{"entity": "label", "iuid": "37a45da85ac849d2b672c7f19ce3f7ba", "timestamp": "2026-10-10T11:16:57.013Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/label/Camilla%20Engblom.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/label/Camilla%20Engblom"}}, "value": "Camilla Engblom", "created": "2023-05-23T12:38:09.737Z", "modified": "2023-05-23T12:38:09.744Z", "accounts": [{"entity": "account", "iuid": "872f3f09c9cf41169e3d649d74502776", "timestamp": "2026-10-10T11:16:57.013Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/camilla.engblom%40ki.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/camilla.engblom%40ki.se"}}, "email": "camilla.engblom@ki.se", "name": "Camilla Engblom", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-12-01T15:29:12.384Z", "created": "2023-05-23T12:38:40.863Z", "modified": "2025-12-01T15:29:12.384Z"}], "publications_count": 18, "publications": [{"entity": "publication", "iuid": "8846d92f48ef4728b42be2ccbf41fb61", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8846d92f48ef4728b42be2ccbf41fb61.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8846d92f48ef4728b42be2ccbf41fb61"}}, "title": "Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.", "authors": [{"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Yang", "given": "Qiao", "initials": "Q"}, {"family": "Acs", "given": "Balazs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d642b1db48643f497be9a35a71dadde.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d232b4567694b6f80b59ad262e7ff54.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Steen", "given": "Sanna", "initials": "S"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "310", "issn-l": null}, "abstract": "Breast cancer is a highly heterogeneous disease with diverse outcomes, and intra-tumoral heterogeneity plays a significant role in both diagnosis and treatment. Despite its importance, the spatial distribution of intra-tumoral heterogeneity is not fully elucidated. Spatial transcriptomics has emerged as a promising tool to study the molecular mechanisms behind many diseases. It offers accurate measurements of RNA abundance, providing powerful tools to correlate the morphologies of cellular neighborhoods with localized gene expression patterns. However, the spot-based spatial transcriptomic tools, including the most widely used platform, Visium, do not achieve single-cell resolution readouts, which hinders data interpretability. In this study, we present a computational pathology image analysis pipeline (i.e., computational tissue annotation, CTA) that utilizes machine learning algorithms to accurately map tumor, stroma, and immune compartments within Visium-assayed tumor sections. Using a cohort of 23 breast tumor sections from four patients, we demonstrate that CTA can provide high-resolution annotations on the hematoxylin-and-eosin-stained images alongside the paired sequencing data, support the evaluation of deconvolution methods, deepen insights into intra-tumoral heterogeneity by increasing data analysis resolution, assist with spatially resolved intrinsic subtyping, and enhance the visualization of lymphocyte clones at single-cell resolution. The proposed pipeline provides valuable insights into the complex spatial architecture of breast cancer, contributing to more personalized diagnostics and treatment strategies.", "doi": "10.1038/s41698-025-01104-3", "pmid": "40925915", "labels": {"Camilla Engblom": "", "SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC12420830"}, {"db": "pii", "key": "10.1038/s41698-025-01104-3"}], "notes": [], "created": "2025-12-01T15:33:06.973Z", "modified": "2026-09-23T11:37:05.380Z"}, {"entity": "publication", "iuid": "fe9cf0f6d04a4cd6aedfa01c32fc97b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe9cf0f6d04a4cd6aedfa01c32fc97b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe9cf0f6d04a4cd6aedfa01c32fc97b9"}}, "title": "Tertiary lymphoid structures in Merkel cell carcinoma facilitate na\u00efve and central memory T-cell infiltration linked to immunotherapy response", "authors": [{"family": "Srinivas", "given": "Nalini", "initials": "N"}, {"family": "Spassova", "given": "Ivelina", "initials": "I"}, {"family": "Lei", "given": "Kuan Cheok", "initials": "KC"}, {"family": "Gao", "given": "Jiwei", "initials": "J"}, {"family": "Pino", "given": "Mar\u00eda