{"entity": "researcher", "timestamp": "2026-08-09T07:59:18.077Z", "family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "affiliations": ["Center for Hematology and Regenerative Medicine, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.", "Hematology Center, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f"}}, "publications": [{"entity": "publication", "iuid": "b16a5df99b634091a39abab2b83d0afc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b16a5df99b634091a39abab2b83d0afc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b16a5df99b634091a39abab2b83d0afc"}}, "title": "Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.", "authors": [{"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Hauenstein", "given": "Julia", "initials": "J"}, {"family": "F\u00e4llmar", "given": "Helena", "initials": "H"}, {"family": "Lindell", "given": "Magnus", "initials": "M"}, {"family": "Natanaelsson", "given": "Christian", "initials": "C"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "M\u00e5nsson Welinder", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}], "type": "journal article", "published": "2026-06-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "issn-l": null, "volume": "8", "issue": "2", "pages": "lqag053"}, "abstract": "Element Biosciences' avidity sequencing has emerged as a competing technology to Illumina's short-read sequencing platform. Prior benchmarks of avidity sequencing have not included the latest Illumina NovaSeq X/X Plus instruments with XLEAP chemistry. Here, we have run polymerase chain reaction-free whole-genome sequencing on four human tumor cell lines using both Illumina NovaSeq X Plus and Element AVITI instruments. AVITI showed low duplication rates and reported higher base qualities; the latter contributed to improved mapping confidence and fewer spurious variant candidates. Both platforms were found to be highly comparable when benchmarking variant calling, with AVITI only providing a minor improvement on INDELs at lower coverages. Stratifying by genomic context revealed further differences, where AVITI genome coverage and variant calls were superior in high-GC regions while being inferior in GC homopolymers. Error-rate analysis highlighted further differences between the platforms; in particular, AVITI in some instances displayed an increased error rate on read 2 related to short fragments. AVITI error rate was also found to be more stable downstream of repetitive regions, except for GC homopolymers. We further found that AVITI sequencing was sensitive to G-quadruplex motifs. Overall, despite these identified differences, both platforms performed highly comparable for variant analysis.", "doi": "10.1093/nargab/lqag053", "pmid": "42206012", "labels": {"NGI Stockholm (Genomics Production)": "Technology development", "National Genomics Infrastructure": "Technology development", "NGI Short read": "Technology development", "NGI Stockholm (Genomics Applications)": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC13202175"}, {"db": "pii", "key": "lqag053"}], "notes": [], "created": "2026-06-08T17:20:13.126Z", "modified": "2026-06-24T14:03:11.081Z"}, {"entity": "publication", "iuid": "57fc3379fa7d498cbf6dfb3d1a9a5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0"}}, "title": "The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.", "authors": [{"family": "Rekha", "given": "Rokeya Sultana", "initials": "RS"}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Agerberth", "given": "Birgitta", "initials": "B"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}, {"family": "Gu\u00f0mundsson", "given": "Gu\u00f0mundur H", "initials": "GH"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}], "type": "journal article", "published": "2025-01-28", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "1", "pages": "115031", "issn-l": null}, "abstract": "The human cathelicidin peptide LL-37 induces autophagy in human macrophages. Different post-translational modifications (PTMs) such as citrullination, acetylation, and formylation impact LL-37, yet their effect on autophagy remains unknown. Thus, we set out to study how the cellular source could impact PTM of LL-37 and subsequent effects on autophagy initiation. Neutrophil-released LL-37 failed to induce autophagy, unlike macrophage-released LL-37. Mass spectrometry analysis revealed modifications on neutrophil-derived LL-37, especially at the N terminus, while macrophage-derived LL-37 remained mostly native. Native LL-37 initiated autophagy, while formylated and acetylated versions did not. Truncated peptides lacking the N-terminal di-leucine motif or substituted with di-alanine did not initiate autophagy. Native LL-37 failed to initiate autophagy in macrophages with genetic inactivation of dipeptidyl peptidase-1. An intact N-terminal di-leucine motif in LL-37 was crucial for autophagy initiation, and modifications abrogated the effects. This pathway presents a novel way to regulate the effects of LL-37 in infection or