{"entity": "researcher", "timestamp": "2026-05-17T09:45:14.518Z", "family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "affiliations": ["Department of Protein Science, Science for Life Laboratory, KTH\u2013Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8"}}, "publications": [{"entity": "publication", "iuid": "ba2006e120954777a021042ee6d1b63e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e"}}, "title": "Cell shapes decode molecular phenotypes in image-based spatial proteomics.", "authors": [{"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Leineweber", "given": "William D", "initials": "WD", "orcid": "0000-0003-3069-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6f5dd2023994301867b8bb3948a2274.json"}}, {"family": "Viana", "given": "Matheus P", "initials": "MP", "orcid": "0000-0001-9288-2108", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b1be92b4f549df8b09af4a7532493f.json"}}, {"family": "Cesnik", "given": "Anthony", "initials": "A", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Hansen", "given": "Jan N", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4047064d44674e229a3b2dd10f241607.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Rafelski", "given": "Susanne M", "initials": "SM", "orcid": "0000-0002-1399-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f5be9729bf4ff280b958d85df287d4.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The diversity of cellular and tissue structures can arise from a few basic cell shapes, which undergo various transformations based on biophysical constraints on cytoskeletal organization. While cellular geometry has been linked with selected biological processes such as polarity, signaling or morphogenesis, the orchestration of the whole proteome in association to cell shape is still poorly understood. In this study, using more than 1 million images of single cells stained for 11,998 proteins across 10 cell lines in the Human Protein Atlas database, we performed an integrated analysis of organelle, pathway and single protein levels in association to a 2D cellular shapespace. We found that cell and nuclear shapes across cell lines exist in a shared continuum. We also found that the subcellular organelle topology varies across cell lines, but remains robust within each cell line's shapespace. At the single protein level, we found that cells of different shapes in the same cell cycle phase might be preparing for different fates, and that many non-cell cycle proteins expressed shape-based abundance variation. Using the same coordinate framework defined by shape, we could analyze the distribution shift of protein spatial localization under drug perturbation.", "doi": "10.1101/2025.05.13.653868", "pmid": "40463127", "labels": {"Wei Ouyang": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12132440"}, {"db": "pii", "key": "2025.05.13.653868"}], "notes": [], "created": "2025-12-15T10:06:41.544Z", "modified": "2025-12-15T10:06:41.690Z"}, {"entity": "publication", "iuid": "df293d53882b4896bf5c0e2b9fc40e8a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a"}}, "title": "Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2022-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "608", "issue": "7924", "pages": "E32", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/s41586-022-05180-4", "pmid": "35931766", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-022-05180-4"}], "notes": [], "created": "2023-12-04T14:58:17.819Z", "modified": "2023-12-04T14:58:17.937Z"}, {"entity": "publication", "iuid": "a56bfb5717d746eea1722911e715cfe6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Shutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "590", "issue": "7847", "pages": "649-654", "issn-l": "0028-0836"}, "abstract": "The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.", "doi": "10.1038/s41586-021-03232-9", "pmid": "33627808", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03232-9"}], "notes": [], "created": "2021-10-08T14:12:30.416Z", "modified": "2022-11-04T11:32:13.601Z"}, {"entity": "publication", "iuid": "b88c28292c524760a32c286f42bb228b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b88c28292c524760a32c286f42bb228b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b88c28292c524760a32c286f42bb228b"}}, "title": "The human secretome.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b93284f942e44f1086616357d77267c3.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06cbc187628340278395a00ab9dd6c89.json"}}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Scheffel", "given": "Julia", "initials": "J", "orcid": "0000-0001-8353-3774", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26054d5035214c8ab2b7e449c8402fc0.json"}}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ffb1140aaa42c5ac63fe76653fc63b.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794215a6625b4fe4b652ec08bcab98ec.json"}}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0001-5386-5460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ea4741b77234afe83e92c3dfff0a799.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Ekblad", "given": "Siri", "initials": "S", "orcid": "0000-0002-0582-7141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/172a0df6d88347b499f6dd25b5602194.json"}}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M", "orcid": "0000-0001-9542-601X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/262cf0a008ac4ced8969d35e33628fe5.json"}}, {"family": "Kanje", "given": "Sara", "initials": "S", "orcid": "0000-0002-4751-2519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28e34a13f8f748a38a5ca6241205a878.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M", "orcid": "0000-0002-7875-2822", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57ae4837a9a947709093067a0456f715.json"}}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a69f7651977a4b4a92bdf5f9d6408d04.json"}}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL", "orcid": "0000-0003-1096-9061", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce3e9610155a4814add604d22b11ae04.