Jos\u00e9", "initials": "MJ", "orcid": "0009-0004-0516-6867", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb929c821d834477b1b474d8d1423706.json"}}, {"family": "Giglio", "given": "Giovanni", "initials": "G"}, {"family": "Kitanovski", "given": "Simo", "initials": "S"}, {"family": "Dalkoohi", "given": "Mazdak", "initials": "M"}, {"family": "Livingstone", "given": "Elisabeth", "initials": "E"}, {"family": "Leiter", "given": "Ulrike", "initials": "U"}, {"family": "Mohr", "given": "Peter", "initials": "P"}, {"family": "Gambichler", "given": "Thilo", "initials": "T"}, {"family": "Stoffels", "given": "Ingo", "initials": "I"}, {"family": "Ugurel", "given": "Selma", "initials": "S", "orcid": "0000-0002-9384-6704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd5e687b8ade4fd3901fc5f0488a1127.json"}}, {"family": "Cheung", "given": "Phyllis Fung Yi", "initials": "PFY"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Lui", "given": "Weng Onn", "initials": "WO"}, {"family": "Becker", "given": "J\u00fcrgen Christian", "initials": "JC", "orcid": "0000-0001-9183-653X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7197f45a2a7c4f16a45bb196e9b32fba.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "9", "pages": "e012224", "issn-l": null}, "abstract": "The presence of tertiary lymphoid structures (TLS) in solid tumors, including Merkel cell carcinoma (MCC), is associated with a better prognosis and a better response to immunotherapy with immune checkpoint inhibition (ICI). The detailed mechanisms by which TLS influence antitumor immune responses are only partially understood.\n\nClinically annotated tumor tissues of 27 patients with MCC were obtained prior to ICI therapy. Tumor samples were subjected to transcriptomic and multiplex immuno-visual profiling, T-cell receptor (TCR) clonotype mapping, as well as-in selected cases-spatial transcriptomics to comprehensively characterize the tumor immune microenvironment.\n\nWeighted gene co-expression network analysis (WGCNA) of transcriptomic data in combination with topological overlap measures indicated a higher abundance of TLS in tumors of patients with MCC responding to ICI therapy. This concept was substantiated through immunomorphological analyses, revealing mature B-cell follicle-like structures characterized by high endothelial venules (HEVs). Further supporting HEVs as critical entry points for na\u00efve T cells, the presence of TLS was correlated with a pronounced infiltration of CD4+ and CD8+ T cells, exhibiting both na\u00efve and central memory phenotypes. The TCR repertoire of these infiltrates exhibited enhanced richness and diversity with a pronounced reactivity toward Merkel cell polyomavirus-derived T-cell epitopes. Spatially resolved RNA and V(D)J sequencing revealed the expression of genes associated with T-cell recruitment within TLS, alongside the presence of na\u00efve and central memory T-cell markers. Notably, individual clonally expanded TCR transcripts were detected both within TLS and among tumor-infiltrating lymphocytes. The latter were associated with low expression of memory cell markers and high expression of effector cell markers. Additionally, a spatial gradient in the expression of genes linked to immune stress in MCC cells-such as those involved in the interferon-\u03b3 response and antigen processing and presentation machinery-originated in proximity to the TLS.\n\nOur findings are consistent with a key role of TLS in shaping immune interactions within the MCC microenvironment, driving the recruitment of diverse tumor-reactive T cells. These insights hold promise for advancing immunotherapeutic strategies.", "doi": "10.1136/jitc-2025-012224", "pmid": "40992783", "labels": {"Camilla Engblom": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12458699"}, {"db": "pii", "key": "jitc-2025-012224"}], "notes": [], "created": "2025-12-01T15:32:17.638Z", "modified": "2026-06-30T11:26:30.155Z"}, {"entity": "publication", "iuid": "80625326e9a047959c1d1f617b678ff2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/80625326e9a047959c1d1f617b678ff2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/80625326e9a047959c1d1f617b678ff2"}}, "title": "Putting cancer immunotherapy into spatial context in the clinic.", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "43", "issue": "4", "pages": "471-476", "issn-l": "1087-0156"}, "abstract": null, "doi": "10.1038/s41587-025-02596-x", "pmid": "40229365", "labels": {"Camilla Engblom": "", "SciLifeLab Fellow": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-025-02596-x"}], "notes": [], "created": "2025-12-01T15:30:56.177Z", "modified": "2026-09-23T11:28:25.353Z"}, {"entity": "publication", "iuid": "dc33d8f3be6e4fc8becb981c8f8f4434", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dc33d8f3be6e4fc8becb981c8f8f4434.