inflammation.", "doi": "10.1016/j.celrep.2024.115031", "pmid": "39708316", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(24)01382-2"}], "notes": [], "created": "2025-02-28T14:11:56.119Z", "modified": "2025-11-28T10:42:15.993Z"}, {"entity": "publication", "iuid": "b9461e2dab3c45d891518478219868dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9461e2dab3c45d891518478219868dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9461e2dab3c45d891518478219868dd"}}, "title": "Three Adult Cases of STAT1 Gain-of-Function with Chronic Mucocutaneous Candidiasis Treated with JAK Inhibitors.", "authors": [{"family": "Borgstr\u00f6m", "given": "Emilie W", "initials": "EW", "orcid": "0000-0002-4269-5475", "researcher": {"href": "https://publications.scilifelab.se/researcher/4833a08012f642b098ba90c88ae74e3d.json"}}, {"family": "Edvinsson", "given": "Marie", "initials": "M"}, {"family": "P\u00e9rez", "given": "Luc\u00eda P", "initials": "LP"}, {"family": "Norlin", "given": "Anna C", "initials": "AC", "orcid": "0000-0001-5503-1689", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c0fe142669148538fd228de442b87a2.json"}}, {"family": "Enoksson", "given": "Sara L", "initials": "SL"}, {"family": "Hansen", "given": "Susanne", "initials": "S"}, {"family": "Fasth", "given": "Anders", "initials": "A", "orcid": "0000-0002-0033-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57576e445b0844f287e58d868dd22574.json"}}, {"family": "Friman", "given": "Vanda", "initials": "V"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}, {"family": "Estupi\u00f1\u00e1n", "given": "Hernando Y", "initials": "HY"}, {"family": "Wang", "given": "Qing", "initials": "Q"}, {"family": "Ziyang", "given": "Tan", "initials": "T"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Smith", "given": "Carl Inge E", "initials": "CIE", "orcid": "0000-0003-1907-3392", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3ea998a87b44c218f91701cf3019af1.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}], "type": "journal article", "published": "2023-01-00", "journal": {"title": "J Clin Immunol", "issn": "1573-2592", "volume": "43", "issue": "1", "pages": "136-150", "issn-l": "0271-9142"}, "abstract": "The aim of this study was to characterize clinical effects and biomarkers in three patients with chronic mucocutaneous candidiasis (CMC) caused by gain-of-function (GOF) mutations in the STAT1 gene during treatment with Janus kinase (JAK) inhibitors.\n\nMass cytometry (CyTOF) was used to characterize mononuclear leukocyte populations and Olink assay to quantify 265 plasma proteins. Flow-cytometric Assay for Specific Cell-mediated Immune-response in Activated whole blood (FASCIA) was used to quantify the reactivity against Candida albicans.\n\nOverall, JAK inhibitors improved clinical symptoms of CMC, but caused side effects in two patients. Absolute numbers of neutrophils, T cells, B cells, and NK cells were sustained during baricitinib treatment. Detailed analysis of cellular subsets, using CyTOF, revealed increased expression of CD45, CD52, and CD99 in NK cells, reflecting a more functional phenotype. Conversely, monocytes and eosinophils downregulated CD16, consistent with reduced inflammation. Moreover, T and B cells showed increased expression of activation markers during treatment. In one patient with a remarkable clinical effect of baricitinib treatment, the immune response to C. albicans increased after 7 weeks of treatment. Alterations in plasma biomarkers involved downregulation of cellular markers CXCL10, annexin A1, granzyme B, granzyme H, and oncostatin M, whereas FGF21 was the only upregulated marker after 7 weeks. After 3 months, IFN-\u0263 and CXCL10 were downregulated.\n\nThe clinical effect of JAK inhibitor treatment of CMC is promising. Several biological variables were altered during baricitinib treatment demonstrating that lymphocytes, NK cells, monocytes, and eosinophils were affected. In parallel, cellular reactivity against C. albicans was enhanced.", "doi": "10.1007/s10875-022-01351-0", "pmid": "36050429", "labels": {"Cellular Immunomonitoring": "Collaborative", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9840596"}, {"db": "pii", "key": "10.1007/s10875-022-01351-0"}], "notes": [], "created": "2022-09-04T08:15:08.566Z", "modified": "2024-01-16T13:48:34.251Z"}, {"entity": "publication", "iuid": "8e627a82e39d4c059ca3d5e9ae6a57d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8"}}, "title": "Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.", "authors": [{"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L", "orcid": "0000-0002-5044-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/111f8a8c4c6d4d2ea60e5fc76831b7fa.json"}}, {"family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "Gran", "given": "Charlotte", "initials": "C"}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F", "orcid": "0000-0001-7198-5116", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a3bc9c440024ec994e534c3a6627f55.