{"entity": "researcher", "timestamp": "2026-08-09T07:59:42.100Z", "family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d"}}, "publications": [{"entity": "publication", "iuid": "92f0abc9e79944d2bebd0d108d67ca04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f0abc9e79944d2bebd0d108d67ca04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f0abc9e79944d2bebd0d108d67ca04"}}, "title": "Spatiotemporal gene expression and cellular dynamics of the developing human heart.", "authors": [{"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d"}, {"family": "Foyer", "given": "Julia", "initials": "J"}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Shakari", "given": "Nick", "initials": "N", "orcid": "0009-0003-2192-769X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c36fc495bd4e16829c53630137b3c2.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Sariyar", "given": "Sanem", "initials": "S"}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications.scilifelab.se/researcher/272dfc4476064018bc7ed0235b7d3e55.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Bergmann", "given": "Olaf", "initials": "O", "orcid": "0000-0003-1065-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb61ad666a3427193e07c6274e8c3a1.json"}}, {"family": "Sylv\u00e9n", "given": "Christer", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.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": "2025-11-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "57", "issue": "11", "pages": "2756-2771"}, "abstract": "Heart development relies on topologically orchestrated cellular transitions and interactions, many of which remain poorly characterized in humans. Here, we combined unbiased spatial and single-cell transcriptomics with imaging-based validation across postconceptional weeks 5.5 to 14 to uncover the molecular landscape of human early cardiogenesis. We present a high-resolution transcriptomic map of the developing human heart, revealing the spatial arrangements of 31 coarse-grained and 72 fine-grained cell states organized into distinct functional niches. Our findings illuminate key insights into the formation of the cardiac pacemaker-conduction system, heart valves and atrial septum, and uncover unexpected diversity among cardiac mesenchymal cells. We also trace the emergence of autonomic innervation and provide the first spatial account of chromaffin cells in the fetal heart. Our study, supported by an open-access spatially centric interactive viewer, offers a unique resource to explore the cellular and molecular blueprint of human heart development, offering links to genetic causes of heart disease.", "doi": "10.1038/s41588-025-02352-6", "pmid": "41162788", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12597827"}, {"db": "pii", "key": "10.1038/s41588-025-02352-6"}], "notes": [], "created": "2025-11-24T12:14:25.565Z", "modified": "2025-11-24T12:48:57.768Z"}, {"entity": "publication", "iuid": "07cd66044bbe4799bb39d2ca83fa2edf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf"}}, "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.scilifelab.se/researcher/5a057942e8804bd19530d9faf484c72f.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications.scilifelab.se/researcher/272dfc4476064018bc7ed0235b7d3e55.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Mardamshina", "given": "Mariya", "initials": "M", "orcid": "0000-0003-0066-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff68d3499c01447b8a48d99b86bd882b.json"}}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Ballllosera Navarro", "given": "Frederic", "initials": "F"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z", "orcid": "0000-0002-4350-2524", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89be535ddfa4c6ab46201fb383f4a2b.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b9ccd9ae84cdfbcb663591f39a77b.json"}}], "type": "journal article", "published": "2024-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "9381"}, "abstract": "The respiratory system, including the lungs, is essential for terrestrial life. While recent research has advanced our understanding of lung development, much still relies on animal models and transcriptome analyses. In this study conducted within the Human Developmental Cell Atlas (HDCA) initiative, we describe the protein-level spatiotemporal organization of the lung during the first trimester of human gestation. Using high-parametric tissue imaging with a 30-plex antibody panel, we analyzed human lung samples from 6 to 13 post-conception weeks, generating data from over 2 million cells across five developmental timepoints. We present a resource detailing spatially resolved cell type composition of the developing human lung, including proliferative states, immune cell patterns, spatial arrangement traits, and their temporal evolution. This represents an extensive single-cell resolved protein-level examination of the developing human