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dc33d8f3be6e4fc8becb981c8f8f4434"}}, "title": "Author Correction: Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.", "authors": [{"family": "Shafighi", "given": "Shadi", "initials": "S"}, {"family": "Geras", "given": "Agnieszka", "initials": "A"}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Sahaf Naeini", "given": "Alireza", "initials": "A"}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "R\u0105czkowska", "given": "Alicja", "initials": "A"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ee63256b2504f11b09a23542183fcf7.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c76f0c2ef08414786315bccea70fc40.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb88b057a1f4bfb87358f0ad55bcd7a.json"}}], "type": "published erratum", "published": "2025-03-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2801", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-025-58177-8", "pmid": "40118850", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC11928600"}, {"db": "pii", "key": "10.1038/s41467-025-58177-8"}], "notes": [], "created": "2026-08-20T08:53:53.581Z", "modified": "2026-09-23T15:46:21.785Z"}, {"entity": "publication", "iuid": "6659339299c543fc9fb89e3a822a940b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6659339299c543fc9fb89e3a822a940b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6659339299c543fc9fb89e3a822a940b"}}, "title": "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.", "authors": [{"family": "Shafighi", "given": "Shadi", "initials": "S"}, {"family": "Geras", "given": "Agnieszka", "initials": "A"}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Sahaf Naeini", "given": "Alireza", "initials": "A"}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "R\u0105czkowska", "given": "Alicja", "initials": "A"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ee63256b2504f11b09a23542183fcf7.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c76f0c2ef08414786315bccea70fc40.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb88b057a1f4bfb87358f0ad55bcd7a.json"}}], "type": "journal article", "published": "2024-10-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9343", "issn-l": "2041-1723"}, "abstract": "Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.", "doi": "10.1038/s41467-024-53374-3", "pmid": "39472583", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC11522407"}, {"db": "pii", "key": "10.1038/s41467-024-53374-3"}], "notes": [], "created": "2026-09-23T09:06:01.939Z", "modified": "2026-09-23T09:06:02.122Z"}, {"entity": "publication", "iuid": "e35b4f54df724359a55bb9c829e1623a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e35b4f54df724359a55bb9c829e1623a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e35b4f54df724359a55bb9c829e1623a"}}, "title": "Location matters: mapping antigen receptors within tissues.", "authors": [{"family": "Lin", "given": "Qirong", "initials": "Q"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Nat. Rev. Immunol.", "issn": "1474-1741", "volume": "24", "issue": "9", "pages": "617", "issn-l": "1474-1733"}, "abstract": null, "doi": "10.1038/s41577-024-01069-7", "pmid": "39075196", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pii", "key": "10.1038/s41577-024-01069-7"}], "notes": [], "created": "2026-08-20T08:55:53.543Z", "modified": "2026-09-23T13:36:19.655Z"}, {"entity": "publication", "iuid": "dc59e58e41dc44b3b814c09615125218", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dc59e58e41dc44b3b814c09615125218.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dc59e58e41dc44b3b814c09615125218"}}, "title": "CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.", "authors": [{"family": "Kurt", "given": "Semih", "initials": "S", "orcid": "0000-0002-9760-9140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb8ea49a9e234226930bb0fab7e9a05e.json"}}, {"family": "Chen", "given": "Mandi", "initials": "M", "orcid": "0000-0003-1880-1730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7bddfe2c3b84279aba6f3553210315d.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "5", "issn-l": "1367-4803"}, "abstract": "Copy number variations (CNVs) are common genetic alterations in tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of cancer progression. Moreover, accurate inference of CNVs from single-cell sequencing data is essential for unravelling intratumoral heterogeneity. However, existing inference methods face limitations in resolution and sensitivity.\n\nTo address these challenges, we present CopyVAE, a deep learning framework based on a variational autoencoder architecture. Through experiments, we demonstrated that CopyVAE can accurately and reliably detect CNVs from data obtained using single-cell RNA sequencing. CopyVAE surpasses existing methods in terms of sensitivity and specificity. We also discussed CopyVAE's potential to advance our understanding of genetic alterations and their impact on disease advancement.