{"entity": "researcher", "timestamp": "2026-08-20T20:45:33.232Z", "family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "affiliations": ["SciLifeLab and Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479"}}, "publications": [{"entity": "publication", "iuid": "e7049b1e01f1419e9f26134ae55daedd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e7049b1e01f1419e9f26134ae55daedd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e7049b1e01f1419e9f26134ae55daedd"}}, "title": "Probe set selection for targeted spatial transcriptomics.", "authors": [{"family": "Kuemmerle", "given": "Louis B", "initials": "LB", "orcid": "0000-0002-9193-1243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31e2ab0bc76a4fb1bf1cf184b487c222.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/573854d96a9e4e21a3b96135c11c6efc.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB"}, {"family": "Barros de Andrade E Sousa", "given": "Lisa", "initials": "L"}, {"family": "Stra\u00dfer", "given": "Lena", "initials": "L"}, {"family": "Mekki", "given": "Ilhem Isra", "initials": "II"}, {"family": "Campi", "given": "Francesco", "initials": "F"}, {"family": "Heumos", "given": "Lukas", "initials": "L"}, {"family": "Shulman", "given": "Maiia", "initials": "M", "orcid": "0009-0006-6308-1997", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4bef2f0f2514292b767f2fafd6fed60.json"}}, {"family": "Beliaeva", "given": "Valentina", "initials": "V"}, {"family": "Hediyeh-Zadeh", "given": "Soroor", "initials": "S", "orcid": "0000-0001-7513-6779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9996c51c9d43c6a40db9c46d213399.json"}}, {"family": "Schaar", "given": "Anna C", "initials": "AC"}, {"family": "Mahbubani", "given": "Krishnaa T", "initials": "KT", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de56aac2975a4292b9e6d1eeb8b74d02.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"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": "Piraud", "given": "Marie", "initials": "M"}, {"family": "Ert\u00fcrk", "given": "Ali", "initials": "A", "orcid": "0000-0001-5163-5100", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc5ed46442424675b629587c6ac826d5.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "12", "pages": "2260-2270", "issn-l": "1548-7091"}, "abstract": "Targeted spatial transcriptomic methods capture the topology of cell types and states in tissues at single-cell and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is crucial for capturing the spatial signals present in a tissue. This requires selecting the most informative, yet minimal, set of genes to profile (gene set selection) for which it is possible to build probes (probe design). However, current selections often rely on marker genes, precluding them from detecting continuous spatial signals or new states. We present Spapros, an end-to-end probe set selection pipeline that optimizes both gene set specificity for cell type identification and within-cell type expression variation to resolve spatially distinct populations while considering prior knowledge as well as probe design and expression constraints. We evaluated Spapros and show that it outperforms other selection approaches in both cell type recovery and recovering expression variation beyond cell types. Furthermore, we used Spapros to design a single-cell resolution in situ hybridization on tissues (SCRINSHOT) experiment of adult lung tissue to demonstrate how probes selected with Spapros identify cell types of interest and detect spatial variation even within cell types.", "doi": "10.1038/s41592-024-02496-z", "pmid": "39558096", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11621025"}, {"db": "pii", "key": "10.1038/s41592-024-02496-z"}], "notes": [], "created": "2026-08-20T09:03:14.919Z", "modified": "2026-08-20T09:03:15.285Z"}, {"entity": "publication", "iuid": "0a2b23ff0c444c0f9492aca8082ff178", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a2b23ff0c444c0f9492aca8082ff178.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a2b23ff0c444c0f9492aca8082ff178"}}, "title": "High-parametric protein maps reveal the spatial organization in early-developing human lung", "authors": [{"family": "Sariyar", "given": "Sanem", "initials": "S", "orcid": "0000-0003-0735-5595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/218ce8c5fb3348f9b04304b811808d4b.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4047064d44674e229a3b2dd10f241607.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-0037-5166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/986c7d4c42454d98b6c190a4bdb8b2c9.json"}}, {"family": "Mardamshina", "given": "Mariya", "initials": "M", "orcid": "0000-0003-0066-0861", "researcher": {"href": 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"Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}], "type": "posted-content", "published": "2024-01-25", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.25.577163", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:51:53.380Z", "modified": "2026-08-20T10:51:53.715Z"}, {"entity": "publication", "iuid": "57b68793aa824f6f891b6f7e0f485c6d", "links": {"self": {"href": 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"given": "Werner", "initials": "W", "orcid": "0000-0003-1946-0894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c1a6af6c4240a89064d5a0b5abfc25.json"}}, {"family": "Bellusci", "given": "Saverio", "initials": "S", "orcid": "0000-0001-5987-4579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/775bd6384dc94fc98c87fef871bcaba3.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "posted-content", "published": "2023-12-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.11.571142", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:55.983Z", "modified": "2026-08-20T10:50:56.293Z"}, {"entity": "publication", "iuid": "8dce24ca88a84467b53b954c490959ee", "links": {"self": {"href": 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Barros", "initials": "LB", "orcid": "0000-0001-7702-9782", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a03e4ecd47c410983b707cc8bb7795b.json"}}, {"family": "Stra\u00dfer", "given": "Lena", "initials": "L"}, {"family": "Heumos", "given": "Lukas", "initials": "L", "orcid": "0000-0002-8937-3457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3ea0d64ba024c18afd4f6e13d2277fa.json"}}, {"family": "Mekki", "given": "Ilhem Isra", "initials": "II"}, {"family": "Mahbubani", "given": "Krishnaa T", "initials": "KT", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de56aac2975a4292b9e6d1eeb8b74d02.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Balassa", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Kovacs", "given": "Ferenc", "initials": "F"}, {"family": "Horvath", "given": "Peter", "initials": "P"}, {"family": "Piraud", "given": "Marie", "initials": "M", "orcid": "0000-0002-4917-2458", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d71a57d42dd84b248943d18409a3ce41.json"}}, {"family": "Ert\u00fcrk", "given": "Ali", "initials": "A"}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}], "type": "posted-content", "published": "2022-08-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.08.16.504115", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:13:49.643Z", "modified": "2026-08-20T10:13:49.825Z"}, {"entity": "publication", "iuid": "bcb3f1bfd9ec4b6d814f092b14d5823a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb3f1bfd9ec4b6d814f092b14d5823a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb3f1bfd9ec4b6d814f092b14d5823a"}}, "title": "SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Nguyen", "given": "Hong Phuong", "initials": "HP", "orcid": "0000-0001-9170-9303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91241fcfd1404122a8849adab383514c.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37300f2654d74a5c9b81dd287d47768a.json"}}, {"family": "Seeger", "given": "Werner", "initials": "W"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"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": "2020-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "18", "issue": "11", "pages": "e3000675", "issn-l": "1544-9173"}, "abstract": "Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.", "doi": "10.1371/journal.pbio.3000675", "pmid": "33216742", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7717588"}, {"db": "pii", "key": "PBIOLOGY-D-20-00202"}], "notes": [], "created": "2026-08-20T12:42:40.156Z", "modified": "2026-08-20T12:42:40.301Z"}, {"entity": "publication", "iuid": "9c33bdfb53214af0a4dba29f6385f0ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed"}}, "title": "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Nguyen", "given": "Hong Phuong", "initials": "HP", "orcid": "0000-0001-9170-9303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91241fcfd1404122a8849adab383514c.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Seeger", "given": "Werner", "initials": "W"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "posted-content", "published": "2020-02-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.02.07.938571", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:55:54.959Z", "modified": "2026-08-20T09:55:55.187Z"}]}