{"entity": "researcher", "timestamp": "2026-06-09T02:40:41.112Z", "family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "affiliations": ["Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3"}}, "publications": [{"entity": "publication", "iuid": "e183de5687764f018052867552a12eef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e183de5687764f018052867552a12eef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e183de5687764f018052867552a12eef"}}, "title": "Probabilistic cell typing enables fine mapping of closely related cell types in situ.", "authors": [{"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Harris", "given": "Kenneth D", "initials": "KD", "orcid": "0000-0002-5930-6456", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d82ff0750e140a2820eb51c19eb9437.json"}}, {"family": "Hauling", "given": "Thomas", "initials": "T"}, {"family": "Nicoloutsopoulos", "given": "Dimitris", "initials": "D"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}, {"family": "Skene", "given": "Nathan", "initials": "N", "orcid": "0000-0002-6807-3180", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b4340cc0fa948eda26ce5618ebc0693.json"}}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "17", "issue": "1", "pages": "101-106"}, "abstract": "Understanding the function of a tissue requires knowing the spatial organization of its constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has revealed the genome-wide expression patterns that define its many, closely related neuronal types, but cannot reveal their spatial arrangement. Here we introduce probabilistic cell typing by in situ sequencing (pciSeq), an approach that leverages previous scRNA-seq classification to identify cell types using multiplexed in situ RNA detection. We applied this method by mapping the inhibitory neurons of mouse hippocampal area CA1, for which ground truth is available from extensive previous work identifying their laminar organization. Our method identified these neuronal classes in a spatial arrangement matching ground truth, and further identified multiple classes of isocortical pyramidal cell in a pattern matching their known organization. This method will allow identifying the spatial organization of closely related cell types across the brain and other tissues.", "doi": "10.1038/s41592-019-0631-4", "pmid": "31740815", "labels": {"Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-019-0631-4"}, {"db": "pmc", "key": "PMC6949128"}, {"db": "mid", "key": "EMS84576"}], "notes": [], "created": "2020-01-10T04:54:58.127Z", "modified": "2025-10-17T13:02:18.185Z"}, {"entity": "publication", "iuid": "666d3b0626004dd0978b871abd17db71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/666d3b0626004dd0978b871abd17db71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/666d3b0626004dd0978b871abd17db71"}}, "title": "Profiling surface proteins on individual exosomes using a proximity barcoding assay.", "authors": [{"family": "Wu", "given": "Di", "initials": "D", "orcid": "0000-0003-0293-9057", "researcher": {"href": "https://publications.scilifelab.se/researcher/2664b0c2ac7245508b02bbd8f78998ae.json"}}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Shen", "given": "Xia", "initials": "X", "orcid": "0000-0003-4390-1979", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40d1f7f07ed482b9c95f56c61f0a836.json"}}, {"family": "Sun", "given": "Yu", "initials": "Y", "orcid": "0000-0003-4799-0745", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba9de321f10248a8b81c73daa05c5d48.json"}}, {"family": "Thulin", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0002-2756-3933", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae987ebb24a423392fd51b3ba0166e9.json"}}, {"family": "Cai", "given": "Yanling", "initials": "Y"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Shen", "given": "Qiujin", "initials": "Q"}, {"family": "Oelrich", "given": "Johan", "initials": "J", "orcid": "0000-0002-8591-7728", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e97acea3e040adb1b8ee20cba7cdc0.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Dubois", "given": "K Louise", "initials": "KL"}, {"family": "Ronquist", "given": "K G\u00f6ran", "initials": "KG", "orcid": "0000-0001-5885-8067", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1cdc49a4467457a894cd62c3051306a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2019-08-26", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3854", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Exosomes have been implicated in numerous biological processes, and they may serve as important disease markers. Surface proteins on exosomes carry information about their tissues of origin. Because of the heterogeneity of exosomes it is desirable to investigate them individually, but this has so far remained impractical. Here, we demonstrate a proximity-dependent barcoding assay to profile surface proteins of individual exosomes using antibody-DNA conjugates and next-generation sequencing. We first validate the method using artificial streptavidin-oligonucleotide complexes, followed by analysis of the variable composition of surface proteins on individual exosomes, derived from human body fluids or cell culture media. Exosomes from different sources are characterized by the presence of specific combinations of surface proteins and their abundance, allowing exosomes to be separately quantified in mixed samples to serve as markers for tissue-specific engagement in disease.", "doi": "10.1038/s41467-019-11486-1", "pmid": "31451692", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11486-1"}, {"db": "pmc", "key": "PMC6710248"}], "notes": [], "created": "2020-01-07T15:00:02.216Z", "modified": "2024-01-16T13:48:43.995Z"}, {"entity": "publication", "iuid": "5772fc9a0bde4a55bcf300028482da2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e"}}, "title": "Spatiotemporal structure of cell fate decisions in murine neural