\n\nCopyVAE is implemented and freely available under MIT license at https://github.com/kurtsemih/copyVAE.", "doi": "10.1093/bioinformatics/btae284", "pmid": "38676578", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC11087824"}, {"db": "pii", "key": "7658946"}], "notes": [], "created": "2026-08-20T09:39:52.000Z", "modified": "2026-09-23T12:24:30.207Z"}, {"entity": "publication", "iuid": "f5a13cab1efc4c65bcb105b04185acb8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5a13cab1efc4c65bcb105b04185acb8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5a13cab1efc4c65bcb105b04185acb8"}}, "title": "Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d232b4567694b6f80b59ad262e7ff54.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82aebb401f644b2fbd015827dc916078.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H", "orcid": "0000-0002-5525-4724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a82ccdfe786246c5b813d9361d62c0e2.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Steiner", "given": "Embla", "initials": "E"}, {"family": "Lu", "given": "Chang", "initials": "C", "orcid": "0000-0001-6304-2820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcdd5ebdb20848f9960c0f8d7bacf42f.json"}}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9497b224930b4459aa8915e51c47e919.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642b3b7751434194b4f55f2af8d746a4.json"}}, {"family": "Jangard", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3772-2026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fd4438472764db09961f035401a7d6f.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/504df2e61c124714b9afecf767798a00.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3190bb256fcb4a9eb4f4ef06bb99eb5c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "382", "issue": "6675", "pages": "eadf8486", "issn-l": "0036-8075"}, "abstract": "The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.", "doi": "10.1126/science.adf8486", "pmid": "38060664", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-09-23T07:29:32.990Z", "modified": "2026-09-23T07:29:33.273Z"}, {"entity": "publication", "iuid": "a8f955e41ebd42daa2b3966499fa8248", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0772d0f35bde4d4ca46b93eaaf7b96cf.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4f921580aec4734ad538c0bc3e70b02.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "982", "issn-l": "2041-1723"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-06-01T06:49:27.955Z", "modified": "2026-09-23T10:56:24.585Z"}, {"entity": "publication", "iuid": "241ddb6a6bc141c483880c2f931f97d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/241ddb6a6bc141c483880c2f931f97d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/241ddb6a6bc141c483880c2f931f97d4"}}, "title": "B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing.", "authors": [{"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Bejarano", "given": "David A", "initials": "DA"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO"}, {"family": "Sorini", "given": "Chiara", "initials": "C"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Geerlings", "given": "Laura", "initials": "L"}, {"family": "Novella-Rausell", "given": "Claudio", "initials": "C"}, {"family": "Zagami", "given": "Chiara", "initials": "C"}, {"family": "Kuiper", "given": "Raoul", "initials": "R"}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA"}, {"family": "Castillo", "given": "Francisca", "initials": "F"}, {"family": "Hunt", "given": "Matthew", "initials": "M"}, {"family": "Mariano", "given": "Livia Lacerda", "initials": "LL"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Lennon-Dum\u00e9nil", "given": "Ana-Maria", "initials": "AM"}, {"family": "Mittenzwei", "given": "Romy", "initials": "R"}, {"family": "Westendorf", "given": "Astrid M", "initials": "AM"}, {"family": "H\u00f6velmeyer", "given": "Nadine", "initials": "N"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J"}, {"family": "Schlitzer", "given": "Andreas", "initials": "A"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ"}], "type": "journal article", "published": "2022-12-13", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "55", "issue": "12", "pages": "2336-2351.e12", "issn-l": null}, "abstract": "Therapeutic promotion of intestinal regeneration holds great promise, but defining the cellular mechanisms that influence tissue regeneration remains an unmet challenge. To gain insight into the process of mucosal healing, we longitudinally examined the immune cell composition during intestinal damage and regeneration. B cells were the dominant cell type in the healing colon, and single-cell RNA sequencing (scRNA-seq) revealed expansion of an