lung and provides a valuable resource for further research into the developmental roots of human respiratory health and disease.", "doi": "10.1038/s41467-024-53752-x", "pmid": "39477961", "labels": {"BioImage Informatics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11525936"}, {"db": "pii", "key": "10.1038/s41467-024-53752-x"}], "notes": [], "created": "2024-11-13T10:04:30.594Z", "modified": "2025-12-19T07:56:09.718Z"}, {"entity": "publication", "iuid": "33f0eb0f11f04f6e97e94329b239557e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f0eb0f11f04f6e97e94329b239557e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f0eb0f11f04f6e97e94329b239557e"}}, "title": "Chromatin accessibility during human first-trimester neurodevelopment.", "authors": [{"family": "Mannens", "given": "Camiel C A", "initials": "CCA", "orcid": "0000-0002-1318-2603", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8d4a5ffd743424fab0d3798a8778715.json"}}, {"family": "Hu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-1869-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/49a35358ad6e4b5eaec60d97504102ae.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Schipper", "given": "Marijn", "initials": "M", "orcid": "0000-0002-5170-2796", "researcher": {"href": "https://publications.scilifelab.se/researcher/458e0ee2185d4473bd9bbdd5a9f48e25.json"}}, {"family": "Reagor", "given": "Caleb C", "initials": "CC", "orcid": "0000-0002-8304-1267", "researcher": {"href": "https://publications.scilifelab.se/researcher/981d5cb61a7946f6843e4270576993e9.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "He", "given": "Xiaoling", "initials": "X", "orcid": "0009-0004-1002-8418", "researcher": {"href": "https://publications.scilifelab.se/researcher/aef7b6a77efd410bb696cf988926f4c4.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2024-05-01", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836"}, "abstract": "The human brain develops through a tightly organized cascade of patterning events, induced by transcription factor expression and changes in chromatin accessibility. Although gene expression across the developing brain has been described at single-cell resolution1, similar atlases of chromatin accessibility have been primarily focused on the forebrain2-4. Here we describe chromatin accessibility and paired gene expression across the entire developing human brain during the first trimester (6-13 weeks after conception). We defined 135 clusters and used multiomic measurements to link candidate cis-regulatory elements to gene expression. The number of accessible regions increased both with age and along neuronal differentiation. Using a convolutional neural network, we identified putative functional transcription factor-binding sites in enhancers characterizing neuronal subtypes. We applied this model to cis-regulatory elements linked to ESRRB to elucidate its activation mechanism in the Purkinje cell lineage. Finally, by linking disease-associated single nucleotide polymorphisms to cis-regulatory elements, we validated putative pathogenic mechanisms in several diseases and identified midbrain-derived GABAergic neurons as being the most vulnerable to major depressive disorder-related mutations. Our findings provide a more detailed view of key gene regulatory mechanisms underlying the emergence of brain cell types during the first trimester and a comprehensive reference for future studies related to human neurodevelopment.", "doi": "10.1038/s41586-024-07234-1", "pmid": "38693260", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-024-07234-1"}], "notes": [], "created": "2024-05-17T09:16:14.715Z", "modified": "2024-05-17T09:16:15.854Z"}, {"entity": "publication", "iuid": "e32fd724b739422db6fef1905f9b5493", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493"}}, "title": "Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.", "authors": [{"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Liu", "given": "Yang", "initials": "Y"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Lee", "given": "Hower", "initials": "H"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Kallner", "given": "Helena Kopp", "initials": "HK"}, {"family": "\u00c5kesson", "given": "Elisabet", "initials": "E"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.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": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "26", "issue": "5", "pages": "891-901"}, "abstract": "The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.", "doi": "10.1038/s41593-023-01312-9", "pmid": "37095395", "labels": {"BioImage Informatics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10166856"}, {"db": "pii", "key": "10.1038/s41593-023-01312-9"}], "notes": [], "created": "2023-05-31T11:06:10.725Z", "modified": "2025-10-17T13:02:17.029Z"}, {"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": 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