez", "given": "Sara", "initials": "S", "orcid": "0000-0003-2281-4526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f642f817ac8342f7a8987c27fa061f6a.json"}}, {"family": "Kuksenko", "given": "Olena", "initials": "O"}, {"family": "Smith-Erb", "given": "Matthew", "initials": "M"}, {"family": "Domovic", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4576-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f1072e5f9e44a23b79151629a1c7312.json"}}, {"family": "Van Wittenberghe", "given": "Nicholas", "initials": "N"}, {"family": "Drokhlyansky", "given": "Eugene", "initials": "E"}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Phatnani", "given": "Hemali", "initials": "H", "orcid": "0000-0002-6571-3891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4495ea85d87a45878b4e14c5e23bd361.json"}}, {"family": "Bonneau", "given": "Richard", "initials": "R", "orcid": "0000-0003-4354-7906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7a43f8ee4a542cea7ecb8dcb23d170b.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}], "type": "journal-article", "published": "2025-10-22", "journal": {"title": "Nat Biotechnol", "issn": "1087-0156", "issn-l": "1087-0156"}, "abstract": "Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects but many of the underlying molecular cues remain unclear. Here, we build a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-sequencing profiles. We develop a computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region and sex by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identify cellular and molecular gradients along the adult colonic tract and across the main crypt axis and multicellular programs associated with aging in the large intestine. Our multimodal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.", "doi": "10.1038/s41587-025-02830-6", "pmid": "41125832", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-025-02830-6"}], "notes": [], "created": "2025-10-30T14:08:07.365Z", "modified": "2026-06-03T09:43:48.406Z"}, {"entity": "publication", "iuid": "ab667d31fb0e4bbeb87d2e9af420d3ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab"}}, "title": "SM-Omics is an automated platform for high-throughput spatial multi-omics.", "authors": [{"family": "Vickovic", "given": "S", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "L\u00f6tstedt", "given": "B", "initials": "B", "orcid": "0000-0003-3545-5489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}}, {"family": "Klughammer", "given": "J", "initials": "J", "orcid": "0000-0002-3628-9278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987.json"}}, {"family": "Mages", "given": "S", "initials": "S"}, {"family": "Segerstolpe", "given": "\u00c5", "initials": "\u00c5"}, {"family": "Rozenblatt-Rosen", "given": "O", "initials": "O", "orcid": "0000-0001-6313-3570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d219a623b5d4e46af7841b1f32036c3.json"}}, {"family": "Regev", "given": "A", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}], "type": "journal article", "published": "2022-02-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "795", "issn-l": "2041-1723"}, "abstract": "The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.", "doi": "10.1038/s41467-022-28445-y", "pmid": "35145087", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8831571"}, {"db": "pii", "key": "10.1038/s41467-022-28445-y"}], "notes": [], "created": "2023-12-03T15:46:04.963Z", "modified": "2023-12-03T15:46:05.108Z"}]}