IFN-induced B cell subset during experimental mucosal healing that predominantly located in damaged areas and associated with colitis severity. B cell depletion accelerated recovery upon injury, decreased epithelial ulceration, and enhanced gene expression programs associated with tissue remodeling. scRNA-seq from the epithelial and stromal compartments combined with spatial transcriptomics and multiplex immunostaining showed that B cells decreased interactions between stromal and epithelial cells during mucosal healing. Activated B cells disrupted the epithelial-stromal cross talk required for organoid survival. Thus, B cell expansion during injury impairs epithelial-stromal cell interactions required for mucosal healing, with implications for the treatment of IBD.", "doi": "10.1016/j.immuni.2022.11.002", "pmid": "36462502", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pii", "key": "S1074-7613(22)00592-1"}], "notes": [], "created": "2026-08-20T07:57:12.687Z", "modified": "2026-09-23T07:37:55.136Z"}, {"entity": "publication", "iuid": "b01eeb48ff96488a819c96b07c32fdb4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b01eeb48ff96488a819c96b07c32fdb4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b01eeb48ff96488a819c96b07c32fdb4"}}, "title": "Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d232b4567694b6f80b59ad262e7ff54.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82aebb401f644b2fbd015827dc916078.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Steiner", "given": "Embla", "initials": "E"}, {"family": "Mantovani", "given": "Giulia", "initials": "G"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642b3b7751434194b4f55f2af8d746a4.json"}}, {"family": "Jangard", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3772-2026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fd4438472764db09961f035401a7d6f.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-6948-7281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b1d4eb97634409a99a53c55e2bdcf86.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Mold", "given": "Jeff", "initials": "J", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3190bb256fcb4a9eb4f4ef06bb99eb5c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}], "type": "posted-content", "published": "2022-11-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.11.22.516865", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2023-06-01T06:50:48.655Z", "modified": "2026-09-23T14:08:48.794Z"}, {"entity": "publication", "iuid": "2be4c0bb8c4d4b1ebadf5f42ae2ab3d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2be4c0bb8c4d4b1ebadf5f42ae2ab3d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2be4c0bb8c4d4b1ebadf5f42ae2ab3d4"}}, "title": "Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.", "authors": [{"family": "Classon", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0392-7605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9f51e78f4e04793abac00c22d972363.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9497b224930b4459aa8915e51c47e919.json"}}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Nkulikiyimfura", "given": "Dieudonn\u00e9", "initials": "D"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "16", "issue": "19", "pages": "3452-3464", "issn-l": "1574-7891"}, "abstract": "Prostate cancer is a heterogeneous disease with a need for new prognostic biomarkers. Human leukocyte antigen (HLA) genes are highly polymorphic genes central to antigen presentation to T-cells. Two alleles, HLA-A*02:01 and HLA-A*24:02, have been associated with prognosis in patients diagnosed with de novo metastatic prostate cancer. We leveraged the next-generation sequenced cohorts CPC-GENE and TCGA-PRAD to examine HLA alleles, antiviral T-cell receptors and prostate cancer disease recurrence after prostatectomy. Carrying HLA-A*02:01 (111/229; 48% of patients) was independently associated with disease recurrence in patients with low-intermediate risk prostate cancer. HLA-A*11 (carried by 42/441; 10% of patients) was independently associated with rapid disease recurrence in patients with high-risk prostate cancer. Moreover, HLA-A*02:01 carriers in which anti-cytomegalovirus T-cell receptors (CMV-TCR) were identified in tumors (13/144; 10% of all patients in the cohort) had a higher risk of disease recurrence than CMV-TCR-negative patients. These findings suggest that HLA-type and CMV immunity may be valuable biomarkers for prostate cancer