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ccc9581865849c285b687a4670bbf2b.json"}}, {"family": "Dodig-Crnkovic", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5365873ed6a7463485fb44550a4826ec.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1533d567ad31481fae15627d3b316382.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c4545bd2324b7d9b6696dab5bcb7dd.json"}}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cc0ab2ae97c4f968d6218ca2915389f.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d12504acae5c4f31b83f75c3d7786cd4.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Robinson", "given": "Jonathan", "initials": "J", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/528edd3ba8374bdd8e3187556978c5ef.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bab301bfb3544e69cf96ae4080fc3e9.json"}}, {"family": "Sullivan", "given": "Devin", "initials": "D", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3bff10128d545ff8323e2a701e73eba.json"}}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aff7e9c1d774b8c8bfee2f09a323ed2.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703619132e242aaad263d4ecd80a8ae.json"}}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG", "orcid": "0000-0002-7005-1642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75368e988b364f2ca5e320e0a2c17f82.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b9de19b82b4406d8904cb937a466e8b.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1bdfd8500c4dbea343132bc0d8e44c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6982072448e4e8889c71fc14d214fed.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9397c6e626b1457e8dcd47f037c4cf9d.json"}}], "type": "journal article", "published": "2019-11-26", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "12", "issue": "609", "pages": "eaaz0274"}, "abstract": "The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.", "doi": "10.1126/scisignal.aaz0274", "pmid": "31772123", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "12/609/eaaz0274"}], "notes": [], "created": "2020-09-25T13:06:12.633Z", "modified": "2022-11-04T11:32:15.775Z"}, {"entity": "publication", "iuid": "96c1d5dbe4a04df893cb0a04749db0bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/96c1d5dbe4a04df893cb0a04749db0bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/96c1d5dbe4a04df893cb0a04749db0bb"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c0d15b9219a462a868adab9f428e5fa.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4cfd96c1edb4b7abfc0f25949b9e4ef.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e2ec344c501496796be3250fd563699.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fa0caee72804459be90af5793c7326b.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5219527c2dc6480da474f3c47dff9318.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2806baba4d6477a89ffd4100ae6ea5e.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "357", "issue": "6352", "pages": "eaan2507"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"Affiliated researcher": null, "Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2018-12-03T14:43:54.058Z", "modified": "2022-11-04T11:32:18.582Z"}, {"entity": "publication", "iuid": "6b738021cda643f6bbf791294ece782e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6b738021cda643f6bbf791294ece782e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6b738021cda643f6bbf791294ece782e"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08e64ec3c551482db30e11948c9f6fbc.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1702b107da0f47b48fb407c1168526bc.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7bab301bfb3544e69cf96ae4080fc3e9.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d67702d5965445ce953c729759e689e1.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1234037ea29433184114410b362883f.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c907cab71d247e59c8c8e9d1128830f.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e82a7945c59542f7a80ff2ee1603fe00.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/abbbf8193d5a4376a5c726768d039439.json"}}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Gatto", "given": "Laurent", "initials": "L", "orcid": "0000-0002-1520-2268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e8a6af2989b46fd8f1ba9f8743472bb.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d6d89bd3a43eab43eee98539ed4ad.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c0d15b9219a462a868adab9f428e5fa.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2efbb592ef784fac841437588b0d5e9d.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3db33fa3edb94febb8be7927a16838d0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16beca5822c747128300910b5c74dbfc.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9187c63c52649fb94588ea396eac755.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/770756518b8d49d58ce15957b07c8b46.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9397c6e626b1457e8dcd47f037c4cf9d.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6fb5a1c88b44798144fd2de255fb00.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5aff7e9c1d774b8c8bfee2f09a323ed2.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3bff10128d545ff8323e2a701e73eba.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b9de19b82b4406d8904cb937a466e8b.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edeb3bc6c95d4185bf2098bf1e4a5e3c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456805fa3f4f47328f3923b78bf66996.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2017-05-26", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "356", "issue": "6340", "pages": "eaal3321"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"Affiliated researcher": null, "Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2018-12-03T14:43:09.565Z", "modified": "2022-11-04T11:32:18.775Z"}]}