{"entity": "researcher", "timestamp": "2026-07-13T09:52:34.038Z", "family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9"}}, "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": "c0cac7649e664f42a2dad23b77043ae7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7"}}, "title": "Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2673-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c69d2d421d64a11a719a6fd55c1977a.json"}}, {"family": "Iturritza", "given": "Miren Urrutia", "initials": "MU", "orcid": "0000-0002-3989-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bc5beb14634ef9af3d153c19355794.json"}}, {"family": "Zwicker", "given": "Christian", "initials": "C"}, {"family": "Vanneste", "given": "Bavo", "initials": "B"}, {"family": "Van Hul", "given": "No\u00e9mi", "initials": "N", "orcid": "0000-0003-1410-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1f79e0359b45c9991d14649ad4bc2b.json"}}, {"family": "Semle", "given": "Elisa", "initials": "E"}, {"family": "Quin", "given": "Jaclyn", "initials": "J"}, {"family": "Pascini", "given": "Tales", "initials": "T"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}, {"family": "Scott", "given": "Charlotte L", "initials": "CL", "orcid": "0000-0003-4914-6580", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d25f2a77f9444bb6e57ade9a1388a3.json"}}, {"family": "Vega-Rodriguez", "given": "Joel", "initials": "J", "orcid": "0000-0002-9576-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/a89fc53ed4fb4e179636b66ae8d1caa3.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7105", "issn-l": "2041-1723"}, "abstract": "Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term 'inflammatory hotspots'. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.", "doi": "10.1038/s41467-024-51418-2", "pmid": "39160174", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11333755"}, {"db": "pii", "key": "10.1038/s41467-024-51418-2"}], "notes": [], "created": "2024-11-25T10:17:47.545Z", "modified": "2024-11-25T10:17:47.707Z"}, {"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"}]}