crest", "authors": [{"family": "Soldatov", "given": "Ruslan", "initials": "R", "orcid": "0000-0002-5670-5881", "researcher": {"href": "https://publications.scilifelab.se/researcher/3800b61f5f7042e89514b439e9532a97.json"}}, {"family": "Kaucka", "given": "Marketa", "initials": "M", "orcid": "0000-0002-8781-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/933187e42ddc4ab6a29c46d5cca411e6.json"}}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Petersen", "given": "Julian", "initials": "J", "orcid": "0000-0002-7444-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d20bbfd5a540a58aac82ada8d80b0d.json"}}, {"family": "Chontorotzea", "given": "Tatiana", "initials": "T", "orcid": "0000-0002-6134-1365", "researcher": {"href": "https://publications.scilifelab.se/researcher/7426e1056a94430bb9ab69191e623fd2.json"}}, {"family": "Englmaier", "given": "Lukas", "initials": "L", "orcid": "0000-0002-0082-2616", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba3d0eb3f634ccda4e6562c37bd77f2.json"}}, {"family": "Akkuratova", "given": "Natalia", "initials": "N", "orcid": "0000-0001-6733-8119", "researcher": {"href": "https://publications.scilifelab.se/researcher/68fc565dc99b4e8eb61d39dcef0f3a48.json"}}, {"family": "Yang", "given": "Yunshi", "initials": "Y", "orcid": "0000-0003-0396-5257", "researcher": {"href": "https://publications.scilifelab.se/researcher/4663511b58bd4c0f9c69da8445c7974b.json"}}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M", "orcid": "0000-0003-4949-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafb570acc6d40159228d08f9dcc985f.json"}}, {"family": "Dyachuk", "given": "Viacheslav", "initials": "V", "orcid": "0000-0001-8100-7367", "researcher": {"href": "https://publications.scilifelab.se/researcher/a32abc6aafed40e382beb35f873ae91c.json"}}, {"family": "Bock", "given": "Christoph", "initials": "C", "orcid": "0000-0001-6091-3088", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab95ee1c8284fa7bf2e5a2ee987c835.json"}}, {"family": "Farlik", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0698-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/906ad9a447b64e028f9cf41fbeaea108.json"}}, {"family": "Piacentino", "given": "Michael L", "initials": "ML", "orcid": "0000-0003-1773-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75e58e24dbcf4b8ba91ce39db1491c69.json"}}, {"family": "Boismoreau", "given": "Franck", "initials": "F"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Bronner", "given": "Marianne E", "initials": "ME", "orcid": "0000-0003-4274-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/56516b93bfb047aeab63c9d2fee21d4a.json"}}, {"family": "Croci", "given": "Laura", "initials": "L", "orcid": "0000-0002-7826-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e08f8646894441297506e2a3eb5fb57.json"}}, {"family": "Hsiao", "given": "Wen Yu", "initials": "WY"}, {"family": "Guertin", "given": "David A", "initials": "DA"}, {"family": "Brunet", "given": "Jean Francois", "initials": "JF", "orcid": "0000-0002-1985-6103", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e7516ee3e5a47ed9b6163b10d5baf9a.json"}}, {"family": "Consalez", "given": "Gian Giacomo", "initials": "GG", "orcid": "0000-0003-4594-6273", "researcher": {"href": "https://publications.scilifelab.se/researcher/1eabaebce3194d9c93e65ce4123f4254.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Fried", "given": "Kaj", "initials": "K", "orcid": "0000-0002-9997-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eaae026524ee6b9b589f12846b458.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal-article", "published": "2019-06-07", "journal": {"volume": "364", "issn": "0036-8075", "issue": "6444", "pages": "eaas9536", "title": "Science", "issn-l": null}, "abstract": "Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor Twist1. The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial coactivation of bipotential properties followed by gradual shifts toward commitment. Competing fate programs are coactivated before cells acquire fate-specific phenotypic traits. Determination of a specific fate is achieved by increased synchronization of relevant programs and concurrent repression of competing fate programs.", "doi": "10.1126/science.aas9536", "pmid": "31171666", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "364/6444/eaas9536"}], "notes": [], "created": "2019-06-12T08:11:45.162Z", "modified": "2025-10-17T13:02:18.356Z"}, {"entity": "publication", "iuid": "c712089f45ee420497574a4fbdf3867b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c712089f45ee420497574a4fbdf3867b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c712089f45ee420497574a4fbdf3867b"}}, "title": "Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma.", "authors": [{"family": "Carow", "given": "Berit", "initials": "B", "orcid": "0000-0002-8760-6253", "researcher": {"href": "https://publications.scilifelab.se/researcher/f434d654fb5842708da79b3481017852.json"}}, {"family": "Hauling", "given": "Thomas", "initials": "T"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Kramnik", "given": "Igor", "initials": "I"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}], "type": "journal article", "published": "2019-04-23", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1823", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Granulomas are the pathological hallmark of tuberculosis (TB) and the niche where bacilli can grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here we show 34 immune transcripts align to the morphology of lung sections from Mycobacterium tuberculosis-infected mice at cellular resolution. Colocalizing transcript networks at <10 \u03bcm in C57BL/6 mouse granulomas increase complexity with time after infection. B-cell clusters develop late after infection. Transcripts from activated macrophages are enriched at subcellular distances from M. tuberculosis. Encapsulated C3HeB/FeJ granulomas show necrotic centers with transcripts associated with immunosuppression (Foxp3, Il10), whereas those in the granuloma rims associate with activated T cells and macrophages. We see highly diverse networks with common interactors in similar lesions. Different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion, and the proximity to bacteria are here defined.", "doi": "10.1038/s41467-019-09816-4", "pmid": "31015452", "labels": {"In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09816-4"}, {"db": "pmc", "key": "PMC6479067"}], "notes": [], "created": "2020-01-10T04:54:56.986Z", "modified": "2025-10-17T13:02:18.396Z"}]}