progression.", "doi": "10.1002/1878-0261.13273", "pmid": "35712787", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC9533687"}, {"db": "RefSeq", "key": "NC_006273.2"}], "notes": [], "created": "2026-09-23T12:11:25.234Z", "modified": "2026-09-23T12:11:25.332Z"}, {"entity": "publication", "iuid": "12d6d4f9d51344f08d3eddfd7d981d5d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/12d6d4f9d51344f08d3eddfd7d981d5d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/12d6d4f9d51344f08d3eddfd7d981d5d"}}, "title": "Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues", "authors": [{"family": "Shafighi", "given": "Shadi Darvish", "initials": "SD", "orcid": "0000-0003-0367-8864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec7c2bde8ad94897ac6732da41277705.json"}}, {"family": "Geras", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-3166-2165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2cbd312ebeb4fac9fd004908ccbb5ba.json"}}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Naeini", "given": "Alireza Sahaf", "initials": "AS", "orcid": "0000-0002-3285-4524", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1958ada1c3ee468ebf546a926b36d298.json"}}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "R\u0105czkowski", "given": "\u0141ukasz", "initials": "\u0141", "orcid": "0000-0001-5901-4595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aab710298bfa4642904f1fc63639d28d.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H", "orcid": "0000-0002-5525-4724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a82ccdfe786246c5b813d9361d62c0e2.json"}}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141", "orcid": "0000-0002-9207-6146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5af14234562f4b2db5abdea52b41dac6.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Mold", "given": "Jeff", "initials": "J", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3190bb256fcb4a9eb4f4ef06bb99eb5c.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ee63256b2504f11b09a23542183fcf7.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c76f0c2ef08414786315bccea70fc40.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb88b057a1f4bfb87358f0ad55bcd7a.json"}}], "type": "posted-content", "published": "2022-09-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.09.22.508914", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:14:25.907Z", "modified": "2026-09-23T14:34:19.981Z"}, {"entity": "publication", "iuid": "76128be0f5d7438d8dca82a42c03bb2f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76128be0f5d7438d8dca82a42c03bb2f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76128be0f5d7438d8dca82a42c03bb2f"}}, "title": "The spatial transcriptomic landscape of the healing mouse intestine following damage.", "authors": [{"family": "Parigi", "given": "Sara M", "initials": "SM"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO", "orcid": "0000-0003-0087-371X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da240d88f24d4c6fbdec6c06c1136e74.json"}}, {"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Diaz", "given": "Oscar E", "initials": "OE", "orcid": "0000-0001-7622-7832", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29eecafe74864c759129278a48114c4a.json"}}, {"family": "Selin", "given": "Katja", "initials": "K", "orcid": "0000-0002-8888-0529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0dd08d6ce6af4098acb43cfca72e1667.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32b43121030e4531b11e3b04938e765e.json"}}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Gagliani", "given": "Nicola", "initials": "N", "orcid": "0000-0001-8514-1395", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e512aae891bd4882acbbaef0a76d3457.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/504df2e61c124714b9afecf767798a00.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c90ee0c3d1904ae0933efe3631a651e0.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "828", "issn-l": "2041-1723"}, "abstract": "The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.", "doi": "10.1038/s41467-022-28497-0", "pmid": "35149721", "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [{"db": "pmc", "key": "PMC8837647"}, {"db": "pii", "key": "10.1038/s41467-022-28497-0"}], "notes": [], "created": "2026-09-23T07:32:14.592Z", "modified": "2026-09-23T07:32:14.839Z"}, {"entity": "publication", "iuid": "709815f29bb444d3b23a77ef17185bcf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/709815f29bb444d3b23a77ef17185bcf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/709815f29bb444d3b23a77ef17185bcf"}}, "title": "The spatial transcriptomic landscape of the healing intestine following damage", "authors": [{"family": "Parigi", "given": "Sara M", "initials": "SM"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO", "orcid": "0000-0003-0087-371X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da240d88f24d4c6fbdec6c06c1136e74.json"}}, {"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Diaz", "given": "Oscar E", "initials": "OE"}, {"family": "Selin", "given": "Katja", "initials": "K"}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA"}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Gagliani", "given": "Nicola", "initials": "N"}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/504df2e61c124714b9afecf767798a00.