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Wallblom", "given": "Ann", "initials": "A"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}], "type": "journal article", "published": "2022-09-13", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "6", "issue": "17", "pages": "5009-5023"}, "abstract": "Multiple myeloma (MM) is an incurable and aggressive plasma cell malignancy characterized by a complex karyotype with multiple structural variants (SVs) and copy-number variations (CNVs). Linked-read whole-genome sequencing (lrWGS) allows for refined detection and reconstruction of SVs by providing long-range genetic information from standard short-read sequencing. This makes lrWGS an attractive solution for capturing the full genomic complexity of MM. Here we show that high-quality lrWGS data can be generated from low numbers of cells subjected to fluorescence-activated cell sorting (FACS) without DNA purification. Using this protocol, we analyzed MM cells after FACS from 37 patients with MM using lrWGS. We found high concordance between lrWGS and fluorescence in situ hybridization (FISH) for the detection of recurrent translocations and CNVs. Outside of the regions investigated by FISH, we identified >150 additional SVs and CNVs across the cohort. Analysis of the lrWGS data allowed for resolution of the structure of diverse SVs affecting the MYC and t(11;14) loci, causing the duplication of genes and gene regulatory elements. In addition, we identified private SVs causing the dysregulation of genes recurrently involved in translocations with the IGH locus and show that these can alter the molecular classification of MM. Overall, we conclude that lrWGS allows for the detection of aberrations critical for MM prognostics and provides a feasible route for providing comprehensive genetics. Implementing lrWGS could provide more accurate clinical prognostics, facilitate genomic medicine initiatives, and greatly improve the stratification of patients included in clinical trials.", "doi": "10.1182/bloodadvances.2021006720", "pmid": "35675515", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9631623"}, {"db": "pii", "key": "485485"}], "notes": [], "created": "2022-08-19T08:37:59.788Z", "modified": "2024-01-16T13:48:35.011Z"}, {"entity": "publication", "iuid": "3725797cb1794d6a9449232d6e451b75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3725797cb1794d6a9449232d6e451b75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3725797cb1794d6a9449232d6e451b75"}}, "title": "Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.", "authors": [{"family": "Rauschmeier", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0002-1073-4046", "researcher": {"href": "https://publications.scilifelab.se/researcher/79f8968c617e4d5db26486c2c467b76c.json"}}, {"family": "Reinhardt", "given": "Annika", "initials": "A", "orcid": "0000-0002-7468-9985", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f556d6e77814aa4808f373cfcb01639.json"}}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-4997-6795", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6de7e7552d4d4c9a8bee9e992d3e6b.json"}}, {"family": "Glaros", "given": "Vassilis", "initials": "V", "orcid": "0000-0001-6211-9515", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e51bdbb2d2472582cc6387dc381746.json"}}, {"family": "Artemov", "given": "Artem V", "initials": "AV", "orcid": "0000-0002-0056-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/96355d3e9b394fb790d4f8785dec6d68.json"}}, {"family": "Dunst", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0061-0901", "researcher": {"href": "https://publications.scilifelab.se/researcher/968039236aae4f19b97c4cdac9d5d3d7.json"}}, {"family": "Taneja", "given": "Reshma", "initials": "R", "orcid": "0000-0001-6214-6177", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d94af8d9565471d978e934e90544144.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}, {"family": "Busslinger", "given": "Meinrad", "initials": "M", "orcid": "0000-0002-9111-9351", "researcher": {"href": "https://publications.scilifelab.se/researcher/363a1d70b8a34b55a0d0e57eb7d60550.json"}}, {"family": "Kreslavsky", "given": "Taras", "initials": "T", "orcid": "0000-0002-6672-1914", "researcher": {"href": "https://publications.scilifelab.se/researcher/94bb90e31ed1447a9835a1adae1c8daa.json"}}], "type": "journal article", "published": "2022-02-07", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "219", "issue": "2", "issn-l": "0022-1007"}, "abstract": "The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction, which relies on a complex interplay between specialized effector B and CD4 T lymphocytes, the GC B cells and T follicular helper (TFH) cells. Intriguingly, several positive key regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation, thus limiting the number of TFH cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by the accumulation of monoclonal GC B-like cells and polyclonal TFH cells in various tissues.", "doi": "10.1084/jem.20211406", "pmid": "34919144", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "212923"}, {"db": "pmc", "key": "PMC8689665"}], "notes": [], "created": "2022-11-09T15:55:32.305Z", "modified": "2024-01-16T13:48:37.533Z"}]}