{"entity": "researcher", "timestamp": "2026-08-20T21:12:33.773Z", "family": "Hediyeh-Zadeh", "given": "Soroor", "initials": "S", "orcid": "0000-0001-7513-6779", "affiliations": ["Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany.", "School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9996c51c9d43c6a40db9c46d213399.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9996c51c9d43c6a40db9c46d213399"}}, "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": "05bb661123804612a71398516300deb1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05bb661123804612a71398516300deb1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05bb661123804612a71398516300deb1"}}, "title": "Data from SOX9 Defines Distinct Populations of Cells in SHH Medulloblastoma but Is Not Required for Math1-Driven Tumor Formation", "authors": [{"family": "Adolphe", "given": "Christelle", "initials": "C"}, {"family": "Millar", "given": "Amanda", "initials": "A"}, {"family": "Kojic", "given": "Marija", "initials": "M", "orcid": "0000-0001-6437-283X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77e8f76b0a144796becbc1dab6da9205.json"}}, {"family": "Barkauskas", "given": "Deborah S", "initials": "DS"}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3942-6271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63e6602d2807417684239b93eb065a26.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}, {"family": "Hediyeh-zadeh", "given": "Soroor", "initials": "S", "orcid": "0000-0001-7513-6779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9996c51c9d43c6a40db9c46d213399.json"}}, {"family": "Tan", "given": "Chin Wee", "initials": "CW", "orcid": "0000-0001-9695-7218", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5277887d70f84d1d98fa163ee066817a.json"}}, {"family": "Davis", "given": "Melissa J", "initials": "MJ", "orcid": "0000-0003-4864-7033", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca0ff39b0e06406d9bf637043b2e2221.json"}}, {"family": "Genovesi", "given": "Laura A", "initials": "LA", "orcid": "0000-0001-6277-8422", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35c473636ad549d5a005b2680901551c.json"}}, {"family": "Wainwright", "given": "Brandon J", "initials": "BJ"}], "type": "posted-content", "published": "2023-04-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1158/1541-7786.c.6545124.v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:14:02.202Z", "modified": "2026-08-20T12:14:02.430Z"}, {"entity": "publication", "iuid": "9dcdc4592a8c4e0dab74f807fc254b1b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9dcdc4592a8c4e0dab74f807fc254b1b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9dcdc4592a8c4e0dab74f807fc254b1b"}}, "title": "SOX9 Defines Distinct Populations of Cells in SHH Medulloblastoma but Is Not Required for Math1-Driven Tumor Formation.", "authors": [{"family": "Adolphe", "given": "Christelle", "initials": "C"}, {"family": "Millar", "given": "Amanda", "initials": "A"}, {"family": "Kojic", "given": "Marija", "initials": "M", "orcid": "0000-0001-6437-283X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77e8f76b0a144796becbc1dab6da9205.json"}}, {"family": "Barkauskas", "given": "Deborah S", "initials": "DS"}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3942-6271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63e6602d2807417684239b93eb065a26.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}, {"family": "Hediyeh-Zadeh", "given": "Soroor", "initials": "S", "orcid": "0000-0001-7513-6779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9996c51c9d43c6a40db9c46d213399.json"}}, {"family": "Tan", "given": "Chin Wee", "initials": "CW", "orcid": "0000-0001-9695-7218", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5277887d70f84d1d98fa163ee066817a.json"}}, {"family": "Davis", "given": "Melissa J", "initials": "MJ", "orcid": "0000-0003-4864-7033", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca0ff39b0e06406d9bf637043b2e2221.json"}}, {"family": "Genovesi", "given": "Laura A", "initials": "LA", "orcid": "0000-0001-6277-8422", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35c473636ad549d5a005b2680901551c.json"}}, {"family": "Wainwright", "given": "Brandon J", "initials": "BJ"}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Mol. Cancer Res.", "issn": "1557-3125", "volume": "19", "issue": "11", "pages": "1831-1839", "issn-l": "1541-7786"}, "abstract": "Medulloblastoma is the most common malignant pediatric brain tumor and there is an urgent need for molecularly targeted and subgroup-specific therapies. The stem cell factor SOX9, has been proposed as a potential therapeutic target for the treatment of Sonic Hedgehog medulloblastoma (SHH-MB) subgroup tumors, given its role as a downstream target of Hedgehog signaling and in functionally promoting SHH-MB metastasis and treatment resistance. However, the functional requirement for SOX9 in the genesis of medulloblastoma remains to be determined. Here we report a previously undocumented level of SOX9 expression exclusively in proliferating granule cell precursors (GCP) of the postnatal mouse cerebellum, which function as the medulloblastoma-initiating cells of SHH-MBs. Wild-type GCPs express comparatively lower levels of SOX9 than neural stem cells and mature astroglia and SOX9low GCP-like tumor cells constitute the bulk of both infant (Math1Cre:Ptch1 ) and adult (lox/loxPtch1 ) SHH-MB mouse models. Human medulloblastoma single-cell RNA data analyses reveal three distinct LacZ/+SOX9 populations present in SHH-MB and noticeably absent in other medulloblastoma subgroups: SOX9 + MATH1 + (GCP), SOX9 + GFAP + (astrocytes) and SOX9 + MATH1 + GFAP + (potential tumor-derived astrocytes). To functionally address whether SOX9 is required as a downstream effector of Hedgehog signaling in medulloblastoma tumor cells, we ablated Sox9 using a Math1Cre model system. Surprisingly, targeted ablation of Sox9 in GCPs (Math1Cre:Sox9 ) revealed no overt phenotype and loss of lox/loxSox9 in SHH-MB (Math1Cre:Ptch1 ) does not affect tumor formation. IMPLICATIONS: Despite preclinical data indicating SOX9 plays a key role in SHH-MB biology, our data argue against SOX9 as a viable therapeutic target.lox/lox;Sox9lox/lox", "doi": "10.1158/1541-7786.MCR-21-0117", "pmid": "34330843", "labels": [], "xrefs": [{"db": "pii", "key": "1541-7786.MCR-21-0117"}], "notes": [], "created": "2026-08-20T12:14:25.096Z", "modified": "2026-08-20T12:14:25.210Z"}]}