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c90ee0c3d1904ae0933efe3631a651e0.json"}}], "type": "posted-content", "published": "2021-07-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.07.01.450768", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:05:31.070Z", "modified": "2026-09-23T14:32:16.007Z"}, {"entity": "publication", "iuid": "0335c55d30bd41c3a2710f9557da9b8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0335c55d30bd41c3a2710f9557da9b8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0335c55d30bd41c3a2710f9557da9b8b"}}, "title": "PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data", "authors": [{"family": "Jun", "given": "Seong Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Chen", "given": "Xinsong", "initials": "X"}, {"family": "O\u2019Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Aparicio", "given": "Samuel", "initials": "S"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Roth", "given": "Andrew", "initials": "A"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}], "type": "posted-content", "published": "2021-02-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.02.16.431009", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T10:02:47.611Z", "modified": "2026-09-23T14:45:46.569Z"}, {"entity": "publication", "iuid": "87b5d0b9ef94406ea6311bd755326d5f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/87b5d0b9ef94406ea6311bd755326d5f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/87b5d0b9ef94406ea6311bd755326d5f"}}, "title": "B Cell Expansion Hinders the Stroma-Epithelium Regenerative Crosstalk During Mucosal Healing", "authors": [{"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar Parijat", "initials": "KP", "orcid": "0000-0002-3998-599X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/949d543dbae548cbb5c0310a5f235964.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G", "orcid": "0000-0001-6336-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce06c970b0f84b749499513116913eb6.json"}}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/652b92b02a9448179fb0bf7648ed30b9.json"}}, {"family": "larsson", "given": "ludvig", "initials": "l"}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Novella-Rausell", "given": "Claudio", "initials": "C", "orcid": "0000-0002-7383-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ce5631e59ac468cb9e5d4e8ab16d34e.json"}}, {"family": "Zagami", "given": "Chiara", "initials": "C", "orcid": "0000-0002-5246-3432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18e9f7dd5e0448c49dfe7a3eeaba2b84.json"}}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Mittenzwei", "given": "Romy", "initials": "R"}, {"family": "H\u00f6velmeyer", "given": "Nadine", "initials": "N"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c90ee0c3d1904ae0933efe3631a651e0.json"}}], "type": "posted-content", "published": "2021-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3945928", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T13:01:13.227Z", "modified": "2026-09-23T13:54:24.095Z"}, {"entity": "publication", "iuid": "350d46f4aaa142959aaa64ac1c0440cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/350d46f4aaa142959aaa64ac1c0440cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/350d46f4aaa142959aaa64ac1c0440cb"}}, "title": "Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships", "authors": [{"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82aebb401f644b2fbd015827dc916078.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Stenbeck", "given": "Linnea", "initials": "L"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03acbc899dfb44b88fab0aaad632a35b.json"}}, {"family": "Ehinger", "given": "Anna", "initials": "A"}, {"family": "Wu", "given": "Sunny", "initials": "S"}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G"}, {"family": "Roden", "given": "Daniel", "initials": "D"}, {"family": "Swarbrick", "given": "Alex", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09393c3690dc4ff8b42f5b39ec981a22.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}], "type": "posted-content", "published": "2020-07-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.07.14.200600", "pmid": null, "labels": {"SciLifeLab Fellow": "", "Camilla Engblom": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T09:58:14.066Z", "modified": "2026-09-23T13:43:28.793Z"}]}